diff --git a/_modules/cellpack/autopack/Analysis.html b/_modules/cellpack/autopack/Analysis.html index 08727daf..f353ab3c 100644 --- a/_modules/cellpack/autopack/Analysis.html +++ b/_modules/cellpack/autopack/Analysis.html @@ -956,9 +956,17 @@

Source code for cellpack.autopack.Analysis

 
         get_angles = False
         if ingr.packing_mode == "gradient" and self.env.use_gradient:
-            self.center = center = self.env.gradients[ingr.gradient].mode_settings.get(
-                "center", center
-            )
+            if isinstance(ingr.gradient, list):
+                if len(ingr.gradient) > 1 or len(ingr.gradient) == 0:
+                    self.center = center
+                else:
+                    self.center = center = self.env.gradients[
+                        ingr.gradient[0]
+                    ].mode_settings.get("center", center)
+            else:
+                self.center = center = self.env.gradients[
+                    ingr.gradient
+                ].mode_settings.get("center", center)
             get_angles = True
 
         # get angles wrt gradient
diff --git a/_modules/cellpack/autopack/Environment.html b/_modules/cellpack/autopack/Environment.html
index bf5bf573..93006aa3 100644
--- a/_modules/cellpack/autopack/Environment.html
+++ b/_modules/cellpack/autopack/Environment.html
@@ -1921,7 +1921,9 @@ 
Source code for cellpack.autopack.Environment
# get the most probable point using the gradient
                 # use the gradient weighted map and get mot probabl point
                 self.log.info("pick point from gradients %d", (len(allIngrPts)))
-                ptInd = self.gradients[ingr.gradient].pickPoint(allIngrPts)
+                ptInd = Gradient.pick_point_for_ingredient(
+                    ingr, allIngrPts, self.gradients
+                )
             else:
                 # pick a point randomly among free points
                 # random or uniform?
diff --git a/_modules/cellpack/autopack/Gradient.html b/_modules/cellpack/autopack/Gradient.html
index ee36a38c..600f2fd2 100644
--- a/_modules/cellpack/autopack/Gradient.html
+++ b/_modules/cellpack/autopack/Gradient.html
@@ -133,6 +133,123 @@ 
Source code for cellpack.autopack.Gradient
 
         self.function = self.defaultFunction  # lambda ?
 
+

+[docs]
+    @staticmethod
+    def scale_between_0_and_1(values):
+        """
+        Scale values between 0 and 1
+        """
+        max_value = numpy.nanmax(values)
+        min_value = numpy.nanmin(values)
+        return (values - min_value) / (max_value - min_value)

+
+
+

+[docs]
+    @staticmethod
+    def get_combined_gradient_weight(gradient_list):
+        """
+        Combine the gradient weights
+
+        Parameters
+        ----------
+        gradient_list: list
+            list of gradient objects
+
+        Returns
+        ----------
+        numpy.ndarray
+            the combined gradient weight
+        """
+        weight_list = numpy.zeros((len(gradient_list), len(gradient_list[0].weight)))
+        for i in range(len(gradient_list)):
+            weight_list[i] = Gradient.scale_between_0_and_1(gradient_list[i].weight)
+
+        combined_weight = numpy.mean(weight_list, axis=0)
+        combined_weight = Gradient.scale_between_0_and_1(combined_weight)
+
+        return combined_weight

+
+
+

+[docs]
+    @staticmethod
+    def pick_point_from_weight(weight, points):
+        """
+        Picks a point from a list of points according to the given weight
+
+        Parameters
+        ----------
+        weight: numpy.ndarray
+            the weight of each point
+
+        points: numpy.ndarray
+            list of grid point indices
+
+        Returns
+        ----------
+        int
+            the index of the picked point
+        """
+        weights_to_use = numpy.take(weight, points)
+        weights_to_use = Gradient.scale_between_0_and_1(weights_to_use)
+        weights_to_use[numpy.isnan(weights_to_use)] = 0
+
+        point_probabilities = weights_to_use / numpy.sum(weights_to_use)
+
+        point = numpy.random.choice(points, p=point_probabilities)
+
+        return point

+
+
+

+[docs]
+    @staticmethod
+    def pick_point_for_ingredient(ingr, allIngrPts, all_gradients):
+        """
+        Picks a point for an ingredient according to the gradient
+
+        Parameters
+        ----------
+        ingr: Ingredient
+            the ingredient object
+
+        allIngrPts: numpy.ndarray
+            list of grid point indices
+
+        all_gradients: dict
+            dictionary of all gradient objects
+
+        Returns
+        ----------
+        int
+            the index of the picked point
+        """
+        if isinstance(ingr.gradient, list):
+            if len(ingr.gradient) > 1:
+                if not hasattr(ingr, "combined_weight"):
+                    gradient_list = [
+                        gradient
+                        for gradient_name, gradient in all_gradients.items()
+                        if gradient_name in ingr.gradient
+                    ]
+                    combined_weight = Gradient.get_combined_gradient_weight(
+                        gradient_list
+                    )
+                    ingr.combined_weight = combined_weight
+
+                ptInd = Gradient.pick_point_from_weight(
+                    ingr.combined_weight, allIngrPts
+                )
+            else:
+                ptInd = all_gradients[ingr.gradient[0]].pickPoint(allIngrPts)
+        else:
+            ptInd = all_gradients[ingr.gradient].pickPoint(allIngrPts)
+
+        return ptInd

+
+
 

 [docs]
     def get_center(self):
@@ -164,17 +281,6 @@ 
Source code for cellpack.autopack.Gradient
         return vector / numpy.linalg.norm(vector)

 
 
-

-[docs]
-    def get_normalized_values(self, values):
-        """
-        Scale values between 0 and 1
-        """
-        max_value = numpy.nanmax(values)
-        min_value = numpy.nanmin(values)
-        return (values - min_value) / (max_value - min_value)

-
-
 

 [docs]
     def pickPoint(self, listPts):
@@ -282,7 +388,7 @@ 
Source code for cellpack.autopack.Gradient
 [docs]
     def set_weights_by_mode(self):
 
-        self.scaled_distances = self.get_normalized_values(self.distances)
+        self.scaled_distances = Gradient.scale_between_0_and_1(self.distances)
 
         if (numpy.nanmax(self.scaled_distances) > 1.0) or (
             numpy.nanmin(self.scaled_distances) < 0.0
@@ -309,7 +415,7 @@ 
Source code for cellpack.autopack.Gradient
                 -self.scaled_distances / self.weight_mode_settings["decay_length"]
             )
         # normalize the weight
-        self.weight = self.get_normalized_values(self.weight)
+        self.weight = Gradient.scale_between_0_and_1(self.weight)
 
         if (numpy.nanmax(self.weight) > 1.0) or (numpy.nanmin(self.weight) < 0.0):
             raise ValueError(
@@ -478,7 +584,7 @@ 
Source code for cellpack.autopack.Gradient
             )
             if channel_values is None:
                 continue
-            normalized_values = self.get_normalized_values(channel_values)
+            normalized_values = Gradient.scale_between_0_and_1(channel_values)
             reshaped_values = numpy.reshape(
                 normalized_values, image_writer.image_size, order="F"
             )
diff --git a/_modules/cellpack/autopack/upy/simularium/simularium_helper.html b/_modules/cellpack/autopack/upy/simularium/simularium_helper.html
index a638cadf..8a492c49 100644
--- a/_modules/cellpack/autopack/upy/simularium/simularium_helper.html
+++ b/_modules/cellpack/autopack/upy/simularium/simularium_helper.html
@@ -531,7 +531,10 @@ 
Source code for cellpack.autopack.upy.simularium.simularium_helper
positions, values = self.sort_values(positions, values)
 
-        colormap = matplotlib.cm.Reds(values)
+        normalized_values = (values - np.min(values)) / (
+            np.max(values) - np.min(values)
+        )
+        colormap = matplotlib.cm.Reds(normalized_values)
 
         for index, value in enumerate(values):
             name = f"{incoming_name}#{value:.3f}"
diff --git a/cellpack.autopack.html b/cellpack.autopack.html
index d8597594..1fb4f951 100644
--- a/cellpack.autopack.html
+++ b/cellpack.autopack.html
@@ -3225,15 +3225,26 @@ 
The Gradient class
-

-get_gauss_weights(number_of_points, degree=5)[source]

-
given a number of points compute the gaussian weight for each

+

+static get_combined_gradient_weight(gradient_list)[source]

+
Combine the gradient weights

+

+
Parameters:

+
gradient_list (list) – list of gradient objects

+

+
Returns:

+
the combined gradient weight

+

+
Return type:

+
numpy.ndarray

+

+

 

 
 

-

-get_normalized_values(values)[source]

-
Scale values between 0 and 1

+

+get_gauss_weights(number_of_points, degree=5)[source]

+
given a number of points compute the gaussian weight for each

 

 
 

@@ -3248,6 +3259,53 @@ 
The Gradient class
+

+static pick_point_for_ingredient(ingr, allIngrPts, all_gradients)[source]

+
Picks a point for an ingredient according to the gradient

+

+
Parameters:

+
    
+
  • ingr (Ingredient) – the ingredient object
    • 
+
  • allIngrPts (numpy.ndarray) – list of grid point indices
    • 
+
  • all_gradients (dict) – dictionary of all gradient objects
    • 
+

+

+
Returns:

+
the index of the picked point

+

+
Return type:

+
int

+

+

+

+
+

+

+static pick_point_from_weight(weight, points)[source]

+
Picks a point from a list of points according to the given weight

+

+
Parameters:

+
    
+
  • weight (numpy.ndarray) – the weight of each point
    • 
+
  • points (numpy.ndarray) – list of grid point indices
    • 
+

+

+
Returns:

+
the index of the picked point

+

+
Return type:

+
int

+

+

+

+
+

+

+static scale_between_0_and_1(values)[source]

+
Scale values between 0 and 1

+

+
 

 

 set_weights_by_mode()[source]

@@ -5966,10 +6024,13 @@ 
Table of Contents

 
  • Gradient.getRndWeighted()
    • 
 
  • Gradient.getSubWeighted()
    • 
 
  • Gradient.get_center()
    • 
+
  • Gradient.get_combined_gradient_weight()
    • 
 
  • Gradient.get_gauss_weights()
    • 
-
  • Gradient.get_normalized_values()
    • 
 
  • Gradient.normalize_vector()
    • 
 
  • Gradient.pickPoint()
    • 
+
  • Gradient.pick_point_for_ingredient()
    • 
+
  • Gradient.pick_point_from_weight()
    • 
+
  • Gradient.scale_between_0_and_1()
    • 
 
  • Gradient.set_weights_by_mode()
    • 
 
 
diff --git a/cellpack.html b/cellpack.html
index 45bc4ca7..24e093f5 100644
--- a/cellpack.html
+++ b/cellpack.html
@@ -528,10 +528,13 @@ 
    SubpackagesGradient.getRndWeighted()
 
  • Gradient.getSubWeighted()
    • 
 
  • Gradient.get_center()
    • 
+
  • Gradient.get_combined_gradient_weight()
    • 
 
  • Gradient.get_gauss_weights()
    • 
-
  • Gradient.get_normalized_values()
    • 
 
  • Gradient.normalize_vector()
    • 
 
  • Gradient.pickPoint()
    • 
+
  • Gradient.pick_point_for_ingredient()
    • 
+
  • Gradient.pick_point_from_weight()
    • 
+
  • Gradient.scale_between_0_and_1()
    • 
 
  • Gradient.set_weights_by_mode()
    • 
 
 
diff --git a/genindex.html b/genindex.html
index 39e58a34..696fd04a 100644
--- a/genindex.html
+++ b/genindex.html
@@ -1502,6 +1502,8 @@ 
    G
    
       
  • get_collada_material() (cellpack.autopack.MeshStore.MeshStore static method)
 
    • 
       
  • get_collection_id_from_path() (cellpack.autopack.FirebaseHandler.FirebaseHandler static method)
+
    • 
+      
  • get_combined_gradient_weight() (cellpack.autopack.Gradient.Gradient static method)
 
    • 
       
  • get_compartment() (cellpack.autopack.ingredient.Ingredient.Ingredient method)
 
@@ -1620,8 +1622,6 @@ 
    G
    
       
  • get_normal() (cellpack.autopack.MeshStore.MeshStore method)
 
    • 
       
  • get_normal_for_point() (cellpack.autopack.Compartment.Compartment method)
-
    • 
-      
  • get_normalized_values() (cellpack.autopack.Gradient.Gradient method)
 
    • 
       
  • get_nsphere() (cellpack.autopack.MeshStore.MeshStore method)
 
    • 
@@ -2765,6 +2765,10 @@ 
    P
    
       
  • pick_alternate() (cellpack.autopack.ingredient.grow.GrowIngredient method)
 
    • 
       
  • pick_partner_grid_index() (cellpack.autopack.ingredient.agent.Agent method)
+
    • 
+      
  • pick_point_for_ingredient() (cellpack.autopack.Gradient.Gradient static method)
+
    • 
+      
  • pick_point_from_weight() (cellpack.autopack.Gradient.Gradient static method)
 
    • 
       
  • pick_random_alternate() (cellpack.autopack.ingredient.grow.GrowIngredient method)
 
    • 
@@ -2790,14 +2794,14 @@ 
    P
    
 
       
  • place_object() (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper method)
 
    • 
+  
+  
-  
       
  • setParticulesPosition() (cellpack.autopack.upy.hostHelper.Helper method)
-
    • 
-      
  • setProperty() (cellpack.autopack.upy.hostHelper.Helper method)
 
    • 
   
   
      
+      
    • setProperty() (cellpack.autopack.upy.hostHelper.Helper method)
+
      • 
       
    • setPropertyObject() (cellpack.autopack.upy.hostHelper.Helper method)
 
      • 
       
    • SetRBOptions() (cellpack.autopack.Environment.Environment method)
diff --git a/objects.inv b/objects.inv
index 13595e73..84a56e0c 100644
Binary files a/objects.inv and b/objects.inv differ
diff --git a/searchindex.js b/searchindex.js
index 56df98b6..2edc4c1e 100644
--- a/searchindex.js
+++ b/searchindex.js
@@ -1 +1 @@
-Search.setIndex({"alltitles": {"AWS S3": [[11, "aws-s3"]], "Cellpack Recipe Schema 1.0": [[0, "cellpack-recipe-schema-1-0"], [14, "cellpack-recipe-schema-1-0"]], "Contributing": [[10, "contributing"]], "Contributing cheat sheet": [[11, "contributing-cheat-sheet"]], "Created on Fri Jul 20 23:53:00 2012": [[2, "created-on-fri-jul-20-23-53-00-2012"]], "Created on Saturday September 1 1:50:00 2012": [[2, "created-on-saturday-september-1-1-50-00-2012"]], "Deploying": [[10, "deploying"]], "Development": [[11, "development"]], "Documentation": [[11, "documentation"]], "EnviroOnly": [[0, "enviroonly"], [14, "enviroonly"]], "Firebase Firestore": [[11, "firebase-firestore"]], "From sources": [[12, "from-sources"]], "Get Started!": [[10, "get-started"]], "Indices and tables": [[11, "indices-and-tables"]], "Ingredient Properties": [[0, "ingredient-properties"], [14, "ingredient-properties"]], "Installation": [[12, "installation"]], "Introduction to Remote Databases": [[11, "introduction-to-remote-databases"]], "Module contents": [[1, "module-cellpack"], [2, "module-cellpack.autopack"], [3, "module-cellpack.autopack.ingredient"], [4, "module-cellpack.autopack.interface_objects"], [5, "module-cellpack.autopack.loaders"], [6, "module-cellpack.autopack.upy"], [7, "module-cellpack.autopack.upy.simularium"], [8, "module-cellpack.autopack.writers"], [9, "module-cellpack.bin"]], "Options properties": [[0, "options-properties"], [14, "options-properties"]], "Prerequisite": [[11, "prerequisite"]], "Recipe definition properties": [[0, "recipe-definition-properties"], [14, "recipe-definition-properties"]], "Requirements": [[2, "requirements"]], "Run conversion code": [[11, "run-conversion-code"]], "Run pack code": [[11, "run-pack-code"]], "Setup": [[11, "setup"]], "Stable release": [[12, "stable-release"]], "Submodules": [[2, "submodules"], [3, "submodules"], [4, "submodules"], [5, "submodules"], [6, "submodules"], [7, "submodules"], [8, "submodules"], [9, "submodules"]], "Subpackages": [[1, "subpackages"], [2, "subpackages"], [6, "subpackages"]], "The Compartment class": [[2, "the-compartment-class"]], "The CompartmentList class": [[2, "the-compartmentlist-class"]], "The Environment class": [[2, "the-environment-class"]], "The Gradient class": [[2, "the-gradient-class"]], "The Grid class": [[2, "the-grid-class"], [2, "id1"]], "The Helper abstract Object": [[6, "the-helper-abstract-object"]], "The Simularium helper abstract class": [[7, "the-simularium-helper-abstract-class"]], "This object holds the different representation types for an ingredient": [[4, "this-object-holds-the-different-representation-types-for-an-ingredient"]], "This object holds the partner data": [[4, "this-object-holds-the-partner-data"]], "Welcome to cellPack\u2019s documentation!": [[11, "welcome-to-cellpack-s-documentation"]], "_hackFreepts": [[0, "hackfreepts"], [14, "hackfreepts"]], "_timer": [[0, "timer"], [14, "timer"]], "boundingBox": [[0, "boundingbox"], [14, "boundingbox"]], "cancelDialog": [[0, "canceldialog"], [14, "canceldialog"]], "cellPack": [[11, "cellpack"]], "cellpack": [[13, "cellpack"]], "cellpack package": [[1, "cellpack-package"]], "cellpack.autopack package": [[2, "cellpack-autopack-package"]], "cellpack.autopack.AWSHandler module": [[2, "module-cellpack.autopack.AWSHandler"]], "cellpack.autopack.Analysis module": [[2, "module-cellpack.autopack.Analysis"]], "cellpack.autopack.BaseGrid module": [[2, "module-cellpack.autopack.BaseGrid"]], "cellpack.autopack.Compartment module": [[2, "module-cellpack.autopack.Compartment"]], "cellpack.autopack.DBRecipeHandler module": [[2, "module-cellpack.autopack.DBRecipeHandler"]], "cellpack.autopack.Environment module": [[2, "module-cellpack.autopack.Environment"]], "cellpack.autopack.FirebaseHandler module": [[2, "module-cellpack.autopack.FirebaseHandler"]], "cellpack.autopack.GeometryTools module": [[2, "module-cellpack.autopack.GeometryTools"]], "cellpack.autopack.Gradient module": [[2, "module-cellpack.autopack.Gradient"]], "cellpack.autopack.Graphics module": [[2, "module-cellpack.autopack.Graphics"]], "cellpack.autopack.Grid module": [[2, "module-cellpack.autopack.Grid"]], "cellpack.autopack.IOutils module": [[2, "module-cellpack.autopack.IOutils"]], "cellpack.autopack.MeshStore module": [[2, "module-cellpack.autopack.MeshStore"]], "cellpack.autopack.OutputSimularium module": [[2, "cellpack-autopack-outputsimularium-module"]], "cellpack.autopack.Recipe module": [[2, "module-cellpack.autopack.Recipe"]], "cellpack.autopack.Serializable module": [[2, "module-cellpack.autopack.Serializable"]], "cellpack.autopack.binvox_rw module": [[2, "module-cellpack.autopack.binvox_rw"]], "cellpack.autopack.ingredient package": [[3, "cellpack-autopack-ingredient-package"]], "cellpack.autopack.ingredient.Ingredient module": [[3, "module-cellpack.autopack.ingredient.Ingredient"]], "cellpack.autopack.ingredient.agent module": [[3, "module-cellpack.autopack.ingredient.agent"]], "cellpack.autopack.ingredient.grow module": [[3, "module-cellpack.autopack.ingredient.grow"]], "cellpack.autopack.ingredient.multi_cylinder module": [[3, "module-cellpack.autopack.ingredient.multi_cylinder"]], "cellpack.autopack.ingredient.multi_sphere module": [[3, "module-cellpack.autopack.ingredient.multi_sphere"]], "cellpack.autopack.ingredient.single_cube module": [[3, "module-cellpack.autopack.ingredient.single_cube"]], "cellpack.autopack.ingredient.single_cylinder module": [[3, "module-cellpack.autopack.ingredient.single_cylinder"]], "cellpack.autopack.ingredient.single_sphere module": [[3, "module-cellpack.autopack.ingredient.single_sphere"]], "cellpack.autopack.ingredient.utils module": [[3, "module-cellpack.autopack.ingredient.utils"]], "cellpack.autopack.interface_objects package": [[4, "cellpack-autopack-interface-objects-package"]], "cellpack.autopack.interface_objects.database_ids module": [[4, "module-cellpack.autopack.interface_objects.database_ids"]], "cellpack.autopack.interface_objects.default_values module": [[4, "module-cellpack.autopack.interface_objects.default_values"]], "cellpack.autopack.interface_objects.gradient_data module": [[4, "module-cellpack.autopack.interface_objects.gradient_data"]], "cellpack.autopack.interface_objects.ingredient_types module": [[4, "module-cellpack.autopack.interface_objects.ingredient_types"]], "cellpack.autopack.interface_objects.meta_enum module": [[4, "module-cellpack.autopack.interface_objects.meta_enum"]], "cellpack.autopack.interface_objects.packed_objects module": [[4, "module-cellpack.autopack.interface_objects.packed_objects"]], "cellpack.autopack.interface_objects.partners module": [[4, "module-cellpack.autopack.interface_objects.partners"]], "cellpack.autopack.interface_objects.representations module": [[4, "module-cellpack.autopack.interface_objects.representations"]], "cellpack.autopack.ldSequence module": [[2, "module-cellpack.autopack.ldSequence"]], "cellpack.autopack.loaders package": [[5, "cellpack-autopack-loaders-package"]], "cellpack.autopack.loaders.analysis_config_loader module": [[5, "module-cellpack.autopack.loaders.analysis_config_loader"]], "cellpack.autopack.loaders.config_loader module": [[5, "module-cellpack.autopack.loaders.config_loader"]], "cellpack.autopack.loaders.migrate_v1_to_v2 module": [[5, "module-cellpack.autopack.loaders.migrate_v1_to_v2"]], "cellpack.autopack.loaders.migrate_v2_to_v2_1 module": [[5, "module-cellpack.autopack.loaders.migrate_v2_to_v2_1"]], "cellpack.autopack.loaders.recipe_loader module": [[5, "module-cellpack.autopack.loaders.recipe_loader"]], "cellpack.autopack.loaders.utils module": [[5, "module-cellpack.autopack.loaders.utils"]], "cellpack.autopack.loaders.v1_v2_attribute_changes module": [[5, "module-cellpack.autopack.loaders.v1_v2_attribute_changes"]], "cellpack.autopack.octree module": [[2, "module-cellpack.autopack.octree"]], "cellpack.autopack.plotly_result module": [[2, "module-cellpack.autopack.plotly_result"]], "cellpack.autopack.randomRot module": [[2, "module-cellpack.autopack.randomRot"]], "cellpack.autopack.ray module": [[2, "module-cellpack.autopack.ray"]], "cellpack.autopack.trajectory module": [[2, "module-cellpack.autopack.trajectory"]], "cellpack.autopack.transformation module": [[2, "module-cellpack.autopack.transformation"]], "cellpack.autopack.upy package": [[6, "cellpack-autopack-upy-package"]], "cellpack.autopack.upy.colors module": [[6, "module-cellpack.autopack.upy.colors"]], "cellpack.autopack.upy.hostHelper module": [[6, "module-cellpack.autopack.upy.hostHelper"]], "cellpack.autopack.upy.simularium package": [[7, "cellpack-autopack-upy-simularium-package"]], "cellpack.autopack.upy.simularium.plots module": [[7, "module-cellpack.autopack.upy.simularium.plots"]], "cellpack.autopack.upy.simularium.simularium_helper module": [[7, "module-cellpack.autopack.upy.simularium.simularium_helper"]], "cellpack.autopack.utils module": [[2, "module-cellpack.autopack.utils"]], "cellpack.autopack.writers package": [[8, "cellpack-autopack-writers-package"]], "cellpack.autopack.writers.ImageWriter module": [[8, "module-cellpack.autopack.writers.ImageWriter"]], "cellpack.bin package": [[9, "cellpack-bin-package"]], "cellpack.bin.analyze module": [[9, "module-cellpack.bin.analyze"]], "cellpack.bin.clean module": [[9, "module-cellpack.bin.clean"]], "cellpack.bin.cleanup_tasks module": [[9, "module-cellpack.bin.cleanup_tasks"]], "cellpack.bin.get-pdb-offset module": [[9, "cellpack-bin-get-pdb-offset-module"]], "cellpack.bin.pack module": [[9, "module-cellpack.bin.pack"]], "cellpack.bin.simularium_converter module": [[9, "module-cellpack.bin.simularium_converter"]], "cellpack.bin.upload module": [[9, "module-cellpack.bin.upload"]], "color": [[0, "color"], [14, "color"]], "computeGridParams": [[0, "computegridparams"], [14, "computegridparams"]], "coordsystem": [[0, "coordsystem"], [14, "coordsystem"]], "count": [[0, "count"], [14, "count"]], "cutoff_boundary": [[0, "cutoff-boundary"], [14, "cutoff-boundary"]], "cutoff_surface": [[0, "cutoff-surface"], [14, "cutoff-surface"]], "encapsulating_radius": [[0, "encapsulating-radius"], [14, "encapsulating-radius"]], "example Options:": [[0, "example-options"], [14, "example-options"]], "example ingredient": [[0, "example-ingredient"], [14, "example-ingredient"]], "example:": [[0, "example"], [14, "example"]], "excluded_partners_name": [[0, "excluded-partners-name"], [14, "excluded-partners-name"]], "freePtsUpdateThreshold": [[0, "freeptsupdatethreshold"], [14, "freeptsupdatethreshold"]], "gradient": [[0, "gradient"], [14, "gradient"]], "gradients": [[0, "gradients"], [14, "gradients"]], "ingrLookForNeighbours": [[0, "ingrlookforneighbours"], [14, "ingrlookforneighbours"]], "innerGridMethod": [[0, "innergridmethod"], [14, "innergridmethod"]], "is_attractor": [[0, "is-attractor"], [14, "is-attractor"]], "jitter_attempts": [[0, "jitter-attempts"], [14, "jitter-attempts"]], "largestProteinSize": [[0, "largestproteinsize"], [14, "largestproteinsize"]], "max_jitter": [[0, "max-jitter"], [14, "max-jitter"]], "meshFile": [[0, "meshfile"], [14, "meshfile"]], "meshName": [[0, "meshname"], [14, "meshname"]], "molarity": [[0, "molarity"], [14, "molarity"]], "name": [[0, "name"], [0, "id81"], [14, "name"], [14, "id81"]], "offset": [[0, "offset"], [14, "offset"]], "organism": [[0, "organism"], [14, "organism"]], "orientBiasRotRangeMax": [[0, "orientbiasrotrangemax"], [14, "orientbiasrotrangemax"]], "orientBiasRotRangeMin": [[0, "orientbiasrotrangemin"], [14, "orientbiasrotrangemin"]], "overwritePlaceMethod": [[0, "overwriteplacemethod"], [14, "overwriteplacemethod"]], "packing_mode": [[0, "packing-mode"], [14, "packing-mode"]], "partners_name": [[0, "partners-name"], [14, "partners-name"]], "partners_position": [[0, "partners-position"], [14, "partners-position"]], "partners_weight": [[0, "partners-weight"], [14, "partners-weight"]], "pdb": [[0, "pdb"], [14, "pdb"]], "perturb_axis_amplitude": [[0, "perturb-axis-amplitude"], [14, "perturb-axis-amplitude"]], "pickRandPt": [[0, "pickrandpt"], [14, "pickrandpt"]], "pickWeightedIngr": [[0, "pickweightedingr"], [14, "pickweightedingr"]], "place_method": [[0, "place-method"], [0, "id162"], [14, "place-method"], [14, "id162"]], "positions": [[0, "positions"], [14, "positions"]], "positions2": [[0, "positions2"], [14, "positions2"]], "principal_vector": [[0, "principal-vector"], [14, "principal-vector"]], "priority": [[0, "priority"], [14, "priority"]], "proba_binding": [[0, "proba-binding"], [14, "proba-binding"]], "proba_not_binding": [[0, "proba-not-binding"], [14, "proba-not-binding"]], "properties": [[0, "properties"], [14, "properties"]], "radii": [[0, "radii"], [14, "radii"]], "rejection_threshold": [[0, "rejection-threshold"], [14, "rejection-threshold"]], "result_file": [[0, "result-file"], [14, "result-file"]], "rotation_axis": [[0, "rotation-axis"], [14, "rotation-axis"]], "rotation_range": [[0, "rotation-range"], [14, "rotation-range"]], "runTimeDisplay": [[0, "runtimedisplay"], [14, "runtimedisplay"]], "saveResult": [[0, "saveresult"], [14, "saveresult"]], "score": [[0, "score"], [14, "score"]], "smallestProteinSize": [[0, "smallestproteinsize"], [14, "smallestproteinsize"]], "sphereFile": [[0, "spherefile"], [14, "spherefile"]], "type": [[0, "type"], [14, "type"]], "use_gradient": [[0, "use-gradient"], [14, "use-gradient"]], "use_orient_bias": [[0, "use-orient-bias"], [14, "use-orient-bias"]], "use_periodicity": [[0, "use-periodicity"], [14, "use-periodicity"]], "use_rotation_axis": [[0, "use-rotation-axis"], [14, "use-rotation-axis"]], "version": [[0, "version"], [14, "version"]], "weight": [[0, "weight"], [14, "weight"]], "windowsSize": [[0, "windowssize"], [14, "windowssize"]]}, "docnames": ["RECIPE_SCHEMA", "cellpack", "cellpack.autopack", "cellpack.autopack.ingredient", "cellpack.autopack.interface_objects", "cellpack.autopack.loaders", "cellpack.autopack.upy", "cellpack.autopack.upy.simularium", "cellpack.autopack.writers", "cellpack.bin", "contributing", "index", "installation", "modules", "recipe-schema"], "envversion": {"sphinx": 61, "sphinx.domains.c": 3, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 9, "sphinx.domains.index": 1, "sphinx.domains.javascript": 3, "sphinx.domains.math": 2, "sphinx.domains.python": 4, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinx.ext.viewcode": 1}, "filenames": ["RECIPE_SCHEMA.md", "cellpack.rst", "cellpack.autopack.rst", "cellpack.autopack.ingredient.rst", "cellpack.autopack.interface_objects.rst", "cellpack.autopack.loaders.rst", "cellpack.autopack.upy.rst", "cellpack.autopack.upy.simularium.rst", "cellpack.autopack.writers.rst", "cellpack.bin.rst", "contributing.rst", "index.rst", "installation.rst", "modules.rst", "recipe-schema.rst"], "indexentries": {"actiningredient (class in cellpack.autopack.ingredient.grow)": [[3, "cellpack.autopack.ingredient.grow.ActinIngredient", false]], "add() (cellpack.autopack.interface_objects.packed_objects.packedobjects method)": [[4, "cellpack.autopack.interface_objects.packed_objects.PackedObjects.add", false]], "add_circle() (cellpack.autopack.plotly_result.plotlyanalysis method)": [[2, "cellpack.autopack.plotly_result.PlotlyAnalysis.add_circle", false]], "add_compartment() (cellpack.autopack.compartment.compartmentlist static method)": [[2, "cellpack.autopack.Compartment.CompartmentList.add_compartment", false]], "add_compartment_to_scene() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.add_compartment_to_scene", false]], "add_grid_data_to_scene() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.add_grid_data_to_scene", false]], "add_histogram() (cellpack.autopack.upy.simularium.plots.plotdata method)": [[7, "cellpack.autopack.upy.simularium.plots.PlotData.add_histogram", false]], "add_ingredient_positions() (cellpack.autopack.plotly_result.plotlyanalysis method)": [[2, "cellpack.autopack.plotly_result.PlotlyAnalysis.add_ingredient_positions", false]], "add_ingredient_positions_to_plot() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.add_ingredient_positions_to_plot", false]], "add_instance() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.add_instance", false]], "add_mesh_to_scene() (cellpack.autopack.meshstore.meshstore method)": [[2, "cellpack.autopack.MeshStore.MeshStore.add_mesh_to_scene", false]], "add_new_instance_and_update_time() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.add_new_instance_and_update_time", false]], "add_object_to_scene() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.add_object_to_scene", false]], "add_partner() (cellpack.autopack.interface_objects.partners.partners method)": [[4, "cellpack.autopack.interface_objects.partners.Partners.add_partner", false]], "add_scatter() (cellpack.autopack.upy.simularium.plots.plotdata method)": [[7, "cellpack.autopack.upy.simularium.plots.PlotData.add_scatter", false]], "add_seed_number_to_base_name() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.add_seed_number_to_base_name", false]], "add_square() (cellpack.autopack.plotly_result.plotlyanalysis method)": [[2, "cellpack.autopack.plotly_result.PlotlyAnalysis.add_square", false]], "addbone() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.addBone", false]], "addcameratoscene() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.addCameraToScene", false]], "addcameratoscene() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.addCameraToScene", false]], "addcompartment() (cellpack.autopack.serializable.scompartment method)": [[2, "cellpack.autopack.Serializable.sCompartment.addCompartment", false]], "addcompartmentfromgeom() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.addCompartmentFromGeom", false]], "addcompartments() (in module cellpack.autopack.ioutils)": [[2, "cellpack.autopack.IOutils.addCompartments", false]], "addconstraint() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.addConstraint", false]], "addingredient() (cellpack.autopack.recipe.recipe method)": [[2, "cellpack.autopack.Recipe.Recipe.addIngredient", false]], "addingredient() (cellpack.autopack.serializable.singredientgroup method)": [[2, "cellpack.autopack.Serializable.sIngredientGroup.addIngredient", false]], "addingredientfromgeom() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.addIngredientFromGeom", false]], "addingredientgroup() (cellpack.autopack.serializable.scompartment method)": [[2, "cellpack.autopack.Serializable.sCompartment.addIngredientGroup", false]], "addlamptoscene() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.addLampToScene", false]], "addlamptoscene() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.addLampToScene", false]], "addmasteringr() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.addMasterIngr", false]], "addmaterial() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.addMaterial", false]], "addmaterial() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.addMaterial", false]], "addmaterialfromdic() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.addMaterialFromDic", false]], "addmeshedge() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.addMeshEdge", false]], "addmeshedges() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.addMeshEdges", false]], "addmeshface() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.addMeshFace", false]], "addmeshfaces() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.addMeshFaces", false]], "addmeshrborganelle() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.addMeshRBOrganelle", false]], "addmeshvertice() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.addMeshVertice", false]], "addmeshvertices() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.addMeshVertices", false]], "addnode() (cellpack.autopack.octree.octree method)": [[2, "cellpack.autopack.octree.Octree.addNode", false]], "addobject() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.AddObject", false]], "addobjecttoscene() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.addObjectToScene", false]], "addrb() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.addRB", false]], "advance_randpoint_onsphere() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.advance_randpoint_onsphere", false]], "agent (class in cellpack.autopack.ingredient.agent)": [[3, "cellpack.autopack.ingredient.agent.Agent", false]], "alignrotation() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.alignRotation", false]], "analysis (class in cellpack.autopack.analysis)": [[2, "cellpack.autopack.Analysis.Analysis", false]], "analysisconfigloader (class in cellpack.autopack.loaders.analysis_config_loader)": [[5, "cellpack.autopack.loaders.analysis_config_loader.AnalysisConfigLoader", false]], "analyze() (in module cellpack.bin.analyze)": [[9, "cellpack.bin.analyze.analyze", false]], "angle_between_vectors() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.angle_between_vectors", false]], "animationstart() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.animationStart", false]], "animationstop() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.animationStop", false]], "appendingrinstance() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.appendIngrInstance", false]], "apply_rotation() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.apply_rotation", false]], "applymatrix() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.ApplyMatrix", false]], "applymatrix() (in module cellpack.autopack.ingredient.utils)": [[3, "cellpack.autopack.ingredient.utils.ApplyMatrix", false]], "applystate() (cellpack.autopack.trajectory.trajectory method)": [[2, "cellpack.autopack.trajectory.Trajectory.applyState", false]], "applystate_cb() (cellpack.autopack.trajectory.trajectory method)": [[2, "cellpack.autopack.trajectory.Trajectory.applyState_cb", false]], "applystate_name() (cellpack.autopack.trajectory.molbtrajectory method)": [[2, "cellpack.autopack.trajectory.molbTrajectory.applyState_name", false]], "applystate_name() (cellpack.autopack.trajectory.trajectory method)": [[2, "cellpack.autopack.trajectory.Trajectory.applyState_name", false]], "applystate_primitive_name() (cellpack.autopack.trajectory.molbtrajectory method)": [[2, "cellpack.autopack.trajectory.molbTrajectory.applyState_primitive_name", false]], "applystate_primitive_name() (cellpack.autopack.trajectory.trajectory method)": [[2, "cellpack.autopack.trajectory.Trajectory.applyState_primitive_name", false]], "applystep() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.applyStep", false]], "arguments (cellpack.autopack.ingredient.grow.growingredient attribute)": [[3, "cellpack.autopack.ingredient.grow.GrowIngredient.ARGUMENTS", false]], "arguments (cellpack.autopack.ingredient.ingredient.ingredient attribute)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.ARGUMENTS", false]], "armature() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.armature", false]], "as_dict() (cellpack.autopack.dbrecipehandler.compositiondoc method)": [[2, "cellpack.autopack.DBRecipeHandler.CompositionDoc.as_dict", false]], "as_dict() (cellpack.autopack.dbrecipehandler.datadoc method)": [[2, "cellpack.autopack.DBRecipeHandler.DataDoc.as_dict", false]], "as_dict() (cellpack.autopack.dbrecipehandler.objectdoc method)": [[2, "cellpack.autopack.DBRecipeHandler.ObjectDoc.as_dict", false]], "assignmaterial() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.assignMaterial", false]], "assignmaterial() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.assignMaterial", false]], "assignnewmaterial() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.assignNewMaterial", false]], "attempt_to_pack_at_grid_location() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.attempt_to_pack_at_grid_location", false]], "autopackviewer (class in cellpack.autopack.graphics)": [[2, "cellpack.autopack.Graphics.AutopackViewer", false]], "aws (cellpack.autopack.interface_objects.database_ids.database_ids attribute)": [[4, "cellpack.autopack.interface_objects.database_ids.DATABASE_IDS.AWS", false]], "awshandler (class in cellpack.autopack.awshandler)": [[2, "cellpack.autopack.AWSHandler.AWSHandler", false]], "basegrid (class in cellpack.autopack.basegrid)": [[2, "cellpack.autopack.BaseGrid.BaseGrid", false]], "binary (cellpack.autopack.interface_objects.gradient_data.pickmodes attribute)": [[4, "cellpack.autopack.interface_objects.gradient_data.PickModes.BINARY", false]], "bones (cellpack.autopack.upy.hosthelper.helper attribute)": [[6, "cellpack.autopack.upy.hostHelper.Helper.BONES", false]], "box() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.box", false]], "box() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.Box", false], [7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.box", false]], "build_axis_weight_map() (cellpack.autopack.gradient.gradient method)": [[2, "cellpack.autopack.Gradient.Gradient.build_axis_weight_map", false]], "build_compartment_grids() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.build_compartment_grids", false]], "build_directional_weight_map() (cellpack.autopack.gradient.gradient method)": [[2, "cellpack.autopack.Gradient.Gradient.build_directional_weight_map", false]], "build_grid() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.build_grid", false]], "build_grid_sphere() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.build_grid_sphere", false]], "build_mesh() (cellpack.autopack.meshstore.meshstore method)": [[2, "cellpack.autopack.MeshStore.MeshStore.build_mesh", false]], "build_radial_weight_map() (cellpack.autopack.gradient.gradient method)": [[2, "cellpack.autopack.Gradient.Gradient.build_radial_weight_map", false]], "build_surface_distance_weight_map() (cellpack.autopack.gradient.gradient method)": [[2, "cellpack.autopack.Gradient.Gradient.build_surface_distance_weight_map", false]], "build_weight_map() (cellpack.autopack.gradient.gradient method)": [[2, "cellpack.autopack.Gradient.Gradient.build_weight_map", false]], "buildcompartmentsgrids() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.BuildCompartmentsGrids", false]], "buildgrid() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.BuildGrid", false]], "buildgrid() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.buildGrid", false]], "buildgrid_bhtree() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.BuildGrid_bhtree", false]], "buildgrid_binvox() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.BuildGrid_binvox", false]], "buildgrid_box() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.BuildGrid_box", false]], "buildgrid_kevin() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.BuildGrid_kevin", false]], "buildgrid_multisdf() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.BuildGrid_multisdf", false]], "buildgrid_pyray() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.BuildGrid_pyray", false]], "buildgrid_ray() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.BuildGrid_ray", false]], "buildgrid_scanline() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.BuildGrid_scanline", false]], "buildgrid_trimesh() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.BuildGrid_trimesh", false]], "buildgrid_utsdf() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.BuildGrid_utsdf", false]], "buildgridenviroonly() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.BuildGridEnviroOnly", false]], "buildingrprimitive() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.buildIngrPrimitive", false]], "buildmesh() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.buildMesh", false]], "buildmesh() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.buildMesh", false]], "buildsphere() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.buildSphere", false]], "bullet_checkcollision_mp() (in module cellpack.autopack.ingredient.utils)": [[3, "cellpack.autopack.ingredient.utils.bullet_checkCollision_mp", false]], "calc_pairwise_distances() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.calc_pairwise_distances", false]], "calc_scaled_distances_for_positions() (cellpack.autopack.meshstore.meshstore static method)": [[2, "cellpack.autopack.MeshStore.MeshStore.calc_scaled_distances_for_positions", false]], "calc_volume() (cellpack.autopack.geometrytools.geometrytools method)": [[2, "cellpack.autopack.GeometryTools.GeometryTools.calc_volume", false]], "callfunction() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.callFunction", false]], "callfunction() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.callFunction", false]], "cam_options (cellpack.autopack.upy.hosthelper.helper attribute)": [[6, "cellpack.autopack.upy.hostHelper.Helper.CAM_OPTIONS", false]], "cartesian() (cellpack.autopack.basegrid.basegrid method)": [[2, "cellpack.autopack.BaseGrid.BaseGrid.cartesian", false]], "cartesian() (cellpack.autopack.binvox_rw.voxels method)": [[2, "cellpack.autopack.binvox_rw.Voxels.cartesian", false]], "cartesian_to_sph() (cellpack.autopack.analysis.analysis static method)": [[2, "cellpack.autopack.Analysis.Analysis.cartesian_to_sph", false]], "cellpack": [[1, "module-cellpack", false]], "cellpack.autopack": [[2, "module-cellpack.autopack", false]], "cellpack.autopack.analysis": [[2, "module-cellpack.autopack.Analysis", false]], "cellpack.autopack.awshandler": [[2, "module-cellpack.autopack.AWSHandler", false]], "cellpack.autopack.basegrid": [[2, "module-cellpack.autopack.BaseGrid", false]], "cellpack.autopack.binvox_rw": [[2, "module-cellpack.autopack.binvox_rw", false]], "cellpack.autopack.compartment": [[2, "module-cellpack.autopack.Compartment", false]], "cellpack.autopack.dbrecipehandler": [[2, "module-cellpack.autopack.DBRecipeHandler", false]], "cellpack.autopack.environment": [[2, "module-cellpack.autopack.Environment", false]], "cellpack.autopack.firebasehandler": [[2, "module-cellpack.autopack.FirebaseHandler", false]], "cellpack.autopack.geometrytools": [[2, "module-cellpack.autopack.GeometryTools", false]], "cellpack.autopack.gradient": [[2, "module-cellpack.autopack.Gradient", false]], "cellpack.autopack.graphics": [[2, "module-cellpack.autopack.Graphics", false]], "cellpack.autopack.grid": [[2, "module-cellpack.autopack.Grid", false]], "cellpack.autopack.ingredient": [[3, "module-cellpack.autopack.ingredient", false]], "cellpack.autopack.ingredient.agent": [[3, "module-cellpack.autopack.ingredient.agent", false]], "cellpack.autopack.ingredient.grow": [[3, "module-cellpack.autopack.ingredient.grow", false]], "cellpack.autopack.ingredient.ingredient": [[3, "module-cellpack.autopack.ingredient.Ingredient", false]], "cellpack.autopack.ingredient.multi_cylinder": [[3, "module-cellpack.autopack.ingredient.multi_cylinder", false]], "cellpack.autopack.ingredient.multi_sphere": [[3, "module-cellpack.autopack.ingredient.multi_sphere", false]], "cellpack.autopack.ingredient.single_cube": [[3, "module-cellpack.autopack.ingredient.single_cube", false]], "cellpack.autopack.ingredient.single_cylinder": [[3, "module-cellpack.autopack.ingredient.single_cylinder", false]], "cellpack.autopack.ingredient.single_sphere": [[3, "module-cellpack.autopack.ingredient.single_sphere", false]], "cellpack.autopack.ingredient.utils": [[3, "module-cellpack.autopack.ingredient.utils", false]], "cellpack.autopack.interface_objects": [[4, "module-cellpack.autopack.interface_objects", false]], "cellpack.autopack.interface_objects.database_ids": [[4, "module-cellpack.autopack.interface_objects.database_ids", false]], "cellpack.autopack.interface_objects.default_values": [[4, "module-cellpack.autopack.interface_objects.default_values", false]], "cellpack.autopack.interface_objects.gradient_data": [[4, "module-cellpack.autopack.interface_objects.gradient_data", false]], "cellpack.autopack.interface_objects.ingredient_types": [[4, "module-cellpack.autopack.interface_objects.ingredient_types", false]], "cellpack.autopack.interface_objects.meta_enum": [[4, "module-cellpack.autopack.interface_objects.meta_enum", false]], "cellpack.autopack.interface_objects.packed_objects": [[4, "module-cellpack.autopack.interface_objects.packed_objects", false]], "cellpack.autopack.interface_objects.partners": [[4, "module-cellpack.autopack.interface_objects.partners", false]], "cellpack.autopack.interface_objects.representations": [[4, "module-cellpack.autopack.interface_objects.representations", false]], "cellpack.autopack.ioutils": [[2, "module-cellpack.autopack.IOutils", false]], "cellpack.autopack.ldsequence": [[2, "module-cellpack.autopack.ldSequence", false]], "cellpack.autopack.loaders": [[5, "module-cellpack.autopack.loaders", false]], "cellpack.autopack.loaders.analysis_config_loader": [[5, "module-cellpack.autopack.loaders.analysis_config_loader", false]], "cellpack.autopack.loaders.config_loader": [[5, "module-cellpack.autopack.loaders.config_loader", false]], "cellpack.autopack.loaders.migrate_v1_to_v2": [[5, "module-cellpack.autopack.loaders.migrate_v1_to_v2", false]], "cellpack.autopack.loaders.migrate_v2_to_v2_1": [[5, "module-cellpack.autopack.loaders.migrate_v2_to_v2_1", false]], "cellpack.autopack.loaders.recipe_loader": [[5, "module-cellpack.autopack.loaders.recipe_loader", false]], "cellpack.autopack.loaders.utils": [[5, "module-cellpack.autopack.loaders.utils", false]], "cellpack.autopack.loaders.v1_v2_attribute_changes": [[5, "module-cellpack.autopack.loaders.v1_v2_attribute_changes", false]], "cellpack.autopack.meshstore": [[2, "module-cellpack.autopack.MeshStore", false]], "cellpack.autopack.octree": [[2, "module-cellpack.autopack.octree", false]], "cellpack.autopack.plotly_result": [[2, "module-cellpack.autopack.plotly_result", false]], "cellpack.autopack.randomrot": [[2, "module-cellpack.autopack.randomRot", false]], "cellpack.autopack.ray": [[2, "module-cellpack.autopack.ray", false]], "cellpack.autopack.recipe": [[2, "module-cellpack.autopack.Recipe", false]], "cellpack.autopack.serializable": [[2, "module-cellpack.autopack.Serializable", false]], "cellpack.autopack.trajectory": [[2, "module-cellpack.autopack.trajectory", false]], "cellpack.autopack.transformation": [[2, "module-cellpack.autopack.transformation", false]], "cellpack.autopack.upy": [[6, "module-cellpack.autopack.upy", false]], "cellpack.autopack.upy.colors": [[6, "module-cellpack.autopack.upy.colors", false]], "cellpack.autopack.upy.hosthelper": [[6, "module-cellpack.autopack.upy.hostHelper", false]], "cellpack.autopack.upy.simularium": [[7, "module-cellpack.autopack.upy.simularium", false]], "cellpack.autopack.upy.simularium.plots": [[7, "module-cellpack.autopack.upy.simularium.plots", false]], "cellpack.autopack.upy.simularium.simularium_helper": [[7, "module-cellpack.autopack.upy.simularium.simularium_helper", false]], "cellpack.autopack.utils": [[2, "module-cellpack.autopack.utils", false]], "cellpack.autopack.writers": [[8, "module-cellpack.autopack.writers", false]], "cellpack.autopack.writers.imagewriter": [[8, "module-cellpack.autopack.writers.ImageWriter", false]], "cellpack.bin": [[9, "module-cellpack.bin", false]], "cellpack.bin.analyze": [[9, "module-cellpack.bin.analyze", false]], "cellpack.bin.clean": [[9, "module-cellpack.bin.clean", false]], "cellpack.bin.cleanup_tasks": [[9, "module-cellpack.bin.cleanup_tasks", false]], "cellpack.bin.pack": [[9, "module-cellpack.bin.pack", false]], "cellpack.bin.simularium_converter": [[9, "module-cellpack.bin.simularium_converter", false]], "cellpack.bin.upload": [[9, "module-cellpack.bin.upload", false]], "center (cellpack.autopack.interface_objects.gradient_data.modeoptions attribute)": [[4, "cellpack.autopack.interface_objects.gradient_data.ModeOptions.center", false]], "chaltonsequence3 (class in cellpack.autopack.ldsequence)": [[2, "cellpack.autopack.ldSequence.cHaltonSequence3", false]], "changecolor() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.changeColor", false]], "changecolor() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.changeColor", false]], "changecoloro() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.changeColorO", false]], "changematerialproperty() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.changeMaterialProperty", false]], "changeobjcolormat() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.changeObjColorMat", false]], "changeobjcolormat() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.changeObjColorMat", false]], "check_against_one_packed_ingr() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.check_against_one_packed_ingr", false]], "check_and_replace_references() (cellpack.autopack.dbrecipehandler.compositiondoc method)": [[2, "cellpack.autopack.DBRecipeHandler.CompositionDoc.check_and_replace_references", false]], "check_new_placement() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.check_new_placement", false]], "check_paired_key() (in module cellpack.autopack.utils)": [[2, "cellpack.autopack.utils.check_paired_key", false]], "check_rectangle_oustide() (cellpack.autopack.geometrytools.geometrytools method)": [[2, "cellpack.autopack.GeometryTools.GeometryTools.check_rectangle_oustide", false]], "check_required_attributes() (in module cellpack.autopack.loaders.migrate_v1_to_v2)": [[5, "cellpack.autopack.loaders.migrate_v1_to_v2.check_required_attributes", false]], "check_sphere_inside() (cellpack.autopack.geometrytools.geometrytools method)": [[2, "cellpack.autopack.GeometryTools.GeometryTools.check_sphere_inside", false]], "checkcreateempty() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.checkCreateEmpty", false]], "checkcylcollisions() (cellpack.autopack.ingredient.multi_cylinder.multicylindersingr method)": [[3, "cellpack.autopack.ingredient.multi_cylinder.MultiCylindersIngr.checkCylCollisions", false]], "checkcylcollisions() (cellpack.autopack.ingredient.single_cylinder.singlecylinderingr method)": [[3, "cellpack.autopack.ingredient.single_cylinder.SingleCylinderIngr.checkCylCollisions", false]], "checkdistance() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.checkDistance", false]], "checkerrorinpath() (in module cellpack.autopack)": [[2, "cellpack.autopack.checkErrorInPath", false]], "checkifupdate() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.checkIfUpdate", false]], "checkingrpartnerproperties() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.checkIngrPartnerProperties", false]], "checkingrspheres() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.checkIngrSpheres", false]], "checkismesh() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.checkIsMesh", false]], "checkname() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.checkName", false]], "checkpath() (in module cellpack.autopack)": [[2, "cellpack.autopack.checkPath", false]], "checkpointinsidebb() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.checkPointInsideBB", false]], "checkrecipeavailable() (in module cellpack.autopack)": [[2, "cellpack.autopack.checkRecipeAvailable", false]], "checkrotformat() (in module cellpack.autopack.ioutils)": [[2, "cellpack.autopack.IOutils.checkRotFormat", false]], "circle() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.Circle", false]], "clean() (in module cellpack.bin.clean)": [[9, "cellpack.bin.clean.clean", false]], "clean_arguments() (cellpack.autopack.ioutils.ioingredienttool static method)": [[2, "cellpack.autopack.IOutils.IOingredientTool.clean_arguments", false]], "clean_grid_cache() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.clean_grid_cache", false]], "cleanup_results() (cellpack.autopack.dbrecipehandler.dbmaintenance method)": [[2, "cellpack.autopack.DBRecipeHandler.DBMaintenance.cleanup_results", false]], "clear() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.clear", false]], "clear() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.clear", false]], "clearall() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.clearAll", false]], "clearcaches() (in module cellpack.autopack)": [[2, "cellpack.autopack.clearCaches", false]], "clearfill() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.clearFill", false]], "clearingr() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.clearIngr", false]], "clearrbingredient() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.clearRBingredient", false]], "clearrecipe() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.clearRecipe", false]], "clone() (cellpack.autopack.binvox_rw.voxels method)": [[2, "cellpack.autopack.binvox_rw.Voxels.clone", false]], "close_partner_check() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.close_partner_check", false]], "cmp_to_key() (in module cellpack.autopack.utils)": [[2, "cellpack.autopack.utils.cmp_to_key", false]], "colladaexporter (class in cellpack.autopack.graphics)": [[2, "cellpack.autopack.Graphics.ColladaExporter", false]], "collect_and_sort_data() (cellpack.autopack.dbrecipehandler.dbrecipeloader static method)": [[2, "cellpack.autopack.DBRecipeHandler.DBRecipeLoader.collect_and_sort_data", false]], "collect_docs_by_id() (cellpack.autopack.dbrecipehandler.dbrecipeloader method)": [[2, "cellpack.autopack.DBRecipeHandler.DBRecipeLoader.collect_docs_by_id", false]], "collectresult() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.collectResult", false]], "collectresultperingredient() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.collectResultPerIngredient", false]], "collides_with_compartment() (cellpack.autopack.ingredient.multi_cylinder.multicylindersingr method)": [[3, "cellpack.autopack.ingredient.multi_cylinder.MultiCylindersIngr.collides_with_compartment", false]], "collides_with_compartment() (cellpack.autopack.ingredient.multi_sphere.multisphereingr method)": [[3, "cellpack.autopack.ingredient.multi_sphere.MultiSphereIngr.collides_with_compartment", false]], "collides_with_compartment() (cellpack.autopack.ingredient.single_cube.singlecubeingr method)": [[3, "cellpack.autopack.ingredient.single_cube.SingleCubeIngr.collides_with_compartment", false]], "collides_with_compartment() (cellpack.autopack.ingredient.single_cylinder.singlecylinderingr method)": [[3, "cellpack.autopack.ingredient.single_cylinder.SingleCylinderIngr.collides_with_compartment", false]], "collides_with_compartment() (cellpack.autopack.ingredient.single_sphere.singlesphereingr method)": [[3, "cellpack.autopack.ingredient.single_sphere.SingleSphereIngr.collides_with_compartment", false]], "collision_jitter() (cellpack.autopack.ingredient.multi_cylinder.multicylindersingr method)": [[3, "cellpack.autopack.ingredient.multi_cylinder.MultiCylindersIngr.collision_jitter", false]], "collision_jitter() (cellpack.autopack.ingredient.multi_sphere.multisphereingr method)": [[3, "cellpack.autopack.ingredient.multi_sphere.MultiSphereIngr.collision_jitter", false]], "collision_jitter() (cellpack.autopack.ingredient.single_cube.singlecubeingr method)": [[3, "cellpack.autopack.ingredient.single_cube.SingleCubeIngr.collision_jitter", false]], "collision_jitter() (cellpack.autopack.ingredient.single_cylinder.singlecylinderingr method)": [[3, "cellpack.autopack.ingredient.single_cylinder.SingleCylinderIngr.collision_jitter", false]], "collision_jitter() (cellpack.autopack.ingredient.single_sphere.singlesphereingr method)": [[3, "cellpack.autopack.ingredient.single_sphere.SingleSphereIngr.collision_jitter", false]], "color() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.color", false]], "colorbydistancefrom() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.colorByDistanceFrom", false]], "colorbyorder() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.colorByOrder", false]], "colormaterial() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.colorMaterial", false]], "colorobject() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.colorObject", false]], "colorpt() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.colorPT", false]], "combine_results_from_ingredients() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.combine_results_from_ingredients", false]], "combine_results_from_seeds() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.combine_results_from_seeds", false]], "combinedaemeshdata() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.combineDaeMeshData", false]], "compartment (class in cellpack.autopack.compartment)": [[2, "cellpack.autopack.Compartment.Compartment", false]], "compartment_id_for_nearest_grid_point() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.compartment_id_for_nearest_grid_point", false]], "compartmentlist (class in cellpack.autopack.compartment)": [[2, "cellpack.autopack.Compartment.CompartmentList", false]], "compile_db_recipe_data() (cellpack.autopack.dbrecipehandler.dbrecipeloader static method)": [[2, "cellpack.autopack.DBRecipeHandler.DBRecipeLoader.compile_db_recipe_data", false]], "completemapping() (cellpack.autopack.trajectory.trajectory method)": [[2, "cellpack.autopack.trajectory.Trajectory.completeMapping", false]], "compositiondoc (class in cellpack.autopack.dbrecipehandler)": [[2, "cellpack.autopack.DBRecipeHandler.CompositionDoc", false]], "compute_volume_and_set_count() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.compute_volume_and_set_count", false]], "computeexteriorvolume() (cellpack.autopack.basegrid.basegrid method)": [[2, "cellpack.autopack.BaseGrid.BaseGrid.computeExteriorVolume", false]], "computegridnumberofpoint() (cellpack.autopack.basegrid.basegrid method)": [[2, "cellpack.autopack.BaseGrid.BaseGrid.computeGridNumberOfPoint", false]], "computevolume() (cellpack.autopack.basegrid.basegrid method)": [[2, "cellpack.autopack.BaseGrid.BaseGrid.computeVolume", false]], "concatenate_image_data() (cellpack.autopack.writers.imagewriter.imagewriter method)": [[8, "cellpack.autopack.writers.ImageWriter.ImageWriter.concatenate_image_data", false]], "concatobjectmatrix() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.concatObjectMatrix", false]], "concatobjectmatrix() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.concatObjectMatrix", false]], "configloader (class in cellpack.autopack.loaders.config_loader)": [[5, "cellpack.autopack.loaders.config_loader.ConfigLoader", false]], "constraintlookat() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.constraintLookAt", false]], "contains_point() (cellpack.autopack.meshstore.meshstore method)": [[2, "cellpack.autopack.MeshStore.MeshStore.contains_point", false]], "contains_points_mesh() (cellpack.autopack.meshstore.meshstore method)": [[2, "cellpack.autopack.MeshStore.MeshStore.contains_points_mesh", false]], "convert() (in module cellpack.autopack.loaders.migrate_v1_to_v2)": [[5, "cellpack.autopack.loaders.migrate_v1_to_v2.convert", false]], "convert() (in module cellpack.autopack.loaders.migrate_v2_to_v2_1)": [[5, "cellpack.autopack.loaders.migrate_v2_to_v2_1.convert", false]], "convert_db_shortname_to_url() (in module cellpack.autopack)": [[2, "cellpack.autopack.convert_db_shortname_to_url", false]], "convert_gradients() (in module cellpack.autopack.loaders.migrate_v2_to_v2_1)": [[5, "cellpack.autopack.loaders.migrate_v2_to_v2_1.convert_gradients", false]], "convert_partners() (in module cellpack.autopack.loaders.migrate_v2_to_v2_1)": [[5, "cellpack.autopack.loaders.migrate_v2_to_v2_1.convert_partners", false]], "convert_positions_in_representation() (cellpack.autopack.dbrecipehandler.objectdoc static method)": [[2, "cellpack.autopack.DBRecipeHandler.ObjectDoc.convert_positions_in_representation", false]], "convert_representation() (cellpack.autopack.dbrecipehandler.objectdoc static method)": [[2, "cellpack.autopack.DBRecipeHandler.ObjectDoc.convert_representation", false]], "convert_rotation_range() (in module cellpack.autopack.loaders.migrate_v1_to_v2)": [[5, "cellpack.autopack.loaders.migrate_v1_to_v2.convert_rotation_range", false]], "convertcolor() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.convertColor", false]], "convertpickletotext() (cellpack.autopack.environment.environment class method)": [[2, "cellpack.autopack.Environment.Environment.convertPickleToText", false]], "converttosimularium (class in cellpack.bin.simularium_converter)": [[9, "cellpack.bin.simularium_converter.ConvertToSimularium", false]], "convolve_channel() (cellpack.autopack.writers.imagewriter.imagewriter static method)": [[8, "cellpack.autopack.writers.ImageWriter.ImageWriter.convolve_channel", false]], "convolve_image() (cellpack.autopack.writers.imagewriter.imagewriter method)": [[8, "cellpack.autopack.writers.ImageWriter.ImageWriter.convolve_image", false]], "correctbb() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.correctBB", false]], "create3dpointlookup() (cellpack.autopack.basegrid.haltongrid method)": [[2, "cellpack.autopack.BaseGrid.HaltonGrid.create3DPointLookup", false]], "create3dpointlookup() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.create3DPointLookup", false]], "create3dpointlookup() (cellpack.autopack.grid.grid method)": [[2, "cellpack.autopack.Grid.Grid.create3DPointLookup", false]], "create_box_psf() (cellpack.autopack.writers.imagewriter.imagewriter static method)": [[8, "cellpack.autopack.writers.ImageWriter.ImageWriter.create_box_psf", false]], "create_circular_mask() (cellpack.autopack.ingredient.single_sphere.singlesphereingr static method)": [[3, "cellpack.autopack.ingredient.single_sphere.SingleSphereIngr.create_circular_mask", false]], "create_compartment() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.create_compartment", false]], "create_divergent_color_map_with_scaled_values() (in module cellpack.autopack.upy.colors)": [[6, "cellpack.autopack.upy.colors.create_divergent_color_map_with_scaled_values", false]], "create_file_info_object_from_full_path() (in module cellpack.autopack.loaders.utils)": [[5, "cellpack.autopack.loaders.utils.create_file_info_object_from_full_path", false]], "create_gaussian_psf() (cellpack.autopack.writers.imagewriter.imagewriter static method)": [[8, "cellpack.autopack.writers.ImageWriter.ImageWriter.create_gaussian_psf", false]], "create_grid_point_positions() (cellpack.autopack.basegrid.basegrid method)": [[2, "cellpack.autopack.BaseGrid.BaseGrid.create_grid_point_positions", false]], "create_ingredient() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.create_ingredient", false]], "create_mesh() (cellpack.autopack.meshstore.meshstore method)": [[2, "cellpack.autopack.MeshStore.MeshStore.create_mesh", false]], "create_objects() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.create_objects", false]], "create_output_dir() (in module cellpack.autopack.loaders.utils)": [[5, "cellpack.autopack.loaders.utils.create_output_dir", false]], "create_path() (cellpack.autopack.firebasehandler.firebasehandler static method)": [[2, "cellpack.autopack.FirebaseHandler.FirebaseHandler.create_path", false]], "create_presigned_url() (cellpack.autopack.awshandler.awshandler method)": [[2, "cellpack.autopack.AWSHandler.AWSHandler.create_presigned_url", false]], "create_rbnode() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.create_rbnode", false]], "create_report() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.create_report", false]], "create_sphere() (cellpack.autopack.meshstore.meshstore method)": [[2, "cellpack.autopack.MeshStore.MeshStore.create_sphere", false]], "create_sphere_data() (cellpack.autopack.meshstore.meshstore method)": [[2, "cellpack.autopack.MeshStore.MeshStore.create_sphere_data", false]], "create_timestamp() (cellpack.autopack.firebasehandler.firebasehandler static method)": [[2, "cellpack.autopack.FirebaseHandler.FirebaseHandler.create_timestamp", false]], "create_voxelization() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.create_voxelization", false]], "create_voxelization() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.create_voxelization", false]], "create_voxelization() (cellpack.autopack.gradient.gradient method)": [[2, "cellpack.autopack.Gradient.Gradient.create_voxelization", false]], "create_voxelization() (cellpack.autopack.ingredient.single_sphere.singlesphereingr method)": [[3, "cellpack.autopack.ingredient.single_sphere.SingleSphereIngr.create_voxelization", false]], "create_voxelized_mask() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.create_voxelized_mask", false]], "createcolorsmat() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.createColorsMat", false]], "createingrmesh() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.createIngrMesh", false]], "creatematerial() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.createMaterial", false]], "createorganelmesh() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.createOrganelMesh", false]], "createsnmesh() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.createsNmesh", false]], "createspring() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.createSpring", false]], "createsurfacepoints() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.createSurfacePoints", false]], "createtemplate() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.createTemplate", false]], "createtemplatecompartment() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.createTemplateCompartment", false]], "createtexturedmaterial() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.createTexturedMaterial", false]], "cube (cellpack.autopack.interface_objects.gradient_data.weightmodes attribute)": [[4, "cellpack.autopack.interface_objects.gradient_data.WeightModes.CUBE", false]], "cube() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.Cube", false]], "cube_surface_distance() (cellpack.autopack.ingredient.single_cube.singlecubeingr method)": [[3, "cellpack.autopack.ingredient.single_cube.SingleCubeIngr.cube_surface_distance", false]], "cylinder() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.Cylinder", false]], "cylinder() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.cylinder", false]], "cylinderheadtails() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.CylinderHeadTails", false]], "cylinders() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.Cylinders", false]], "database (cellpack.autopack.interface_objects.representations.representations attribute)": [[4, "cellpack.autopack.interface_objects.representations.Representations.DATABASE", false]], "database (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper attribute)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.DATABASE", false]], "database_ids (class in cellpack.autopack.interface_objects.database_ids)": [[4, "cellpack.autopack.interface_objects.database_ids.DATABASE_IDS", false]], "datadoc (class in cellpack.autopack.dbrecipehandler)": [[2, "cellpack.autopack.DBRecipeHandler.DataDoc", false]], "db_name() (cellpack.autopack.firebasehandler.firebasehandler method)": [[2, "cellpack.autopack.FirebaseHandler.FirebaseHandler.db_name", false]], "dbmaintenance (class in cellpack.autopack.dbrecipehandler)": [[2, "cellpack.autopack.DBRecipeHandler.DBMaintenance", false]], "dbrecipeloader (class in cellpack.autopack.dbrecipehandler)": [[2, "cellpack.autopack.DBRecipeHandler.DBRecipeLoader", false]], "dbuploader (class in cellpack.autopack.dbrecipehandler)": [[2, "cellpack.autopack.DBRecipeHandler.DBUploader", false]], "dcd (cellpack.autopack.trajectory.dcdtrajectory attribute)": [[2, "cellpack.autopack.trajectory.dcdTrajectory.dcd", false]], "dcdtrajectory (class in cellpack.autopack.trajectory)": [[2, "cellpack.autopack.trajectory.dcdTrajectory", false]], "debug (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper attribute)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.DEBUG", false]], "decay_length (cellpack.autopack.interface_objects.gradient_data.weightmodeoptions attribute)": [[4, "cellpack.autopack.interface_objects.gradient_data.WeightModeOptions.decay_length", false]], "decompose4x4() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.Decompose4x4", false]], "decompose_mesh() (cellpack.autopack.meshstore.meshstore method)": [[2, "cellpack.autopack.MeshStore.MeshStore.decompose_mesh", false]], "decomposecolladageom() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.decomposeColladaGeom", false]], "decomposemesh() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.DecomposeMesh", false]], "decomposemesh() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.DecomposeMesh", false]], "deep_merge() (in module cellpack.autopack.utils)": [[2, "cellpack.autopack.utils.deep_merge", false]], "default() (cellpack.autopack.writers.numpyarrayencoder method)": [[8, "cellpack.autopack.writers.NumpyArrayEncoder.default", false]], "default_geo_type (cellpack.bin.simularium_converter.converttosimularium attribute)": [[9, "cellpack.bin.simularium_converter.ConvertToSimularium.DEFAULT_GEO_TYPE", false]], "default_input_recipe (cellpack.bin.simularium_converter.converttosimularium attribute)": [[9, "cellpack.bin.simularium_converter.ConvertToSimularium.DEFAULT_INPUT_RECIPE", false]], "default_output_directory (cellpack.bin.simularium_converter.converttosimularium attribute)": [[9, "cellpack.bin.simularium_converter.ConvertToSimularium.DEFAULT_OUTPUT_DIRECTORY", false]], "default_packing_result (cellpack.bin.simularium_converter.converttosimularium attribute)": [[9, "cellpack.bin.simularium_converter.ConvertToSimularium.DEFAULT_PACKING_RESULT", false]], "default_scale_factor (cellpack.bin.simularium_converter.converttosimularium attribute)": [[9, "cellpack.bin.simularium_converter.ConvertToSimularium.DEFAULT_SCALE_FACTOR", false]], "default_values (cellpack.autopack.dbrecipehandler.compositiondoc attribute)": [[2, "cellpack.autopack.DBRecipeHandler.CompositionDoc.DEFAULT_VALUES", false]], "default_values (cellpack.autopack.interface_objects.gradient_data.gradientdata attribute)": [[4, "cellpack.autopack.interface_objects.gradient_data.GradientData.default_values", false]], "default_values (cellpack.autopack.loaders.analysis_config_loader.analysisconfigloader attribute)": [[5, "cellpack.autopack.loaders.analysis_config_loader.AnalysisConfigLoader.default_values", false]], "default_values (cellpack.autopack.loaders.config_loader.configloader attribute)": [[5, "cellpack.autopack.loaders.config_loader.ConfigLoader.default_values", false]], "default_values (cellpack.autopack.loaders.recipe_loader.recipeloader attribute)": [[5, "cellpack.autopack.loaders.recipe_loader.RecipeLoader.default_values", false]], "defaultfunction() (cellpack.autopack.gradient.gradient method)": [[2, "cellpack.autopack.Gradient.Gradient.defaultFunction", false]], "delete_doc() (cellpack.autopack.firebasehandler.firebasehandler method)": [[2, "cellpack.autopack.FirebaseHandler.FirebaseHandler.delete_doc", false]], "deleteblist() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.deleteblist", false]], "deletechildrens() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.deleteChildrens", false]], "deleteinstance() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.deleteInstance", false]], "deletemeshedges() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.deleteMeshEdges", false]], "deletemeshfaces() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.deleteMeshFaces", false]], "deletemeshvertices() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.deleteMeshVertices", false]], "deleteobject() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.deleteObject", false]], "delingr() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.delIngr", false]], "delingredient() (cellpack.autopack.recipe.recipe method)": [[2, "cellpack.autopack.Recipe.Recipe.delIngredient", false]], "delingredientgrow() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.delIngredientGrow", false]], "delrb() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.delRB", false]], "dense_to_sparse() (in module cellpack.autopack.binvox_rw)": [[2, "cellpack.autopack.binvox_rw.dense_to_sparse", false]], "dihedral() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.dihedral", false]], "direction (cellpack.autopack.interface_objects.gradient_data.modeoptions attribute)": [[4, "cellpack.autopack.interface_objects.gradient_data.ModeOptions.direction", false]], "displaycompartment() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.displayCompartment", false]], "displaycompartmentpoints() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.displayCompartmentPoints", false]], "displaycompartments() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.displayCompartments", false]], "displaycompartmentsingredients() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.displayCompartmentsIngredients", false]], "displaycompartmentspoints() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.displayCompartmentsPoints", false]], "displaycytoplasmingredients() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.displayCytoplasmIngredients", false]], "displaydistance() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.displayDistance", false]], "displayenv() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.displayEnv", false]], "displayfill() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.displayFill", false]], "displayfillbox() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.displayFillBox", false]], "displayfreepoints() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.displayFreePoints", false]], "displayfreepointsasps() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.displayFreePointsAsPS", false]], "displaygradient() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.displayGradient", false]], "displayingrcylinders() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.displayIngrCylinders", false]], "displayingredients() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.displayIngredients", false]], "displayingrgrow() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.displayIngrGrow", false]], "displayingrgrows() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.displayIngrGrows", false]], "displayingrmesh() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.displayIngrMesh", false]], "displayingrresults() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.displayIngrResults", false]], "displayingrspheres() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.displayIngrSpheres", false]], "displayinstancesingredient() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.displayInstancesIngredient", false]], "displayleafoctree() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.displayLeafOctree", false]], "displayoctree() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.displayOctree", false]], "displayoctreeleaf() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.displayOctreeLeaf", false]], "displayonenodeoctree() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.displayOneNodeOctree", false]], "displayparticlevolumedistance() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.displayParticleVolumeDistance", false]], "displaypoints() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.displayPoints", false]], "displayprefill() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.displayPreFill", false]], "displayroot() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.displayRoot", false]], "displaysubnode() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.displaysubnode", false]], "distance (cellpack.autopack.interface_objects.gradient_data.invertoptions attribute)": [[4, "cellpack.autopack.interface_objects.gradient_data.InvertOptions.distance", false]], "distance_check_failed() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.distance_check_failed", false]], "distancefunction() (cellpack.autopack.interface_objects.partners.partner method)": [[4, "cellpack.autopack.interface_objects.partners.Partner.distanceFunction", false]], "distributionoptions (class in cellpack.autopack.ingredient.ingredient)": [[3, "cellpack.autopack.ingredient.Ingredient.DistributionOptions", false]], "distributiontypes (class in cellpack.autopack.ingredient.ingredient)": [[3, "cellpack.autopack.ingredient.Ingredient.DistributionTypes", false]], "doc_id() (cellpack.autopack.firebasehandler.firebasehandler static method)": [[2, "cellpack.autopack.FirebaseHandler.FirebaseHandler.doc_id", false]], "doc_to_dict() (cellpack.autopack.firebasehandler.firebasehandler static method)": [[2, "cellpack.autopack.FirebaseHandler.FirebaseHandler.doc_to_dict", false]], "dodecahedron() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.Dodecahedron", false], [6, "cellpack.autopack.upy.hostHelper.Helper.dodecahedron", false]], "doloop() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.doloop", false]], "dot() (in module cellpack.autopack.ray)": [[2, "cellpack.autopack.ray.dot", false]], "dot() (in module cellpack.autopack.upy.hosthelper)": [[6, "cellpack.autopack.upy.hostHelper.dot", false]], "download_file() (cellpack.autopack.awshandler.awshandler method)": [[2, "cellpack.autopack.AWSHandler.AWSHandler.download_file", false]], "download_file() (in module cellpack.autopack)": [[2, "cellpack.autopack.download_file", false]], "drawgradientline() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.drawGradientLine", false]], "drawptcol() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.drawPtCol", false]], "droponeingr() (cellpack.autopack.environment.environment class method)": [[2, "cellpack.autopack.Environment.Environment.dropOneIngr", false]], "droponeingrjson() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.dropOneIngrJson", false]], "dspmesh() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.dspMesh", false]], "dspsph() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.dspSph", false]], "duplivert (cellpack.autopack.upy.hosthelper.helper attribute)": [[6, "cellpack.autopack.upy.hostHelper.Helper.dupliVert", false]], "empty (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper attribute)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.EMPTY", false]], "environment (class in cellpack.autopack.environment)": [[2, "cellpack.autopack.Environment.Environment", false]], "eulertomatrix() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.eulerToMatrix", false]], "expand_object_using_key() (in module cellpack.autopack.utils)": [[2, "cellpack.autopack.utils.expand_object_using_key", false]], "exponential (cellpack.autopack.interface_objects.gradient_data.weightmodes attribute)": [[4, "cellpack.autopack.interface_objects.gradient_data.WeightModes.EXPONENTIAL", false]], "export_image() (cellpack.autopack.writers.imagewriter.imagewriter method)": [[8, "cellpack.autopack.writers.ImageWriter.ImageWriter.export_image", false]], "exportasindexedmeshs() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.exportAsIndexedMeshs", false]], "exportcollada (class in cellpack.autopack.ioutils)": [[2, "cellpack.autopack.IOutils.ExportCollada", false]], "exportingredient() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.exportIngredient", false]], "exportrecipeingredients() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.exportRecipeIngredients", false]], "exporttobd_box() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.exportToBD_BOX", false]], "exporttoreaddy() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.exportToReaDDy", false]], "exporttotem() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.exportToTEM", false]], "exporttotem_sim() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.exportToTEM_SIM", false]], "extend_bounding_box_for_compartments() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.extend_bounding_box_for_compartments", false]], "extendgridarrays() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.extendGridArrays", false]], "extractmeshcomponent() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.extractMeshComponent", false]], "f_dot_product() (in module cellpack.autopack.ray)": [[2, "cellpack.autopack.ray.f_dot_product", false]], "f_ray_intersect_polyhedron() (in module cellpack.autopack.ray)": [[2, "cellpack.autopack.ray.f_ray_intersect_polyhedron", false]], "far_enough_from_surfaces() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.far_enough_from_surfaces", false]], "fill_in_empty_fiber_data() (cellpack.bin.simularium_converter.converttosimularium method)": [[9, "cellpack.bin.simularium_converter.ConvertToSimularium.fill_in_empty_fiber_data", false]], "filltrianglecolor() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.fillTriangleColor", false]], "filter_surface_pts_to_fill_box() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.filter_surface_pts_to_fill_box", false]], "find_nearest() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.find_nearest", false]], "findbranch() (cellpack.autopack.octree.octree method)": [[2, "cellpack.autopack.octree.Octree.findBranch", false]], "findclosestpoint() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.findClosestPoint", false]], "findpointscenter() (in module cellpack.autopack.ray)": [[2, "cellpack.autopack.ray.findPointsCenter", false]], "findposition() (cellpack.autopack.octree.octree method)": [[2, "cellpack.autopack.octree.Octree.findPosition", false]], "finishwithwater() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.finishWithWater", false]], "firebase (cellpack.autopack.interface_objects.database_ids.database_ids attribute)": [[4, "cellpack.autopack.interface_objects.database_ids.DATABASE_IDS.FIREBASE", false]], "firebasehandler (class in cellpack.autopack.firebasehandler)": [[2, "cellpack.autopack.FirebaseHandler.FirebaseHandler", false]], "fit_view3d() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.fit_view3D", false]], "fixnormals() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.FixNormals", false]], "fixonepath() (in module cellpack.autopack)": [[2, "cellpack.autopack.fixOnePath", false]], "fixpath() (in module cellpack.autopack)": [[2, "cellpack.autopack.fixPath", false]], "format_color() (cellpack.autopack.plotly_result.plotlyanalysis static method)": [[2, "cellpack.autopack.plotly_result.PlotlyAnalysis.format_color", false]], "format_rgb_color() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper static method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.format_rgb_color", false]], "frameadvanced() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.frameAdvanced", false]], "fromvec() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.FromVec", false]], "gatherresult() (in module cellpack.autopack.ioutils)": [[2, "cellpack.autopack.IOutils.gatherResult", false]], "gblob (cellpack.autopack.interface_objects.gradient_data.modeoptions attribute)": [[4, "cellpack.autopack.interface_objects.gradient_data.ModeOptions.gblob", false]], "generalapply() (cellpack.autopack.trajectory.trajectory method)": [[2, "cellpack.autopack.trajectory.Trajectory.generalApply", false]], "geom() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.Geom", false]], "geometrytools (class in cellpack.autopack.geometrytools)": [[2, "cellpack.autopack.GeometryTools.GeometryTools", false]], "get() (cellpack.autopack.randomrot.randomrot method)": [[2, "cellpack.autopack.randomRot.RandomRot.get", false]], "get_active() (cellpack.autopack.interface_objects.representations.representations method)": [[4, "cellpack.autopack.interface_objects.representations.Representations.get_active", false]], "get_active_data() (cellpack.autopack.interface_objects.representations.representations method)": [[4, "cellpack.autopack.interface_objects.representations.Representations.get_active_data", false]], "get_adjusted_position() (cellpack.autopack.interface_objects.representations.representations method)": [[4, "cellpack.autopack.interface_objects.representations.Representations.get_adjusted_position", false]], "get_all() (cellpack.autopack.interface_objects.packed_objects.packedobjects method)": [[4, "cellpack.autopack.interface_objects.packed_objects.PackedObjects.get_all", false]], "get_all_distances() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.get_all_distances", false]], "get_all_docs() (cellpack.autopack.firebasehandler.firebasehandler method)": [[2, "cellpack.autopack.FirebaseHandler.FirebaseHandler.get_all_docs", false]], "get_all_ingredients() (cellpack.autopack.loaders.recipe_loader.recipeloader method)": [[5, "cellpack.autopack.loaders.recipe_loader.RecipeLoader.get_all_ingredients", false]], "get_all_positions_to_check() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.get_all_positions_to_check", false]], "get_alternate_position() (cellpack.autopack.ingredient.grow.growingredient method)": [[3, "cellpack.autopack.ingredient.grow.GrowIngredient.get_alternate_position", false]], "get_alternate_position_p() (cellpack.autopack.ingredient.grow.growingredient method)": [[3, "cellpack.autopack.ingredient.grow.GrowIngredient.get_alternate_position_p", false]], "get_and_store_v2_object() (in module cellpack.autopack.loaders.migrate_v1_to_v2)": [[5, "cellpack.autopack.loaders.migrate_v1_to_v2.get_and_store_v2_object", false]], "get_attributes_to_update() (cellpack.autopack.environment.environment static method)": [[2, "cellpack.autopack.Environment.Environment.get_attributes_to_update", false]], "get_aws_object_key() (cellpack.autopack.awshandler.awshandler method)": [[2, "cellpack.autopack.AWSHandler.AWSHandler.get_aws_object_key", false]], "get_bbox() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.get_bbox", false]], "get_bounding_box() (cellpack.bin.simularium_converter.converttosimularium method)": [[9, "cellpack.bin.simularium_converter.ConvertToSimularium.get_bounding_box", false]], "get_bounding_box_limits() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.get_bounding_box_limits", false]], "get_cache_location() (in module cellpack.autopack)": [[2, "cellpack.autopack.get_cache_location", false]], "get_center() (cellpack.autopack.gradient.gradient method)": [[2, "cellpack.autopack.Gradient.Gradient.get_center", false]], "get_centroid() (cellpack.autopack.meshstore.meshstore method)": [[2, "cellpack.autopack.MeshStore.MeshStore.get_centroid", false]], "get_closest_ingredients() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.get_closest_ingredients", false]], "get_collada_material() (cellpack.autopack.meshstore.meshstore static method)": [[2, "cellpack.autopack.MeshStore.MeshStore.get_collada_material", false]], "get_collection_id_from_path() (cellpack.autopack.firebasehandler.firebasehandler static method)": [[2, "cellpack.autopack.FirebaseHandler.FirebaseHandler.get_collection_id_from_path", false]], "get_compartment() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.get_compartment", false]], "get_compartment() (cellpack.autopack.interface_objects.packed_objects.packedobjects method)": [[4, "cellpack.autopack.interface_objects.packed_objects.PackedObjects.get_compartment", false]], "get_compartment_object_by_name() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.get_compartment_object_by_name", false]], "get_creds() (cellpack.autopack.firebasehandler.firebasehandler static method)": [[2, "cellpack.autopack.FirebaseHandler.FirebaseHandler.get_creds", false]], "get_cuttoff_value() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.get_cuttoff_value", false]], "get_cuttoff_value() (cellpack.autopack.ingredient.multi_cylinder.multicylindersingr method)": [[3, "cellpack.autopack.ingredient.multi_cylinder.MultiCylindersIngr.get_cuttoff_value", false]], "get_cuttoff_value() (cellpack.autopack.ingredient.single_cylinder.singlecylinderingr method)": [[3, "cellpack.autopack.ingredient.single_cylinder.SingleCylinderIngr.get_cuttoff_value", false]], "get_deepest_level() (cellpack.autopack.interface_objects.representations.representations method)": [[4, "cellpack.autopack.interface_objects.representations.Representations.get_deepest_level", false]], "get_dev_creds() (cellpack.autopack.firebasehandler.firebasehandler static method)": [[2, "cellpack.autopack.FirebaseHandler.FirebaseHandler.get_dev_creds", false]], "get_display_data() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.get_display_data", false]], "get_distance() (in module cellpack.autopack.utils)": [[2, "cellpack.autopack.utils.get_distance", false]], "get_distances() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.get_distances", false]], "get_distances_and_angles() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.get_distances_and_angles", false]], "get_distances_from_point() (in module cellpack.autopack.utils)": [[2, "cellpack.autopack.utils.get_distances_from_point", false]], "get_doc_by_id() (cellpack.autopack.firebasehandler.firebasehandler method)": [[2, "cellpack.autopack.FirebaseHandler.FirebaseHandler.get_doc_by_id", false]], "get_doc_by_name() (cellpack.autopack.firebasehandler.firebasehandler method)": [[2, "cellpack.autopack.FirebaseHandler.FirebaseHandler.get_doc_by_name", false]], "get_doc_by_ref() (cellpack.autopack.firebasehandler.firebasehandler method)": [[2, "cellpack.autopack.FirebaseHandler.FirebaseHandler.get_doc_by_ref", false]], "get_dpad() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.get_dpad", false]], "get_encapsulating_radii() (cellpack.autopack.interface_objects.packed_objects.packedobjects method)": [[4, "cellpack.autopack.interface_objects.packed_objects.PackedObjects.get_encapsulating_radii", false]], "get_euler() (cellpack.bin.simularium_converter.converttosimularium method)": [[9, "cellpack.bin.simularium_converter.ConvertToSimularium.get_euler", false]], "get_euler_from_matrix() (cellpack.bin.simularium_converter.converttosimularium method)": [[9, "cellpack.bin.simularium_converter.ConvertToSimularium.get_euler_from_matrix", false]], "get_euler_from_quat() (cellpack.bin.simularium_converter.converttosimularium method)": [[9, "cellpack.bin.simularium_converter.ConvertToSimularium.get_euler_from_quat", false]], "get_gauss_weights() (cellpack.autopack.gradient.gradient method)": [[2, "cellpack.autopack.Gradient.Gradient.get_gauss_weights", false]], "get_ingredient_angles() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.get_ingredient_angles", false]], "get_ingredient_by_name() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.get_ingredient_by_name", false]], "get_ingredient_data() (cellpack.bin.simularium_converter.converttosimularium method)": [[9, "cellpack.bin.simularium_converter.ConvertToSimularium.get_ingredient_data", false]], "get_ingredient_display_data() (cellpack.bin.simularium_converter.converttosimularium method)": [[9, "cellpack.bin.simularium_converter.ConvertToSimularium.get_ingredient_display_data", false]], "get_ingredient_key_from_object_or_comp_name() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.get_ingredient_key_from_object_or_comp_name", false]], "get_ingredient_radii() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.get_ingredient_radii", false]], "get_ingredients() (cellpack.autopack.interface_objects.packed_objects.packedobjects method)": [[4, "cellpack.autopack.interface_objects.packed_objects.PackedObjects.get_ingredients", false]], "get_ingredients_in_tree() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.get_ingredients_in_tree", false]], "get_list_of_dims() (cellpack.autopack.analysis.analysis static method)": [[2, "cellpack.autopack.Analysis.Analysis.get_list_of_dims", false]], "get_list_of_free_indices() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.get_list_of_free_indices", false]], "get_local_file_location() (in module cellpack.autopack)": [[2, "cellpack.autopack.get_local_file_location", false]], "get_max_value_from_distribution() (in module cellpack.autopack.utils)": [[2, "cellpack.autopack.utils.get_max_value_from_distribution", false]], "get_mesh() (cellpack.autopack.meshstore.meshstore method)": [[2, "cellpack.autopack.MeshStore.MeshStore.get_mesh", false]], "get_mesh_data() (cellpack.bin.simularium_converter.converttosimularium static method)": [[9, "cellpack.bin.simularium_converter.ConvertToSimularium.get_mesh_data", false]], "get_mesh_filepath_and_extension() (cellpack.autopack.meshstore.meshstore static method)": [[2, "cellpack.autopack.MeshStore.MeshStore.get_mesh_filepath_and_extension", false]], "get_mesh_format() (cellpack.autopack.interface_objects.representations.representations method)": [[4, "cellpack.autopack.interface_objects.representations.Representations.get_mesh_format", false]], "get_mesh_name() (cellpack.autopack.interface_objects.representations.representations method)": [[4, "cellpack.autopack.interface_objects.representations.Representations.get_mesh_name", false]], "get_mesh_path() (cellpack.autopack.interface_objects.representations.representations method)": [[4, "cellpack.autopack.interface_objects.representations.Representations.get_mesh_path", false]], "get_midpoint() (cellpack.autopack.meshstore.meshstore static method)": [[2, "cellpack.autopack.MeshStore.MeshStore.get_midpoint", false]], "get_min_max_radius() (cellpack.autopack.interface_objects.representations.representations method)": [[4, "cellpack.autopack.interface_objects.representations.Representations.get_min_max_radius", false]], "get_min_value_from_distribution() (in module cellpack.autopack.utils)": [[2, "cellpack.autopack.utils.get_min_value_from_distribution", false]], "get_minimum_expected_distance_from_recipe() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.get_minimum_expected_distance_from_recipe", false]], "get_module_version() (in module cellpack)": [[1, "cellpack.get_module_version", false]], "get_new_distance_values() (cellpack.autopack.ingredient.grow.growingredient method)": [[3, "cellpack.autopack.ingredient.grow.GrowIngredient.get_new_distance_values", false]], "get_new_distance_values() (cellpack.autopack.ingredient.multi_sphere.multisphereingr method)": [[3, "cellpack.autopack.ingredient.multi_sphere.MultiSphereIngr.get_new_distance_values", false]], "get_new_distance_values() (cellpack.autopack.ingredient.single_cube.singlecubeingr method)": [[3, "cellpack.autopack.ingredient.single_cube.SingleCubeIngr.get_new_distance_values", false]], "get_new_distance_values() (cellpack.autopack.ingredient.single_sphere.singlesphereingr method)": [[3, "cellpack.autopack.ingredient.single_sphere.SingleSphereIngr.get_new_distance_values", false]], "get_new_distances_and_inside_points() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.get_new_distances_and_inside_points", false]], "get_new_jitter_location_and_rotation() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.get_new_jitter_location_and_rotation", false]], "get_new_pos() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.get_new_pos", false]], "get_noise() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.get_noise", false]], "get_normal() (cellpack.autopack.meshstore.meshstore method)": [[2, "cellpack.autopack.MeshStore.MeshStore.get_normal", false]], "get_normal_for_point() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.get_normal_for_point", false]], "get_normalized_values() (cellpack.autopack.gradient.gradient method)": [[2, "cellpack.autopack.Gradient.Gradient.get_normalized_values", false]], "get_nsphere() (cellpack.autopack.meshstore.meshstore method)": [[2, "cellpack.autopack.MeshStore.MeshStore.get_nsphere", false]], "get_number_of_ingredients_packed() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.get_number_of_ingredients_packed", false]], "get_obj_dict() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.get_obj_dict", false]], "get_object() (cellpack.autopack.meshstore.meshstore method)": [[2, "cellpack.autopack.MeshStore.MeshStore.get_object", false]], "get_packed_minimum_distance() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.get_packed_minimum_distance", false]], "get_paired_key() (in module cellpack.autopack.utils)": [[2, "cellpack.autopack.utils.get_paired_key", false]], "get_partner_by_ingr_name() (cellpack.autopack.interface_objects.partners.partners method)": [[4, "cellpack.autopack.interface_objects.partners.Partners.get_partner_by_ingr_name", false]], "get_partner_pair_dict() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.get_partner_pair_dict", false]], "get_partners() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.get_partners", false]], "get_path_from_ref() (cellpack.autopack.firebasehandler.firebasehandler static method)": [[2, "cellpack.autopack.FirebaseHandler.FirebaseHandler.get_path_from_ref", false]], "get_pdb_path() (cellpack.autopack.interface_objects.representations.representations method)": [[4, "cellpack.autopack.interface_objects.representations.Representations.get_pdb_path", false]], "get_point() (cellpack.autopack.interface_objects.partners.partner method)": [[4, "cellpack.autopack.interface_objects.partners.Partner.get_point", false]], "get_positions() (cellpack.autopack.interface_objects.packed_objects.packedobjects method)": [[4, "cellpack.autopack.interface_objects.packed_objects.PackedObjects.get_positions", false]], "get_positions() (cellpack.autopack.interface_objects.representations.representations method)": [[4, "cellpack.autopack.interface_objects.representations.Representations.get_positions", false]], "get_positions_for_ingredient() (cellpack.autopack.interface_objects.packed_objects.packedobjects method)": [[4, "cellpack.autopack.interface_objects.packed_objects.PackedObjects.get_positions_for_ingredient", false]], "get_positions_per_ingredient() (cellpack.bin.simularium_converter.converttosimularium method)": [[9, "cellpack.bin.simularium_converter.ConvertToSimularium.get_positions_per_ingredient", false]], "get_radii() (cellpack.autopack.interface_objects.packed_objects.packedobjects method)": [[4, "cellpack.autopack.interface_objects.packed_objects.PackedObjects.get_radii", false]], "get_radii() (cellpack.autopack.interface_objects.representations.representations method)": [[4, "cellpack.autopack.interface_objects.representations.Representations.get_radii", false]], "get_radius() (cellpack.autopack.ingredient.multi_sphere.multisphereingr method)": [[3, "cellpack.autopack.ingredient.multi_sphere.MultiSphereIngr.get_radius", false]], "get_radius() (cellpack.autopack.ingredient.single_sphere.singlesphereingr method)": [[3, "cellpack.autopack.ingredient.single_sphere.SingleSphereIngr.get_radius", false]], "get_rb_model() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.get_rb_model", false]], "get_rb_model() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.get_rb_model", false]], "get_rbnodes() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.get_rbNodes", false]], "get_recipe_metadata() (in module cellpack.bin.upload)": [[9, "cellpack.bin.upload.get_recipe_metadata", false]], "get_rectangle_cercle_area() (cellpack.autopack.geometrytools.geometrytools method)": [[2, "cellpack.autopack.GeometryTools.GeometryTools.get_rectangle_cercle_area", false]], "get_reference_data() (cellpack.autopack.dbrecipehandler.compositiondoc static method)": [[2, "cellpack.autopack.DBRecipeHandler.CompositionDoc.get_reference_data", false]], "get_reference_in_obj() (cellpack.autopack.dbrecipehandler.compositiondoc static method)": [[2, "cellpack.autopack.DBRecipeHandler.CompositionDoc.get_reference_in_obj", false]], "get_reflected_point() (in module cellpack.autopack.ingredient.utils)": [[3, "cellpack.autopack.ingredient.utils.get_reflected_point", false]], "get_representations() (in module cellpack.autopack.loaders.migrate_v1_to_v2)": [[5, "cellpack.autopack.loaders.migrate_v1_to_v2.get_representations", false]], "get_rotation() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.get_rotation", false]], "get_rotations_for_ingredient() (cellpack.autopack.interface_objects.packed_objects.packedobjects method)": [[4, "cellpack.autopack.interface_objects.packed_objects.PackedObjects.get_rotations_for_ingredient", false]], "get_scaled_distances_between_surfaces() (cellpack.autopack.meshstore.meshstore method)": [[2, "cellpack.autopack.MeshStore.MeshStore.get_scaled_distances_between_surfaces", false]], "get_seed_list() (in module cellpack.autopack.utils)": [[2, "cellpack.autopack.utils.get_seed_list", false]], "get_signed_distance() (cellpack.autopack.ingredient.grow.growingredient method)": [[3, "cellpack.autopack.ingredient.grow.GrowIngredient.get_signed_distance", false]], "get_signed_distance() (cellpack.autopack.ingredient.multi_sphere.multisphereingr method)": [[3, "cellpack.autopack.ingredient.multi_sphere.MultiSphereIngr.get_signed_distance", false]], "get_signed_distance() (cellpack.autopack.ingredient.single_cube.singlecubeingr method)": [[3, "cellpack.autopack.ingredient.single_cube.SingleCubeIngr.get_signed_distance", false]], "get_signed_distance() (cellpack.autopack.ingredient.single_cylinder.singlecylinderingr method)": [[3, "cellpack.autopack.ingredient.single_cylinder.SingleCylinderIngr.get_signed_distance", false]], "get_signed_distance() (cellpack.autopack.ingredient.single_sphere.singlesphereingr method)": [[3, "cellpack.autopack.ingredient.single_sphere.SingleSphereIngr.get_signed_distance", false]], "get_size_of_bounding_box() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.get_size_of_bounding_box", false]], "get_smallest_radius() (cellpack.autopack.meshstore.meshstore method)": [[2, "cellpack.autopack.MeshStore.MeshStore.get_smallest_radius", false]], "get_staging_creds() (cellpack.autopack.firebasehandler.firebasehandler static method)": [[2, "cellpack.autopack.FirebaseHandler.FirebaseHandler.get_staging_creds", false]], "get_username() (cellpack.autopack.firebasehandler.firebasehandler static method)": [[2, "cellpack.autopack.FirebaseHandler.FirebaseHandler.get_username", false]], "get_value() (cellpack.autopack.firebasehandler.firebasehandler method)": [[2, "cellpack.autopack.FirebaseHandler.FirebaseHandler.get_value", false]], "get_value_from_distribution() (in module cellpack.autopack.utils)": [[2, "cellpack.autopack.utils.get_value_from_distribution", false]], "get_weights_by_distance() (cellpack.autopack.ingredient.agent.agent method)": [[3, "cellpack.autopack.ingredient.agent.Agent.get_weights_by_distance", false]], "geta() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.getA", false]], "getabsposuntilroot() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.GetAbsPosUntilRoot", false]], "getactiveing() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.getActiveIng", false]], "getallmaterials() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.getAllMaterials", false]], "getallmaterials() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.getAllMaterials", false]], "getallposrot() (in module cellpack.autopack.ioutils)": [[2, "cellpack.autopack.IOutils.getAllPosRot", false]], "getangleaxis() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.getAngleAxis", false]], "getaxisrotation() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.getAxisRotation", false]], "getbiasedrotation() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.getBiasedRotation", false]], "getbigbb() (cellpack.autopack.ingredient.multi_cylinder.multicylindersingr method)": [[3, "cellpack.autopack.ingredient.multi_cylinder.MultiCylindersIngr.getBigBB", false]], "getbigbb() (cellpack.autopack.ingredient.single_cylinder.singlecylinderingr method)": [[3, "cellpack.autopack.ingredient.single_cylinder.SingleCylinderIngr.getBigBB", false]], "getbinaryweighted() (cellpack.autopack.gradient.gradient method)": [[2, "cellpack.autopack.Gradient.Gradient.getBinaryWeighted", false]], "getboundary() (cellpack.autopack.geometrytools.geometrytools method)": [[2, "cellpack.autopack.GeometryTools.GeometryTools.getBoundary", false]], "getboundingbox() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.getBoundingBox", false]], "getboxsize() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.getBoxSize", false]], "getcenter() (cellpack.autopack.basegrid.basegrid method)": [[2, "cellpack.autopack.BaseGrid.BaseGrid.getCenter", false]], "getcenter() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.getCenter", false]], "getcenter() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.getCenter", false]], "getchilds() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.getChilds", false]], "getclosestfreegridpoint() (cellpack.autopack.basegrid.basegrid method)": [[2, "cellpack.autopack.BaseGrid.BaseGrid.getClosestFreeGridPoint", false]], "getclosestgridpoint() (cellpack.autopack.basegrid.basegrid method)": [[2, "cellpack.autopack.BaseGrid.BaseGrid.getClosestGridPoint", false]], "getcolladamaterial() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.getColladaMaterial", false]], "getcornerpointcube() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.getCornerPointCube", false]], "getcornerpointcube() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.getCornerPointCube", false]], "getcurrentscene() (cellpack.autopack.upy.hosthelper.helper class method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.getCurrentScene", false]], "getcurrentscene() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.getCurrentScene", false]], "getcurrentscenename() (cellpack.autopack.upy.hosthelper.helper class method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.getCurrentSceneName", false]], "getcurrentselection() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.getCurrentSelection", false]], "getcurrentselection() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.getCurrentSelection", false]], "getdata() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.getData", false]], "getdiagonal() (cellpack.autopack.basegrid.basegrid method)": [[2, "cellpack.autopack.BaseGrid.BaseGrid.getDiagonal", false]], "getdihedral() (in module cellpack.autopack.ingredient.utils)": [[3, "cellpack.autopack.ingredient.utils.getDihedral", false]], "getdistance() (cellpack.autopack.geometrytools.geometrytools method)": [[2, "cellpack.autopack.GeometryTools.GeometryTools.GetDistance", false]], "getencapsulatingradius() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.getEncapsulatingRadius", false]], "getface() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.getFace", false]], "getface() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.getFace", false]], "getfaceedges() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.getFaceEdges", false]], "getfacenormals() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.getFaceNormals", false]], "getfacenormalsarea() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.getFaceNormalsArea", false]], "getfaces() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.getFaces", false]], "getfacesfromv() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.getFacesfromV", false]], "getfacesnfromv() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.getFacesNfromV", false]], "getfirstpoint() (cellpack.autopack.ingredient.grow.growingredient method)": [[3, "cellpack.autopack.ingredient.grow.GrowIngredient.getFirstPoint", false]], "getforwweight() (cellpack.autopack.gradient.gradient method)": [[2, "cellpack.autopack.Gradient.Gradient.getForwWeight", false]], "gethaltonunique() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.getHaltonUnique", false]], "gethclass() (in module cellpack.autopack.upy)": [[6, "cellpack.autopack.upy.getHClass", false]], "gethelperclass() (in module cellpack.autopack.upy)": [[6, "cellpack.autopack.upy.getHelperClass", false]], "getijk() (cellpack.autopack.basegrid.basegrid method)": [[2, "cellpack.autopack.BaseGrid.BaseGrid.getIJK", false]], "getijk() (cellpack.autopack.grid.grid method)": [[2, "cellpack.autopack.Grid.Grid.getIJK", false]], "getimage() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.getImage", false]], "getindex() (cellpack.autopack.binvox_rw.voxels method)": [[2, "cellpack.autopack.binvox_rw.Voxels.getIndex", false]], "getindexdata() (cellpack.autopack.binvox_rw.voxels method)": [[2, "cellpack.autopack.binvox_rw.Voxels.getIndexData", false]], "getingredientinstancepos() (cellpack.autopack.trajectory.trajectory method)": [[2, "cellpack.autopack.trajectory.Trajectory.getIngredientInstancePos", false]], "getingredientsinbox() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.getIngredientsInBox", false]], "getingrfromnameinrecipe() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.getIngrFromNameInRecipe", false]], "getinterpolatednormal() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.getInterpolatedNormal", false]], "getinterpolatedsphere() (cellpack.autopack.ingredient.grow.growingredient method)": [[3, "cellpack.autopack.ingredient.grow.GrowIngredient.getInterpolatedSphere", false]], "getjtransrot() (cellpack.autopack.ingredient.grow.growingredient method)": [[3, "cellpack.autopack.ingredient.grow.GrowIngredient.getJtransRot", false]], "getjtransrot_r() (cellpack.autopack.ingredient.grow.growingredient method)": [[3, "cellpack.autopack.ingredient.grow.GrowIngredient.getJtransRot_r", false]], "getlayers() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.getLayers", false]], "getlinearweighted() (cellpack.autopack.gradient.gradient method)": [[2, "cellpack.autopack.Gradient.Gradient.getLinearWeighted", false]], "getlistcompfrommask() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.getListCompFromMask", false]], "getmasterinstance() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.getMasterInstance", false]], "getmaterial() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.getMaterial", false]], "getmaterial() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.getMaterial", false]], "getmaterialname() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.getMaterialName", false]], "getmaterialobject() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.getMaterialObject", false]], "getmaterialproperty() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.getMaterialProperty", false]], "getmaxjitter() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.getMaxJitter", false]], "getmaxweight() (cellpack.autopack.gradient.gradient method)": [[2, "cellpack.autopack.Gradient.Gradient.getMaxWeight", false]], "getmesh() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.getMesh", false]], "getmesh() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.getMesh", false]], "getmesh() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.getMesh", false]], "getmesh() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.getMesh", false]], "getmeshedge() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.getMeshEdge", false]], "getmeshedges() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.getMeshEdges", false]], "getmeshedges() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.getMeshEdges", false]], "getmeshfaces() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.getMeshFaces", false]], "getmeshfaces() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.getMeshFaces", false]], "getmeshnormales() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.getMeshNormales", false]], "getmeshnormales() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.getMeshNormales", false]], "getmeshvertice() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.getMeshVertice", false]], "getmeshvertices() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.getMeshVertices", false]], "getmeshvertices() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.getMeshVertices", false]], "getminmaxproteinsize() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.getMinMaxProteinSize", false]], "getminmaxproteinsize() (cellpack.autopack.recipe.recipe method)": [[2, "cellpack.autopack.Recipe.Recipe.getMinMaxProteinSize", false]], "getminweight() (cellpack.autopack.gradient.gradient method)": [[2, "cellpack.autopack.Gradient.Gradient.getMinWeight", false]], "getname() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.getName", false]], "getname() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.getName", false]], "getnbgridpoints() (cellpack.autopack.basegrid.haltongrid method)": [[2, "cellpack.autopack.BaseGrid.HaltonGrid.getNBgridPoints", false]], "getnextpoint() (cellpack.autopack.ingredient.grow.growingredient method)": [[3, "cellpack.autopack.ingredient.grow.GrowIngredient.getNextPoint", false]], "getnextptindcyl() (cellpack.autopack.ingredient.grow.growingredient method)": [[3, "cellpack.autopack.ingredient.grow.GrowIngredient.getNextPtIndCyl", false]], "getnormals() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.getNormals", false]], "getnormedvector() (in module cellpack.autopack.ingredient.utils)": [[3, "cellpack.autopack.ingredient.utils.getNormedVector", false]], "getnormedvectorones() (in module cellpack.autopack.ingredient.utils)": [[3, "cellpack.autopack.ingredient.utils.getNormedVectorOnes", false]], "getnormedvectoru() (in module cellpack.autopack.ingredient.utils)": [[3, "cellpack.autopack.ingredient.utils.getNormedVectorU", false]], "getobject() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.getObject", false]], "getobject() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.getObject", false]], "getobjectname() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.getObjectName", false]], "getold() (cellpack.autopack.randomrot.randomrot method)": [[2, "cellpack.autopack.randomRot.RandomRot.getOld", false]], "getoneingr() (cellpack.autopack.environment.environment class method)": [[2, "cellpack.autopack.Environment.Environment.getOneIngr", false]], "getoneingrjson() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.getOneIngrJson", false]], "getorder() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.getOrder", false]], "getparticles() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.getParticles", false]], "getparticulesposition() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.getParticulesPosition", false]], "getpointfrom3d() (cellpack.autopack.basegrid.basegrid method)": [[2, "cellpack.autopack.BaseGrid.BaseGrid.getPointFrom3D", false]], "getpointfrom3d() (cellpack.autopack.basegrid.haltongrid method)": [[2, "cellpack.autopack.BaseGrid.HaltonGrid.getPointFrom3D", false]], "getpointsincube() (cellpack.autopack.basegrid.basegrid method)": [[2, "cellpack.autopack.BaseGrid.BaseGrid.getPointsInCube", false]], "getpointsincubefillbb() (cellpack.autopack.basegrid.basegrid method)": [[2, "cellpack.autopack.BaseGrid.BaseGrid.getPointsInCubeFillBB", false]], "getpointsinsphere() (cellpack.autopack.basegrid.basegrid method)": [[2, "cellpack.autopack.BaseGrid.BaseGrid.getPointsInSphere", false]], "getpointtodrop() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.getPointToDrop", false]], "getposat() (cellpack.autopack.trajectory.dcdtrajectory method)": [[2, "cellpack.autopack.trajectory.dcdTrajectory.getPosAt", false]], "getposat() (cellpack.autopack.trajectory.molbtrajectory method)": [[2, "cellpack.autopack.trajectory.molbTrajectory.getPosAt", false]], "getposat() (cellpack.autopack.trajectory.xyztrajectory method)": [[2, "cellpack.autopack.trajectory.xyzTrajectory.getPosAt", false]], "getpositionperidocity() (cellpack.autopack.basegrid.basegrid method)": [[2, "cellpack.autopack.BaseGrid.BaseGrid.getPositionPeridocity", false]], "getposline() (cellpack.autopack.trajectory.xyztrajectory method)": [[2, "cellpack.autopack.trajectory.xyzTrajectory.getPosLine", false]], "getposuntilroot() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.getPosUntilRoot", false]], "getproperty() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.getProperty", false]], "getpropertyobject() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.getPropertyObject", false]], "getradius() (cellpack.autopack.basegrid.basegrid method)": [[2, "cellpack.autopack.BaseGrid.BaseGrid.getRadius", false]], "getradius() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.getRadius", false]], "getramp() (in module cellpack.autopack.upy.colors)": [[6, "cellpack.autopack.upy.colors.getRamp", false]], "getrndweighted() (cellpack.autopack.gradient.gradient method)": [[2, "cellpack.autopack.Gradient.Gradient.getRndWeighted", false]], "getrottransrb() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.getRotTransRB", false]], "getscale() (cellpack.autopack.basegrid.haltongrid method)": [[2, "cellpack.autopack.BaseGrid.HaltonGrid.getScale", false]], "getscale() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.getScale", false]], "getsize() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.getSize", false]], "getsizexyz() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.getSizeXYZ", false]], "getsortedactiveingredients() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.getSortedActiveIngredients", false]], "getstringvalueoptions() (in module cellpack.autopack.ioutils)": [[2, "cellpack.autopack.IOutils.getStringValueOptions", false]], "getsubweighted() (cellpack.autopack.gradient.gradient method)": [[2, "cellpack.autopack.Gradient.Gradient.getSubWeighted", false]], "getsubweighted() (cellpack.autopack.ingredient.agent.agent method)": [[3, "cellpack.autopack.ingredient.agent.Agent.getSubWeighted", false]], "getsurfaceinnerpoints() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.getSurfaceInnerPoints", false]], "getsurfaceinnerpoints_kevin() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.getSurfaceInnerPoints_kevin", false]], "getsurfaceinnerpoints_sdf() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.getSurfaceInnerPoints_sdf", false]], "getsurfaceinnerpoints_sdf_interpolate() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.getSurfaceInnerPoints_sdf_interpolate", false]], "getsurfacepoint() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.getSurfacePoint", false]], "gettotalnbobject() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.getTotalNbObject", false]], "gettransformation() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.getTransformation", false]], "gettranslation() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.getTranslation", false]], "gettranslation() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.getTranslation", false]], "gettubeproperties() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.getTubeProperties", false]], "gettubepropertiesmatrix() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.getTubePropertiesMatrix", false]], "gettype() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.getType", false]], "getuv() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.getUV", false]], "getuvs() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.getUVs", false]], "getv3() (cellpack.autopack.ingredient.grow.growingredient method)": [[3, "cellpack.autopack.ingredient.grow.GrowIngredient.getV3", false]], "getvertexnormals() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.getVertexNormals", false]], "getvisibility() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.getVisibility", false]], "getvisibility() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.getVisibility", false]], "getvnfromf() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.getVNfromF", false]], "github (cellpack.autopack.interface_objects.database_ids.database_ids attribute)": [[4, "cellpack.autopack.interface_objects.database_ids.DATABASE_IDS.GITHUB", false]], "grab() (cellpack.autopack.ioutils.grabresult method)": [[2, "cellpack.autopack.IOutils.GrabResult.grab", false]], "grabresult (class in cellpack.autopack.ioutils)": [[2, "cellpack.autopack.IOutils.GrabResult", false]], "gradient (class in cellpack.autopack.gradient)": [[2, "cellpack.autopack.Gradient.Gradient", false]], "gradient_list_to_dict() (cellpack.autopack.dbrecipehandler.compositiondoc static method)": [[2, "cellpack.autopack.DBRecipeHandler.CompositionDoc.gradient_list_to_dict", false]], "gradientdata (class in cellpack.autopack.interface_objects.gradient_data)": [[4, "cellpack.autopack.interface_objects.gradient_data.GradientData", false]], "gradientdoc (class in cellpack.autopack.dbrecipehandler)": [[2, "cellpack.autopack.DBRecipeHandler.GradientDoc", false]], "gradientmodes (class in cellpack.autopack.interface_objects.gradient_data)": [[4, "cellpack.autopack.interface_objects.gradient_data.GradientModes", false]], "grid (class in cellpack.autopack.grid)": [[2, "cellpack.autopack.Grid.Grid", false]], "gridpoint (class in cellpack.autopack.basegrid)": [[2, "cellpack.autopack.BaseGrid.gridPoint", false]], "grow (cellpack.autopack.interface_objects.ingredient_types.ingredient_type attribute)": [[4, "cellpack.autopack.interface_objects.ingredient_types.INGREDIENT_TYPE.GROW", false]], "grow() (cellpack.autopack.ingredient.grow.growingredient method)": [[3, "cellpack.autopack.ingredient.grow.GrowIngredient.grow", false]], "grow_place() (cellpack.autopack.ingredient.grow.growingredient method)": [[3, "cellpack.autopack.ingredient.grow.GrowIngredient.grow_place", false]], "growingredient (class in cellpack.autopack.ingredient.grow)": [[3, "cellpack.autopack.ingredient.grow.GrowIngredient", false]], "halton() (in module cellpack.autopack.ldsequence)": [[2, "cellpack.autopack.ldSequence.halton", false]], "halton2() (in module cellpack.autopack.ldsequence)": [[2, "cellpack.autopack.ldSequence.halton2", false]], "halton3() (in module cellpack.autopack.ldsequence)": [[2, "cellpack.autopack.ldSequence.halton3", false]], "halton_sequence() (in module cellpack.autopack.ldsequence)": [[2, "cellpack.autopack.ldSequence.halton_sequence", false]], "haltongrid (class in cellpack.autopack.basegrid)": [[2, "cellpack.autopack.BaseGrid.HaltonGrid", false]], "haltonsequence (class in cellpack.autopack.ldsequence)": [[2, "cellpack.autopack.ldSequence.HaltonSequence", false]], "haltonterm() (in module cellpack.autopack.ldsequence)": [[2, "cellpack.autopack.ldSequence.haltonterm", false]], "handle_expired_results() (cellpack.autopack.dbrecipehandler.resultdoc method)": [[2, "cellpack.autopack.DBRecipeHandler.ResultDoc.handle_expired_results", false]], "handle_real_time_visualization() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.handle_real_time_visualization", false]], "handlers() (cellpack.autopack.interface_objects.database_ids.database_ids class method)": [[4, "cellpack.autopack.interface_objects.database_ids.DATABASE_IDS.handlers", false]], "has_mesh() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.has_mesh", false]], "has_mesh() (cellpack.autopack.interface_objects.representations.representations method)": [[4, "cellpack.autopack.interface_objects.representations.Representations.has_mesh", false]], "has_pdb() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.has_pdb", false]], "has_pdb() (cellpack.autopack.interface_objects.representations.representations method)": [[4, "cellpack.autopack.interface_objects.representations.Representations.has_pdb", false]], "helper (class in cellpack.autopack.upy.hosthelper)": [[6, "cellpack.autopack.upy.hostHelper.Helper", false]], "hexahedron() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.Hexahedron", false], [6, "cellpack.autopack.upy.hostHelper.Helper.hexahedron", false]], "hextorgb() (in module cellpack.autopack.upy.colors)": [[6, "cellpack.autopack.upy.colors.hexToRgb", false]], "hideingrprimitive() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.hideIngrPrimitive", false]], "histogram() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.histogram", false]], "host (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper attribute)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.host", false]], "icosahedron() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.Icosahedron", false], [6, "cellpack.autopack.upy.hostHelper.Helper.icosahedron", false]], "ijktoindex() (cellpack.autopack.binvox_rw.voxels method)": [[2, "cellpack.autopack.binvox_rw.Voxels.ijkToIndex", false]], "ijktoxyz() (cellpack.autopack.binvox_rw.voxels method)": [[2, "cellpack.autopack.binvox_rw.Voxels.ijkToxyz", false]], "ik (cellpack.autopack.upy.hosthelper.helper attribute)": [[6, "cellpack.autopack.upy.hostHelper.Helper.IK", false]], "imagewriter (class in cellpack.autopack.writers.imagewriter)": [[8, "cellpack.autopack.writers.ImageWriter.ImageWriter", false]], "inbox() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.inBox", false]], "inc() (cellpack.autopack.ldsequence.chaltonsequence3 method)": [[2, "cellpack.autopack.ldSequence.cHaltonSequence3.inc", false]], "includeingredientrecipe() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.includeIngredientRecipe", false]], "includeingrrecipe() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.includeIngrRecipe", false]], "includeingrrecipes() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.includeIngrRecipes", false]], "increment_static() (cellpack.autopack.upy.simularium.simularium_helper.instance method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.Instance.increment_static", false]], "increment_static_objects() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.increment_static_objects", false]], "increment_time() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.increment_time", false]], "indexedpolgonstotripoints() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.IndexedPolgonsToTriPoints", false]], "indexedpolygons() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.IndexedPolygons", false]], "ingredient (class in cellpack.autopack.ingredient.ingredient)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient", false]], "ingredient_compare0() (in module cellpack.autopack.utils)": [[2, "cellpack.autopack.utils.ingredient_compare0", false]], "ingredient_compare1() (in module cellpack.autopack.utils)": [[2, "cellpack.autopack.utils.ingredient_compare1", false]], "ingredient_compare2() (in module cellpack.autopack.utils)": [[2, "cellpack.autopack.utils.ingredient_compare2", false]], "ingredient_type (class in cellpack.autopack.interface_objects.ingredient_types)": [[4, "cellpack.autopack.interface_objects.ingredient_types.INGREDIENT_TYPE", false]], "ingredientinstancedrop (class in cellpack.autopack.ingredient.ingredient)": [[3, "cellpack.autopack.ingredient.Ingredient.IngredientInstanceDrop", false]], "ingrid() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.inGrid", false]], "ingrjsonnode() (cellpack.autopack.ioutils.ioingredienttool method)": [[2, "cellpack.autopack.IOutils.IOingredientTool.ingrJsonNode", false]], "ingrjsonnode() (cellpack.autopack.writers.ioingredienttool method)": [[8, "cellpack.autopack.writers.IOingredientTool.ingrJsonNode", false]], "ingrpythonnode() (cellpack.autopack.ioutils.ioingredienttool method)": [[2, "cellpack.autopack.IOutils.IOingredientTool.ingrPythonNode", false]], "init_scene_with_objects() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.init_scene_with_objects", false]], "initialize_mesh() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.initialize_mesh", false]], "initialize_mesh() (cellpack.autopack.ingredient.multi_cylinder.multicylindersingr method)": [[3, "cellpack.autopack.ingredient.multi_cylinder.MultiCylindersIngr.initialize_mesh", false]], "initialize_mesh() (cellpack.autopack.ingredient.single_cylinder.singlecylinderingr method)": [[3, "cellpack.autopack.ingredient.single_cylinder.SingleCylinderIngr.initialize_mesh", false]], "initialize_mesh() (cellpack.autopack.ingredient.single_sphere.singlesphereingr method)": [[3, "cellpack.autopack.ingredient.single_sphere.SingleSphereIngr.initialize_mesh", false]], "initialize_shape() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.initialize_shape", false]], "inner_grid_methods (class in cellpack.autopack.loaders.config_loader)": [[5, "cellpack.autopack.loaders.config_loader.Inner_Grid_Methods", false]], "insertnode() (cellpack.autopack.octree.octree method)": [[2, "cellpack.autopack.octree.Octree.insertNode", false]], "instance (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper attribute)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.INSTANCE", false]], "instance (class in cellpack.autopack.upy.simularium.simularium_helper)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.Instance", false]], "instancepolygon() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.instancePolygon", false]], "instancescylinder() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.instancesCylinder", false]], "instancessphere() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.instancesSphere", false]], "instancestocollada() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.instancesToCollada", false]], "invertoptions (class in cellpack.autopack.interface_objects.gradient_data)": [[4, "cellpack.autopack.interface_objects.gradient_data.InvertOptions", false]], "ioingredienttool (class in cellpack.autopack.ioutils)": [[2, "cellpack.autopack.IOutils.IOingredientTool", false]], "ioingredienttool (class in cellpack.autopack.writers)": [[8, "cellpack.autopack.writers.IOingredientTool", false]], "is_db_dict() (cellpack.autopack.dbrecipehandler.datadoc static method)": [[2, "cellpack.autopack.DBRecipeHandler.DataDoc.is_db_dict", false]], "is_fiber() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper static method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.is_fiber", false]], "is_firebase_obj() (cellpack.autopack.firebasehandler.firebasehandler static method)": [[2, "cellpack.autopack.FirebaseHandler.FirebaseHandler.is_firebase_obj", false]], "is_full_url() (in module cellpack.autopack)": [[2, "cellpack.autopack.is_full_url", false]], "is_key() (cellpack.autopack.dbrecipehandler.datadoc static method)": [[2, "cellpack.autopack.DBRecipeHandler.DataDoc.is_key", false]], "is_key() (cellpack.autopack.recipe.recipe static method)": [[2, "cellpack.autopack.Recipe.Recipe.is_key", false]], "is_matrix() (cellpack.bin.simularium_converter.converttosimularium method)": [[9, "cellpack.bin.simularium_converter.ConvertToSimularium.is_matrix", false]], "is_member() (cellpack.autopack.interface_objects.meta_enum.metaenum class method)": [[4, "cellpack.autopack.interface_objects.meta_enum.MetaEnum.is_member", false]], "is_nested_list() (cellpack.autopack.dbrecipehandler.datadoc static method)": [[2, "cellpack.autopack.DBRecipeHandler.DataDoc.is_nested_list", false]], "is_obj() (cellpack.autopack.dbrecipehandler.datadoc static method)": [[2, "cellpack.autopack.DBRecipeHandler.DataDoc.is_obj", false]], "is_partner() (cellpack.autopack.interface_objects.partners.partners method)": [[4, "cellpack.autopack.interface_objects.partners.Partners.is_partner", false]], "is_point_in_correct_region() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.is_point_in_correct_region", false]], "is_point_inside_bb() (cellpack.autopack.basegrid.basegrid method)": [[2, "cellpack.autopack.BaseGrid.BaseGrid.is_point_inside_bb", false]], "is_point_inside_mesh() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.is_point_inside_mesh", false]], "is_reference() (cellpack.autopack.firebasehandler.firebasehandler static method)": [[2, "cellpack.autopack.FirebaseHandler.FirebaseHandler.is_reference", false]], "is_remote_path() (in module cellpack.autopack)": [[2, "cellpack.autopack.is_remote_path", false]], "is_s3_url() (in module cellpack.autopack)": [[2, "cellpack.autopack.is_s3_url", false]], "is_two_d() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.is_two_d", false]], "is_url_valid() (cellpack.autopack.awshandler.awshandler method)": [[2, "cellpack.autopack.AWSHandler.AWSHandler.is_url_valid", false]], "isindexedpolyon() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.isIndexedPolyon", false]], "issphere() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.isSphere", false]], "jitter (cellpack.autopack.loaders.config_loader.place_methods attribute)": [[5, "cellpack.autopack.loaders.config_loader.Place_Methods.JITTER", false]], "jitter_place() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.jitter_place", false]], "jitterposition() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.jitterPosition", false]], "joinsobjects() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.JoinsObjects", false]], "key_to_dict_mapping (cellpack.autopack.dbrecipehandler.compositiondoc attribute)": [[2, "cellpack.autopack.DBRecipeHandler.CompositionDoc.KEY_TO_DICT_MAPPING", false]], "labels() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.Labels", false]], "light_options (cellpack.autopack.upy.hosthelper.helper attribute)": [[6, "cellpack.autopack.upy.hostHelper.Helper.LIGHT_OPTIONS", false]], "linear (cellpack.autopack.interface_objects.gradient_data.pickmodes attribute)": [[4, "cellpack.autopack.interface_objects.gradient_data.PickModes.LINEAR", false]], "linear (cellpack.autopack.interface_objects.gradient_data.weightmodes attribute)": [[4, "cellpack.autopack.interface_objects.gradient_data.WeightModes.LINEAR", false]], "linktraj() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.linkTraj", false]], "list (cellpack.autopack.ingredient.ingredient.distributiontypes attribute)": [[3, "cellpack.autopack.ingredient.Ingredient.DistributionTypes.LIST", false]], "list_values (cellpack.autopack.ingredient.ingredient.distributionoptions attribute)": [[3, "cellpack.autopack.ingredient.Ingredient.DistributionOptions.LIST_VALUES", false]], "load_asjson() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.load_asJson", false]], "load_astxt() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.load_asTxt", false]], "load_file() (in module cellpack.autopack)": [[2, "cellpack.autopack.load_file", false]], "load_json() (in module cellpack.autopack.ioutils)": [[2, "cellpack.autopack.IOutils.load_Json", false]], "load_jsonstring() (in module cellpack.autopack.ioutils)": [[2, "cellpack.autopack.IOutils.load_JsonString", false]], "load_mixedasjson() (in module cellpack.autopack.ioutils)": [[2, "cellpack.autopack.IOutils.load_MixedasJson", false]], "load_object_from_pickle() (in module cellpack.autopack.utils)": [[2, "cellpack.autopack.utils.load_object_from_pickle", false]], "loadfreepoint() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.loadFreePoint", false]], "loadjson() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.loadJSON", false]], "loadresult() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.loadResult", false]], "lookforneighbours() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.lookForNeighbours", false]], "loopthroughingr() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.loopThroughIngr", false]], "lowercirclefunction() (cellpack.autopack.geometrytools.geometrytools method)": [[2, "cellpack.autopack.GeometryTools.GeometryTools.LowerCircleFunction", false]], "lowerrectanglefunction() (cellpack.autopack.geometrytools.geometrytools method)": [[2, "cellpack.autopack.GeometryTools.GeometryTools.LowerRectangleFunction", false]], "main() (in module cellpack.bin.analyze)": [[9, "cellpack.bin.analyze.main", false]], "main() (in module cellpack.bin.clean)": [[9, "cellpack.bin.clean.main", false]], "main() (in module cellpack.bin.pack)": [[9, "cellpack.bin.pack.main", false]], "main() (in module cellpack.bin.simularium_converter)": [[9, "cellpack.bin.simularium_converter.main", false]], "main() (in module cellpack.bin.upload)": [[9, "cellpack.bin.upload.main", false]], "make_and_show_heatmap() (cellpack.autopack.plotly_result.plotlyanalysis method)": [[2, "cellpack.autopack.plotly_result.PlotlyAnalysis.make_and_show_heatmap", false]], "make_directory_if_needed() (in module cellpack.autopack)": [[2, "cellpack.autopack.make_directory_if_needed", false]], "make_grid_heatmap() (cellpack.autopack.plotly_result.plotlyanalysis method)": [[2, "cellpack.autopack.plotly_result.PlotlyAnalysis.make_grid_heatmap", false]], "makeingredient() (cellpack.autopack.ioutils.ioingredienttool method)": [[2, "cellpack.autopack.IOutils.IOingredientTool.makeIngredient", false]], "makeingredientfromjson() (cellpack.autopack.ioutils.ioingredienttool method)": [[2, "cellpack.autopack.IOutils.IOingredientTool.makeIngredientFromJson", false]], "makeingrmapping() (cellpack.autopack.trajectory.trajectory method)": [[2, "cellpack.autopack.trajectory.Trajectory.makeIngrMapping", false]], "makemarchingcube() (in module cellpack.autopack.ray)": [[2, "cellpack.autopack.ray.makeMarchingCube", false]], "maketexture() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.makeTexture", false]], "map_colors() (in module cellpack.autopack.upy.colors)": [[6, "cellpack.autopack.upy.colors.map_colors", false]], "mask_sphere_points() (cellpack.autopack.ingredient.grow.growingredient method)": [[3, "cellpack.autopack.ingredient.grow.GrowIngredient.mask_sphere_points", false]], "mask_sphere_points_angle() (cellpack.autopack.ingredient.grow.growingredient method)": [[3, "cellpack.autopack.ingredient.grow.GrowIngredient.mask_sphere_points_angle", false]], "mask_sphere_points_boundary() (cellpack.autopack.ingredient.grow.growingredient method)": [[3, "cellpack.autopack.ingredient.grow.GrowIngredient.mask_sphere_points_boundary", false]], "mask_sphere_points_dihedral() (cellpack.autopack.ingredient.grow.growingredient method)": [[3, "cellpack.autopack.ingredient.grow.GrowIngredient.mask_sphere_points_dihedral", false]], "mask_sphere_points_ingredients() (cellpack.autopack.ingredient.grow.growingredient method)": [[3, "cellpack.autopack.ingredient.grow.GrowIngredient.mask_sphere_points_ingredients", false]], "mask_sphere_points_vector() (cellpack.autopack.ingredient.grow.growingredient method)": [[3, "cellpack.autopack.ingredient.grow.GrowIngredient.mask_sphere_points_vector", false]], "matrixtofacesmesh() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.matrixToFacesMesh", false]], "matrixtovnmesh() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.matrixToVNMesh", false]], "max (cellpack.autopack.ingredient.ingredient.distributionoptions attribute)": [[3, "cellpack.autopack.ingredient.Ingredient.DistributionOptions.MAX", false]], "max (cellpack.autopack.interface_objects.gradient_data.pickmodes attribute)": [[4, "cellpack.autopack.interface_objects.gradient_data.PickModes.MAX", false]], "mean (cellpack.autopack.ingredient.ingredient.distributionoptions attribute)": [[3, "cellpack.autopack.ingredient.Ingredient.DistributionOptions.MEAN", false]], "measure_distance() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.measure_distance", false]], "merge_place_results() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.merge_place_results", false]], "mesh (cellpack.autopack.interface_objects.ingredient_types.ingredient_type attribute)": [[4, "cellpack.autopack.interface_objects.ingredient_types.INGREDIENT_TYPE.MESH", false]], "meshstore (class in cellpack.autopack.meshstore)": [[2, "cellpack.autopack.MeshStore.MeshStore", false]], "metaballs() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.metaballs", false]], "metaenum (class in cellpack.autopack.interface_objects.meta_enum)": [[4, "cellpack.autopack.interface_objects.meta_enum.MetaEnum", false]], "midpoint() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.MidPoint", false]], "migrate_ingredient() (in module cellpack.autopack.loaders.migrate_v1_to_v2)": [[5, "cellpack.autopack.loaders.migrate_v1_to_v2.migrate_ingredient", false]], "min (cellpack.autopack.ingredient.ingredient.distributionoptions attribute)": [[3, "cellpack.autopack.ingredient.Ingredient.DistributionOptions.MIN", false]], "min (cellpack.autopack.interface_objects.gradient_data.pickmodes attribute)": [[4, "cellpack.autopack.interface_objects.gradient_data.PickModes.MIN", false]], "modeoptions (class in cellpack.autopack.interface_objects.gradient_data)": [[4, "cellpack.autopack.interface_objects.gradient_data.ModeOptions", false]], "module": [[1, "module-cellpack", false], [2, "module-cellpack.autopack", false], [2, "module-cellpack.autopack.AWSHandler", false], [2, "module-cellpack.autopack.Analysis", false], [2, "module-cellpack.autopack.BaseGrid", false], [2, "module-cellpack.autopack.Compartment", false], [2, "module-cellpack.autopack.DBRecipeHandler", false], [2, "module-cellpack.autopack.Environment", false], [2, "module-cellpack.autopack.FirebaseHandler", false], [2, "module-cellpack.autopack.GeometryTools", false], [2, "module-cellpack.autopack.Gradient", false], [2, "module-cellpack.autopack.Graphics", false], [2, "module-cellpack.autopack.Grid", false], [2, "module-cellpack.autopack.IOutils", false], [2, "module-cellpack.autopack.MeshStore", false], [2, "module-cellpack.autopack.Recipe", false], [2, "module-cellpack.autopack.Serializable", false], [2, "module-cellpack.autopack.binvox_rw", false], [2, "module-cellpack.autopack.ldSequence", false], [2, "module-cellpack.autopack.octree", false], [2, "module-cellpack.autopack.plotly_result", false], [2, "module-cellpack.autopack.randomRot", false], [2, "module-cellpack.autopack.ray", false], [2, "module-cellpack.autopack.trajectory", false], [2, "module-cellpack.autopack.transformation", false], [2, "module-cellpack.autopack.utils", false], [3, "module-cellpack.autopack.ingredient", false], [3, "module-cellpack.autopack.ingredient.Ingredient", false], [3, "module-cellpack.autopack.ingredient.agent", false], [3, "module-cellpack.autopack.ingredient.grow", false], [3, "module-cellpack.autopack.ingredient.multi_cylinder", false], [3, "module-cellpack.autopack.ingredient.multi_sphere", false], [3, "module-cellpack.autopack.ingredient.single_cube", false], [3, "module-cellpack.autopack.ingredient.single_cylinder", false], [3, "module-cellpack.autopack.ingredient.single_sphere", false], [3, "module-cellpack.autopack.ingredient.utils", false], [4, "module-cellpack.autopack.interface_objects", false], [4, "module-cellpack.autopack.interface_objects.database_ids", false], [4, "module-cellpack.autopack.interface_objects.default_values", false], [4, "module-cellpack.autopack.interface_objects.gradient_data", false], [4, "module-cellpack.autopack.interface_objects.ingredient_types", false], [4, "module-cellpack.autopack.interface_objects.meta_enum", false], [4, "module-cellpack.autopack.interface_objects.packed_objects", false], [4, "module-cellpack.autopack.interface_objects.partners", false], [4, "module-cellpack.autopack.interface_objects.representations", false], [5, "module-cellpack.autopack.loaders", false], [5, "module-cellpack.autopack.loaders.analysis_config_loader", false], [5, "module-cellpack.autopack.loaders.config_loader", false], [5, "module-cellpack.autopack.loaders.migrate_v1_to_v2", false], [5, "module-cellpack.autopack.loaders.migrate_v2_to_v2_1", false], [5, "module-cellpack.autopack.loaders.recipe_loader", false], [5, "module-cellpack.autopack.loaders.utils", false], [5, "module-cellpack.autopack.loaders.v1_v2_attribute_changes", false], [6, "module-cellpack.autopack.upy", false], [6, "module-cellpack.autopack.upy.colors", false], [6, "module-cellpack.autopack.upy.hostHelper", false], [7, "module-cellpack.autopack.upy.simularium", false], [7, "module-cellpack.autopack.upy.simularium.plots", false], [7, "module-cellpack.autopack.upy.simularium.simularium_helper", false], [8, "module-cellpack.autopack.writers", false], [8, "module-cellpack.autopack.writers.ImageWriter", false], [9, "module-cellpack.bin", false], [9, "module-cellpack.bin.analyze", false], [9, "module-cellpack.bin.clean", false], [9, "module-cellpack.bin.cleanup_tasks", false], [9, "module-cellpack.bin.pack", false], [9, "module-cellpack.bin.simularium_converter", false], [9, "module-cellpack.bin.upload", false]], "molbtrajectory (class in cellpack.autopack.trajectory)": [[2, "cellpack.autopack.trajectory.molbTrajectory", false]], "move() (cellpack.autopack.upy.simularium.simularium_helper.instance method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.Instance.move", false]], "move_object() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.move_object", false]], "moverbnode() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.moveRBnode", false]], "multi_cylinder (cellpack.autopack.interface_objects.ingredient_types.ingredient_type attribute)": [[4, "cellpack.autopack.interface_objects.ingredient_types.INGREDIENT_TYPE.MULTI_CYLINDER", false]], "multi_sphere (cellpack.autopack.interface_objects.ingredient_types.ingredient_type attribute)": [[4, "cellpack.autopack.interface_objects.ingredient_types.INGREDIENT_TYPE.MULTI_SPHERE", false]], "multicylindersingr (class in cellpack.autopack.ingredient.multi_cylinder)": [[3, "cellpack.autopack.ingredient.multi_cylinder.MultiCylindersIngr", false]], "multisphereingr (class in cellpack.autopack.ingredient.multi_sphere)": [[3, "cellpack.autopack.ingredient.multi_sphere.MultiSphereIngr", false]], "newempty() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.newEmpty", false]], "newempty() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.newEmpty", false]], "newinstance() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.newInstance", false]], "nodetogeom() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.nodeToGeom", false]], "norm() (cellpack.autopack.meshstore.meshstore static method)": [[2, "cellpack.autopack.MeshStore.MeshStore.norm", false]], "norm() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.norm", false]], "normal (cellpack.autopack.ingredient.ingredient.distributiontypes attribute)": [[3, "cellpack.autopack.ingredient.Ingredient.DistributionTypes.NORMAL", false]], "normal_array() (cellpack.autopack.meshstore.meshstore static method)": [[2, "cellpack.autopack.MeshStore.MeshStore.normal_array", false]], "normal_array() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.normal_array", false]], "normalize() (cellpack.autopack.meshstore.meshstore static method)": [[2, "cellpack.autopack.MeshStore.MeshStore.normalize", false]], "normalize() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.normalize", false]], "normalize_v3() (cellpack.autopack.meshstore.meshstore static method)": [[2, "cellpack.autopack.MeshStore.MeshStore.normalize_v3", false]], "normalize_v3() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.normalize_v3", false]], "normalize_vector() (cellpack.autopack.gradient.gradient method)": [[2, "cellpack.autopack.Gradient.Gradient.normalize_vector", false]], "np_check_collision() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.np_check_collision", false]], "numpyarrayencoder (class in cellpack.autopack.writers)": [[8, "cellpack.autopack.writers.NumpyArrayEncoder", false]], "object (cellpack.autopack.interface_objects.gradient_data.modeoptions attribute)": [[4, "cellpack.autopack.interface_objects.gradient_data.ModeOptions.object", false]], "objectdoc (class in cellpack.autopack.dbrecipehandler)": [[2, "cellpack.autopack.DBRecipeHandler.ObjectDoc", false]], "objectsselection() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.ObjectsSelection", false]], "objectsselection() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.ObjectsSelection", false]], "octahedron() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.Octahedron", false], [6, "cellpack.autopack.upy.hostHelper.Helper.octahedron", false]], "octnode (class in cellpack.autopack.octree)": [[2, "cellpack.autopack.octree.OctNode", false]], "octree (class in cellpack.autopack.octree)": [[2, "cellpack.autopack.octree.Octree", false]], "onecolladageom() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.oneColladaGeom", false]], "onecylinder() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.oneCylinder", false]], "onejitter() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.oneJitter", false]], "onemetaball() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.oneMetaBall", false]], "oneprevingredient() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.onePrevIngredient", false]], "open_in_simularium() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper static method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.open_in_simularium", false]], "pack() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.pack", false]], "pack() (in module cellpack.bin.pack)": [[9, "cellpack.bin.pack.pack", false]], "pack_at_grid_pt_location() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.pack_at_grid_pt_location", false]], "pack_at_grid_pt_location() (cellpack.autopack.ingredient.multi_sphere.multisphereingr method)": [[3, "cellpack.autopack.ingredient.multi_sphere.MultiSphereIngr.pack_at_grid_pt_location", false]], "pack_grid() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.pack_grid", false]], "pack_one_seed() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.pack_one_seed", false]], "packedobject (class in cellpack.autopack.interface_objects.packed_objects)": [[4, "cellpack.autopack.interface_objects.packed_objects.PackedObject", false]], "packedobjects (class in cellpack.autopack.interface_objects.packed_objects)": [[4, "cellpack.autopack.interface_objects.packed_objects.PackedObjects", false]], "parse() (cellpack.autopack.trajectory.dcdtrajectory method)": [[2, "cellpack.autopack.trajectory.dcdTrajectory.parse", false]], "parse() (cellpack.autopack.trajectory.molbtrajectory method)": [[2, "cellpack.autopack.trajectory.molbTrajectory.parse", false]], "parse() (cellpack.autopack.trajectory.xyztrajectory method)": [[2, "cellpack.autopack.trajectory.xyzTrajectory.parse", false]], "parse_one_mol() (cellpack.autopack.trajectory.molbtrajectory method)": [[2, "cellpack.autopack.trajectory.molbTrajectory.parse_one_mol", false]], "parse_s3_uri() (in module cellpack.autopack)": [[2, "cellpack.autopack.parse_s3_uri", false]], "particle() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.particle", false]], "partner (class in cellpack.autopack.interface_objects.partners)": [[4, "cellpack.autopack.interface_objects.partners.Partner", false]], "partners (class in cellpack.autopack.interface_objects.partners)": [[4, "cellpack.autopack.interface_objects.partners.Partners", false]], "pathdeform() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.pathDeform", false]], "pathdeform() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.pathDeform", false]], "pb (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper attribute)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.pb", false]], "perturbaxis() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.perturbAxis", false]], "pick_alternate() (cellpack.autopack.ingredient.grow.growingredient method)": [[3, "cellpack.autopack.ingredient.grow.GrowIngredient.pick_alternate", false]], "pick_partner_grid_index() (cellpack.autopack.ingredient.agent.agent method)": [[3, "cellpack.autopack.ingredient.agent.Agent.pick_partner_grid_index", false]], "pick_random_alternate() (cellpack.autopack.ingredient.grow.growingredient method)": [[3, "cellpack.autopack.ingredient.grow.GrowIngredient.pick_random_alternate", false]], "pickalternatehalton() (cellpack.autopack.ingredient.grow.growingredient method)": [[3, "cellpack.autopack.ingredient.grow.GrowIngredient.pickAlternateHalton", false]], "pickhalton() (cellpack.autopack.ingredient.grow.growingredient method)": [[3, "cellpack.autopack.ingredient.grow.GrowIngredient.pickHalton", false]], "pickingredient() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.pickIngredient", false]], "pickmodes (class in cellpack.autopack.interface_objects.gradient_data)": [[4, "cellpack.autopack.interface_objects.gradient_data.PickModes", false]], "pickpoint() (cellpack.autopack.gradient.gradient method)": [[2, "cellpack.autopack.Gradient.Gradient.pickPoint", false]], "pickrandomsphere() (cellpack.autopack.ingredient.grow.growingredient method)": [[3, "cellpack.autopack.ingredient.grow.GrowIngredient.pickRandomSphere", false]], "place() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.place", false]], "place_alternate() (cellpack.autopack.ingredient.grow.growingredient method)": [[3, "cellpack.autopack.ingredient.grow.GrowIngredient.place_alternate", false]], "place_alternate_p() (cellpack.autopack.ingredient.grow.growingredient method)": [[3, "cellpack.autopack.ingredient.grow.GrowIngredient.place_alternate_p", false]], "place_methods (class in cellpack.autopack.loaders.config_loader)": [[5, "cellpack.autopack.loaders.config_loader.Place_Methods", false]], "place_object() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.place_object", false]], "plane() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.plane", false]], "plane() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.plane", false]], "platonic() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.Platonic", false]], "plot() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.plot", false]], "plot_distance_distribution() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.plot_distance_distribution", false]], "plot_occurence_distribution() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.plot_occurence_distribution", false]], "plot_position_distribution() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.plot_position_distribution", false]], "plot_position_distribution_total() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.plot_position_distribution_total", false]], "plotdata (class in cellpack.autopack.upy.simularium.plots)": [[7, "cellpack.autopack.upy.simularium.plots.PlotData", false]], "plotlyanalysis (class in cellpack.autopack.plotly_result)": [[2, "cellpack.autopack.plotly_result.PlotlyAnalysis", false]], "point_is_available() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.point_is_available", false]], "pointcloudobject() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.PointCloudObject", false]], "points() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.Points", false]], "polygon (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper attribute)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.POLYGON", false]], "polylines() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.Polylines", false]], "post_and_open_file() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.post_and_open_file", false]], "power (cellpack.autopack.interface_objects.gradient_data.weightmodeoptions attribute)": [[4, "cellpack.autopack.interface_objects.gradient_data.WeightModeOptions.power", false]], "power (cellpack.autopack.interface_objects.gradient_data.weightmodes attribute)": [[4, "cellpack.autopack.interface_objects.gradient_data.WeightModes.POWER", false]], "prep_data_for_db() (cellpack.autopack.dbrecipehandler.dbuploader static method)": [[2, "cellpack.autopack.DBRecipeHandler.DBUploader.prep_data_for_db", false]], "prep_db_doc_for_download() (cellpack.autopack.dbrecipehandler.dbrecipeloader method)": [[2, "cellpack.autopack.DBRecipeHandler.DBRecipeLoader.prep_db_doc_for_download", false]], "prep_molecules_for_save() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.prep_molecules_for_save", false]], "prepare_alternates() (cellpack.autopack.ingredient.grow.growingredient method)": [[3, "cellpack.autopack.ingredient.grow.GrowIngredient.prepare_alternates", false]], "prepare_alternates_proba() (cellpack.autopack.ingredient.grow.growingredient method)": [[3, "cellpack.autopack.ingredient.grow.GrowIngredient.prepare_alternates_proba", false]], "prepare_buildgrid_box() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.prepare_buildgrid_box", false]], "preparedynamic() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.prepareDynamic", false]], "prepareingredient() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.prepareIngredient", false]], "preparemaster() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.prepareMaster", false]], "printfillinfo() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.printFillInfo", false]], "printfillinfo() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.printFillInfo", false]], "printfillinfo() (cellpack.autopack.recipe.recipe method)": [[2, "cellpack.autopack.Recipe.Recipe.printFillInfo", false]], "printingredients() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.printIngredients", false]], "printoneingr() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.printOneIngr", false]], "process_ingredients_in_recipe() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.process_ingredients_in_recipe", false]], "process_one_ingredient() (cellpack.bin.simularium_converter.converttosimularium method)": [[9, "cellpack.bin.simularium_converter.ConvertToSimularium.process_one_ingredient", false]], "progressbar() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.progressBar", false]], "progressbar() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.progressBar", false]], "quaternion_matrix() (cellpack.autopack.randomrot.randomrot method)": [[2, "cellpack.autopack.randomRot.RandomRot.quaternion_matrix", false]], "radial (cellpack.autopack.interface_objects.gradient_data.gradientmodes attribute)": [[4, "cellpack.autopack.interface_objects.gradient_data.GradientModes.RADIAL", false]], "radius (cellpack.autopack.interface_objects.gradient_data.modeoptions attribute)": [[4, "cellpack.autopack.interface_objects.gradient_data.ModeOptions.radius", false]], "random() (in module cellpack.autopack.environment)": [[2, "cellpack.autopack.Environment.random", false]], "random() (in module cellpack.autopack.gradient)": [[2, "cellpack.autopack.Gradient.random", false]], "random() (in module cellpack.autopack.ingredient.agent)": [[3, "cellpack.autopack.ingredient.agent.random", false]], "random() (in module cellpack.autopack.ingredient.grow)": [[3, "cellpack.autopack.ingredient.grow.random", false]], "random() (in module cellpack.autopack.ingredient.ingredient)": [[3, "cellpack.autopack.ingredient.Ingredient.random", false]], "random() (in module cellpack.autopack.recipe)": [[2, "cellpack.autopack.Recipe.random", false]], "random_quaternion() (cellpack.autopack.randomrot.randomrot method)": [[2, "cellpack.autopack.randomRot.RandomRot.random_quaternion", false]], "random_rotation_matrix() (cellpack.autopack.randomrot.randomrot method)": [[2, "cellpack.autopack.randomRot.RandomRot.random_rotation_matrix", false]], "randomize_rotation() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.randomize_rotation", false]], "randomize_translation() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.randomize_translation", false]], "randomrot (class in cellpack.autopack.randomrot)": [[2, "cellpack.autopack.randomRot.RandomRot", false]], "randpoint_onsphere() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.randpoint_onsphere", false]], "ray_intersect_polygon() (in module cellpack.autopack.ray)": [[2, "cellpack.autopack.ray.ray_intersect_polygon", false]], "ray_intersect_polyhedron() (in module cellpack.autopack.ray)": [[2, "cellpack.autopack.ray.ray_intersect_polyhedron", false]], "raycast() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.raycast", false]], "raycast() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.raycast", false]], "raycast_test() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.raycast_test", false]], "raytrace (cellpack.autopack.loaders.config_loader.inner_grid_methods attribute)": [[5, "cellpack.autopack.loaders.config_loader.Inner_Grid_Methods.RAYTRACE", false]], "read() (cellpack.autopack.ioutils.ioingredienttool method)": [[2, "cellpack.autopack.IOutils.IOingredientTool.read", false]], "read() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.read", false]], "read() (in module cellpack.autopack.binvox_rw)": [[2, "cellpack.autopack.binvox_rw.read", false]], "read_as_3d_array() (in module cellpack.autopack.binvox_rw)": [[2, "cellpack.autopack.binvox_rw.read_as_3d_array", false]], "read_as_coord_array() (in module cellpack.autopack.binvox_rw)": [[2, "cellpack.autopack.binvox_rw.read_as_coord_array", false]], "read_dict_from_glob_file() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.read_dict_from_glob_file", false]], "read_header() (in module cellpack.autopack.binvox_rw)": [[2, "cellpack.autopack.binvox_rw.read_header", false]], "read_json_file() (in module cellpack.autopack.loaders.utils)": [[5, "cellpack.autopack.loaders.utils.read_json_file", false]], "read_mesh_file() (cellpack.autopack.meshstore.meshstore method)": [[2, "cellpack.autopack.MeshStore.MeshStore.read_mesh_file", false]], "read_text_file() (in module cellpack.autopack)": [[2, "cellpack.autopack.read_text_file", false]], "readarraysfromfile() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.readArraysFromFile", false]], "readgridfromfile() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.readGridFromFile", false]], "readme_url() (cellpack.autopack.dbrecipehandler.dbmaintenance method)": [[2, "cellpack.autopack.DBRecipeHandler.DBMaintenance.readme_url", false]], "readmeshfromfile() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.readMeshFromFile", false]], "recalc_normals() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.recalc_normals", false]], "recipe (class in cellpack.autopack.recipe)": [[2, "cellpack.autopack.Recipe.Recipe", false]], "recipeloader (class in cellpack.autopack.loaders.recipe_loader)": [[5, "cellpack.autopack.loaders.recipe_loader.RecipeLoader", false]], "rectangle (class in cellpack.autopack.geometrytools)": [[2, "cellpack.autopack.GeometryTools.Rectangle", false]], "redwhiteblueramp() (in module cellpack.autopack.upy.colors)": [[6, "cellpack.autopack.upy.colors.RedWhiteBlueRamp", false]], "reg (cellpack.autopack.interface_objects.gradient_data.pickmodes attribute)": [[4, "cellpack.autopack.interface_objects.gradient_data.PickModes.REG", false]], "reg (cellpack.autopack.trajectory.trajectory attribute)": [[2, "cellpack.autopack.trajectory.Trajectory.reg", false]], "region_1() (cellpack.autopack.geometrytools.geometrytools method)": [[2, "cellpack.autopack.GeometryTools.GeometryTools.region_1", false]], "region_1_2_theta() (cellpack.autopack.geometrytools.geometrytools method)": [[2, "cellpack.autopack.GeometryTools.GeometryTools.region_1_2_theta", false]], "region_2() (cellpack.autopack.geometrytools.geometrytools method)": [[2, "cellpack.autopack.GeometryTools.GeometryTools.region_2", false]], "region_2_integrand() (cellpack.autopack.geometrytools.geometrytools method)": [[2, "cellpack.autopack.GeometryTools.GeometryTools.region_2_integrand", false]], "region_3() (cellpack.autopack.geometrytools.geometrytools method)": [[2, "cellpack.autopack.GeometryTools.GeometryTools.region_3", false]], "region_3_integrand() (cellpack.autopack.geometrytools.geometrytools method)": [[2, "cellpack.autopack.GeometryTools.GeometryTools.region_3_integrand", false]], "reject() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.reject", false]], "remove_from_realtime_display() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.remove_from_realtime_display", false]], "remove_nans() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper static method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.remove_nans", false]], "removefreepoint() (cellpack.autopack.basegrid.basegrid method)": [[2, "cellpack.autopack.BaseGrid.BaseGrid.removeFreePoint", false]], "removeonepoint() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.removeOnePoint", false]], "reorder_free_points() (cellpack.autopack.basegrid.basegrid static method)": [[2, "cellpack.autopack.BaseGrid.BaseGrid.reorder_free_points", false]], "reparent() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.reParent", false]], "reparent() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.reParent", false]], "replaceingrmesh() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.replaceIngrMesh", false]], "reporthook() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.reporthook", false]], "reportprogress() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.reportprogress", false]], "representations (class in cellpack.autopack.interface_objects.representations)": [[4, "cellpack.autopack.interface_objects.representations.Representations", false]], "rerieveaxis() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.rerieveAxis", false]], "reset() (cellpack.autopack.basegrid.basegrid method)": [[2, "cellpack.autopack.BaseGrid.BaseGrid.reset", false]], "reset() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.reset", false]], "reset() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.reset", false]], "reset() (cellpack.autopack.grid.grid method)": [[2, "cellpack.autopack.Grid.Grid.reset", false]], "reset() (cellpack.autopack.ingredient.grow.growingredient method)": [[3, "cellpack.autopack.ingredient.grow.GrowIngredient.reset", false]], "reset() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.reset", false]], "reset() (cellpack.autopack.ioutils.grabresult method)": [[2, "cellpack.autopack.IOutils.GrabResult.reset", false]], "reset() (cellpack.autopack.ldsequence.chaltonsequence3 method)": [[2, "cellpack.autopack.ldSequence.cHaltonSequence3.reset", false]], "resetdefault() (in module cellpack.autopack)": [[2, "cellpack.autopack.resetDefault", false]], "resetingrrecip() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.resetIngrRecip", false]], "resetingrs() (cellpack.autopack.recipe.recipe method)": [[2, "cellpack.autopack.Recipe.Recipe.resetIngrs", false]], "resetlastpoint() (cellpack.autopack.ingredient.grow.growingredient method)": [[3, "cellpack.autopack.ingredient.grow.GrowIngredient.resetLastPoint", false]], "resetprogressbar() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.resetProgressBar", false]], "resetprogressbar() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.resetProgressBar", false]], "resetspheredistribution() (cellpack.autopack.ingredient.grow.growingredient method)": [[3, "cellpack.autopack.ingredient.grow.GrowIngredient.resetSphereDistribution", false]], "resettransformation() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.resetTransformation", false]], "resolution (cellpack.autopack.geometrytools.geometrytools attribute)": [[2, "cellpack.autopack.GeometryTools.GeometryTools.Resolution", false]], "resolve_composition() (cellpack.autopack.recipe.recipe static method)": [[2, "cellpack.autopack.Recipe.Recipe.resolve_composition", false]], "resolve_db_regions() (cellpack.autopack.dbrecipehandler.compositiondoc method)": [[2, "cellpack.autopack.DBRecipeHandler.CompositionDoc.resolve_db_regions", false]], "resolve_gradient_data_objects() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.resolve_gradient_data_objects", false]], "resolve_inheritance() (cellpack.autopack.loaders.recipe_loader.recipeloader static method)": [[5, "cellpack.autopack.loaders.recipe_loader.RecipeLoader.resolve_inheritance", false]], "resolve_local_regions() (cellpack.autopack.dbrecipehandler.compositiondoc method)": [[2, "cellpack.autopack.DBRecipeHandler.CompositionDoc.resolve_local_regions", false]], "resolve_object_data() (cellpack.autopack.dbrecipehandler.compositiondoc method)": [[2, "cellpack.autopack.DBRecipeHandler.CompositionDoc.resolve_object_data", false]], "restore() (cellpack.autopack.basegrid.basegrid method)": [[2, "cellpack.autopack.BaseGrid.BaseGrid.restore", false]], "restore() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.restore", false]], "restore() (cellpack.autopack.grid.grid method)": [[2, "cellpack.autopack.Grid.Grid.restore", false]], "restore_grids_from_pickle() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.restore_grids_from_pickle", false]], "restore_molecules_array() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.restore_molecules_array", false]], "restoreeditmode() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.restoreEditMode", false]], "restorefreepoints() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.restoreFreePoints", false]], "restoregridfromfile() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.restoreGridFromFile", false]], "resultdoc (class in cellpack.autopack.dbrecipehandler)": [[2, "cellpack.autopack.DBRecipeHandler.ResultDoc", false]], "retrievecolormat() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.retrieveColorMat", false]], "retrievehost() (in module cellpack.autopack.upy)": [[6, "cellpack.autopack.upy.retrieveHost", false]], "return_object_value() (cellpack.autopack.writers.writer static method)": [[8, "cellpack.autopack.writers.Writer.return_object_value", false]], "rigid_place() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.rigid_place", false]], "rnd (cellpack.autopack.interface_objects.gradient_data.pickmodes attribute)": [[4, "cellpack.autopack.interface_objects.gradient_data.PickModes.RND", false]], "rotate_about_axis() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.rotate_about_axis", false]], "rotateobj() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.rotateObj", false]], "rotateobj() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.rotateObj", false]], "rotatepoint() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.rotatePoint", false]], "rotation_matrix() (cellpack.autopack.upy.hosthelper.helper class method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.rotation_matrix", false]], "rotax() (in module cellpack.autopack.ingredient.utils)": [[3, "cellpack.autopack.ingredient.utils.rotax", false]], "rotvecttovect() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.rotVectToVect", false]], "rotvecttovect() (in module cellpack.autopack.ingredient.utils)": [[3, "cellpack.autopack.ingredient.utils.rotVectToVect", false]], "run_analysis_workflow() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.run_analysis_workflow", false]], "run_cleanup() (in module cellpack.bin.cleanup_tasks)": [[9, "cellpack.bin.cleanup_tasks.run_cleanup", false]], "run_distance_analysis() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.run_distance_analysis", false]], "run_partner_analysis() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.run_partner_analysis", false]], "runbullet() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.runBullet", false]], "save() (cellpack.autopack.basegrid.basegrid method)": [[2, "cellpack.autopack.BaseGrid.BaseGrid.save", false]], "save() (cellpack.autopack.grid.grid method)": [[2, "cellpack.autopack.Grid.Grid.save", false]], "save() (cellpack.autopack.writers.writer method)": [[8, "cellpack.autopack.writers.Writer.save", false]], "save_as_simularium() (cellpack.autopack.writers.writer method)": [[8, "cellpack.autopack.writers.Writer.save_as_simularium", false]], "save_aspython() (in module cellpack.autopack.ioutils)": [[2, "cellpack.autopack.IOutils.save_asPython", false]], "save_file_and_get_url() (cellpack.autopack.awshandler.awshandler method)": [[2, "cellpack.autopack.AWSHandler.AWSHandler.save_file_and_get_url", false]], "save_grids_to_pickle() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.save_grids_to_pickle", false]], "save_mixed_asjson() (cellpack.autopack.writers.writer method)": [[8, "cellpack.autopack.writers.Writer.save_Mixed_asJson", false]], "save_result() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.save_result", false]], "savedejavumesh() (cellpack.autopack.upy.hosthelper.helper class method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.saveDejaVuMesh", false]], "savegridlogsasjson() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.saveGridLogsAsJson", false]], "savegridtofile() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.saveGridToFile", false]], "savegridtofile() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.saveGridToFile", false]], "saveobjmesh() (cellpack.autopack.upy.hosthelper.helper class method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.saveObjMesh", false]], "saverecipeavailable() (in module cellpack.autopack)": [[2, "cellpack.autopack.saveRecipeAvailable", false]], "saverecipeavailablejson() (in module cellpack.autopack)": [[2, "cellpack.autopack.saveRecipeAvailableJSON", false]], "saveresultbinary() (in module cellpack.autopack.ioutils)": [[2, "cellpack.autopack.IOutils.saveResultBinary", false]], "saveresultbinarydic() (in module cellpack.autopack.ioutils)": [[2, "cellpack.autopack.IOutils.saveResultBinaryDic", false]], "scalar() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.scalar", false]], "scale_distance_between (cellpack.autopack.interface_objects.gradient_data.modeoptions attribute)": [[4, "cellpack.autopack.interface_objects.gradient_data.ModeOptions.scale_distance_between", false]], "scaleobj() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.scaleObj", false]], "scaleobj() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.scaleObj", false]], "scanline (cellpack.autopack.loaders.config_loader.inner_grid_methods attribute)": [[5, "cellpack.autopack.loaders.config_loader.Inner_Grid_Methods.SCANLINE", false]], "scompartment (class in cellpack.autopack.serializable)": [[2, "cellpack.autopack.Serializable.sCompartment", false]], "selectedge() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.selectEdge", false]], "selectedges() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.selectEdges", false]], "selectface() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.selectFace", false]], "selectfaces() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.selectFaces", false]], "selectvertice() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.selectVertice", false]], "selectvertices() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.selectVertices", false]], "serializedfromresult() (in module cellpack.autopack.ioutils)": [[2, "cellpack.autopack.IOutils.serializedFromResult", false]], "serializedrecipe() (in module cellpack.autopack.ioutils)": [[2, "cellpack.autopack.IOutils.serializedRecipe", false]], "serializedrecipe_group() (in module cellpack.autopack.ioutils)": [[2, "cellpack.autopack.IOutils.serializedRecipe_group", false]], "serializedrecipe_group_dic() (in module cellpack.autopack.ioutils)": [[2, "cellpack.autopack.IOutils.serializedRecipe_group_dic", false]], "set_active() (cellpack.autopack.interface_objects.representations.representations method)": [[4, "cellpack.autopack.interface_objects.representations.Representations.set_active", false]], "set_doc() (cellpack.autopack.firebasehandler.firebasehandler method)": [[2, "cellpack.autopack.FirebaseHandler.FirebaseHandler.set_doc", false]], "set_gradient() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.set_gradient", false]], "set_ingredient() (cellpack.autopack.interface_objects.partners.partner method)": [[4, "cellpack.autopack.interface_objects.partners.Partner.set_ingredient", false]], "set_ingredient_color() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.set_ingredient_color", false]], "set_mode_properties() (cellpack.autopack.interface_objects.gradient_data.gradientdata method)": [[4, "cellpack.autopack.interface_objects.gradient_data.GradientData.set_mode_properties", false]], "set_object_static() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.set_object_static", false]], "set_partners_ingredient() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.set_partners_ingredient", false]], "set_recipe_ingredient() (cellpack.autopack.ioutils.ioingredienttool method)": [[2, "cellpack.autopack.IOutils.IOingredientTool.set_recipe_ingredient", false]], "set_result_file_name() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.set_result_file_name", false]], "set_sphere_positions() (cellpack.autopack.interface_objects.representations.representations method)": [[4, "cellpack.autopack.interface_objects.representations.Representations.set_sphere_positions", false]], "set_static() (cellpack.autopack.upy.simularium.simularium_helper.instance method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.Instance.set_static", false]], "set_surface_distances() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.set_surface_distances", false]], "set_surfptsbht() (cellpack.autopack.basegrid.basegrid method)": [[2, "cellpack.autopack.BaseGrid.BaseGrid.set_surfPtsBht", false]], "set_surfptscht() (cellpack.autopack.basegrid.basegrid method)": [[2, "cellpack.autopack.BaseGrid.BaseGrid.set_surfPtscht", false]], "set_weights_by_mode() (cellpack.autopack.gradient.gradient method)": [[2, "cellpack.autopack.Gradient.Gradient.set_weights_by_mode", false]], "setcount() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.setCount", false]], "setcount() (cellpack.autopack.recipe.recipe method)": [[2, "cellpack.autopack.Recipe.Recipe.setCount", false]], "setcurrentselection() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.setCurrentSelection", false]], "setexteriorrecipe() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.setExteriorRecipe", false]], "setframe() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.setFrame", false]], "setgeomfaces() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.setGeomFaces", false]], "setgeomfaces() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.setGeomFaces", false]], "sethistovol() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.SetHistoVol", false]], "setinnerrecipe() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.setInnerRecipe", false]], "setinstance() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.setInstance", false]], "setkeyframe() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.setKeyFrame", false]], "setlayers() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.setLayers", false]], "setmesh() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.setMesh", false]], "setmeshedge() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.setMeshEdge", false]], "setmeshedges() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.setMeshEdges", false]], "setmeshface() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.setMeshFace", false]], "setmeshfaces() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.setMeshFaces", false]], "setmeshvertice() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.setMeshVertice", false]], "setmeshvertices() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.setMeshVertices", false]], "setname() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.setName", false]], "setnumber() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.setNumber", false]], "setobjectmatrix() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.setObjectMatrix", false]], "setobjectmatrix() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.setObjectMatrix", false]], "setparticulesposition() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.setParticulesPosition", false]], "setproperty() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.setProperty", false]], "setpropertyobject() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.setPropertyObject", false]], "setrboptions() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.SetRBOptions", false]], "setrigidbody() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.setRigidBody", false]], "setrigidbody() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.setRigidBody", false]], "setseed() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.setSeed", false]], "setseed() (cellpack.autopack.randomrot.randomrot method)": [[2, "cellpack.autopack.randomRot.RandomRot.setSeed", false]], "setsoftbody() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.setSoftBody", false]], "setspringoptions() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.SetSpringOptions", false]], "setsurfacerecipe() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.setSurfaceRecipe", false]], "settilling() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.setTilling", false]], "settransformation() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.setTransformation", false]], "settranslation() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.setTranslation", false]], "settranslation() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.setTranslation", false]], "setup() (cellpack.autopack.basegrid.basegrid method)": [[2, "cellpack.autopack.BaseGrid.BaseGrid.setup", false]], "setupboundaryperiodicity() (cellpack.autopack.basegrid.basegrid method)": [[2, "cellpack.autopack.BaseGrid.BaseGrid.setupBoundaryPeriodicity", false]], "setupfromjsondic() (in module cellpack.autopack.ioutils)": [[2, "cellpack.autopack.IOutils.setupFromJsonDic", false]], "setupoctree() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.setupOctree", false]], "setuprboptions() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.setupRBOptions", false]], "setuv() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.setUV", false]], "setuvs() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.setUVs", false]], "setvaluetojsonnode() (cellpack.autopack.writers.writer static method)": [[8, "cellpack.autopack.writers.Writer.setValueToJsonNode", false]], "setvaluetopythonstr() (in module cellpack.autopack.ioutils)": [[2, "cellpack.autopack.IOutils.setValueToPythonStr", false]], "setviewer() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.setViewer", false]], "setviewport() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.setViewport", false]], "shallow_match (cellpack.autopack.dbrecipehandler.compositiondoc attribute)": [[2, "cellpack.autopack.DBRecipeHandler.CompositionDoc.SHALLOW_MATCH", false]], "should_write() (cellpack.autopack.dbrecipehandler.compositiondoc method)": [[2, "cellpack.autopack.DBRecipeHandler.CompositionDoc.should_write", false]], "should_write() (cellpack.autopack.dbrecipehandler.datadoc method)": [[2, "cellpack.autopack.DBRecipeHandler.DataDoc.should_write", false]], "should_write() (cellpack.autopack.dbrecipehandler.gradientdoc method)": [[2, "cellpack.autopack.DBRecipeHandler.GradientDoc.should_write", false]], "should_write() (cellpack.autopack.dbrecipehandler.objectdoc method)": [[2, "cellpack.autopack.DBRecipeHandler.ObjectDoc.should_write", false]], "show() (cellpack.autopack.plotly_result.plotlyanalysis method)": [[2, "cellpack.autopack.plotly_result.PlotlyAnalysis.show", false]], "showhide() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.showHide", false]], "showingrprimitive() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.showIngrPrimitive", false]], "simpleplot() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.simpleplot", false]], "simulariumhelper (class in cellpack.autopack.upy.simularium.simularium_helper)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper", false]], "single_cube (cellpack.autopack.interface_objects.ingredient_types.ingredient_type attribute)": [[4, "cellpack.autopack.interface_objects.ingredient_types.INGREDIENT_TYPE.SINGLE_CUBE", false]], "single_cylinder (cellpack.autopack.interface_objects.ingredient_types.ingredient_type attribute)": [[4, "cellpack.autopack.interface_objects.ingredient_types.INGREDIENT_TYPE.SINGLE_CYLINDER", false]], "single_sphere (cellpack.autopack.interface_objects.ingredient_types.ingredient_type attribute)": [[4, "cellpack.autopack.interface_objects.ingredient_types.INGREDIENT_TYPE.SINGLE_SPHERE", false]], "singlecubeingr (class in cellpack.autopack.ingredient.single_cube)": [[3, "cellpack.autopack.ingredient.single_cube.SingleCubeIngr", false]], "singlecylinderingr (class in cellpack.autopack.ingredient.single_cylinder)": [[3, "cellpack.autopack.ingredient.single_cylinder.SingleCylinderIngr", false]], "singlesphereingr (class in cellpack.autopack.ingredient.single_sphere)": [[3, "cellpack.autopack.ingredient.single_sphere.SingleSphereIngr", false]], "singredient (class in cellpack.autopack.serializable)": [[2, "cellpack.autopack.Serializable.sIngredient", false]], "singredientfiber (class in cellpack.autopack.serializable)": [[2, "cellpack.autopack.Serializable.sIngredientFiber", false]], "singredientgroup (class in cellpack.autopack.serializable)": [[2, "cellpack.autopack.Serializable.sIngredientGroup", false]], "slow_box_fill() (cellpack.autopack.basegrid.basegrid method)": [[2, "cellpack.autopack.BaseGrid.BaseGrid.slow_box_fill", false]], "sort() (cellpack.autopack.recipe.recipe method)": [[2, "cellpack.autopack.Recipe.Recipe.sort", false]], "sort_values() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper static method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.sort_values", false]], "sortingredient() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.sortIngredient", false]], "sparse_to_dense() (in module cellpack.autopack.binvox_rw)": [[2, "cellpack.autopack.binvox_rw.sparse_to_dense", false]], "sphere (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper attribute)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.SPHERE", false]], "sphere() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.Sphere", false]], "sphere() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.sphere", false]], "spherehalton() (in module cellpack.autopack.ldsequence)": [[2, "cellpack.autopack.ldSequence.SphereHalton", false]], "spheres() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.Spheres", false]], "spheres_sst (cellpack.autopack.loaders.config_loader.place_methods attribute)": [[5, "cellpack.autopack.loaders.config_loader.Place_Methods.SPHERES_SST", false]], "spheres_sst_place() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.spheres_SST_place", false]], "spline (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper attribute)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.SPLINE", false]], "spline() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.spline", false]], "spline() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.spline", false]], "split_ingredient_data() (in module cellpack.autopack.loaders.migrate_v1_to_v2)": [[5, "cellpack.autopack.loaders.migrate_v1_to_v2.split_ingredient_data", false]], "square (cellpack.autopack.interface_objects.gradient_data.weightmodes attribute)": [[4, "cellpack.autopack.interface_objects.gradient_data.WeightModes.SQUARE", false]], "static_id (cellpack.autopack.ingredient.ingredient.ingredient attribute)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.static_id", false]], "static_id (cellpack.autopack.serializable.scompartment attribute)": [[2, "cellpack.autopack.Serializable.sCompartment.static_id", false]], "static_id (cellpack.autopack.serializable.singredient attribute)": [[2, "cellpack.autopack.Serializable.sIngredient.static_id", false]], "static_id (cellpack.autopack.serializable.singredientfiber attribute)": [[2, "cellpack.autopack.Serializable.sIngredientFiber.static_id", false]], "static_id (cellpack.autopack.serializable.singredientgroup attribute)": [[2, "cellpack.autopack.Serializable.sIngredientGroup.static_id", false]], "std (cellpack.autopack.ingredient.ingredient.distributionoptions attribute)": [[3, "cellpack.autopack.ingredient.Ingredient.DistributionOptions.STD", false]], "store() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.store", false]], "store_asjson() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.store_asJson", false]], "store_metadata() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper static method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.store_metadata", false]], "store_packed_object() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.store_packed_object", false]], "store_packed_object() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.store_packed_object", false]], "store_result_file() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper static method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.store_result_file", false]], "sub (cellpack.autopack.interface_objects.gradient_data.pickmodes attribute)": [[4, "cellpack.autopack.interface_objects.gradient_data.PickModes.SUB", false]], "surface (cellpack.autopack.interface_objects.gradient_data.gradientmodes attribute)": [[4, "cellpack.autopack.interface_objects.gradient_data.GradientModes.SURFACE", false]], "swap() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.swap", false]], "test_points_in_bb() (cellpack.autopack.basegrid.basegrid method)": [[2, "cellpack.autopack.BaseGrid.BaseGrid.test_points_in_bb", false]], "testforescape() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.testForEscape", false]], "tetrahedron() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.Tetrahedron", false], [6, "cellpack.autopack.upy.hostHelper.Helper.tetrahedron", false]], "text() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.Text", false]], "texturefacecoordintestovertexcoordinates() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.TextureFaceCoordintesToVertexCoordinates", false]], "threecolorramp() (in module cellpack.autopack.upy.colors)": [[6, "cellpack.autopack.upy.colors.ThreeColorRamp", false]], "timefunction() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.timeFunction", false]], "timefunction() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.timeFunction", false]], "to_json() (cellpack.autopack.serializable.scompartment method)": [[2, "cellpack.autopack.Serializable.sCompartment.to_JSON", false]], "to_json() (cellpack.autopack.serializable.singredient method)": [[2, "cellpack.autopack.Serializable.sIngredient.to_JSON", false]], "to_json() (cellpack.autopack.serializable.singredientfiber method)": [[2, "cellpack.autopack.Serializable.sIngredientFiber.to_JSON", false]], "to_json() (cellpack.autopack.serializable.singredientgroup method)": [[2, "cellpack.autopack.Serializable.sIngredientGroup.to_JSON", false]], "tobinary() (in module cellpack.autopack.ioutils)": [[2, "cellpack.autopack.IOutils.toBinary", false]], "toggle() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.toggle", false]], "toggledisplay() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.toggleDisplay", false]], "toggledisplay() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.toggleDisplay", false]], "toggleeditmode() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.toggleEditMode", false]], "toggleorganelmatr() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.toggleOrganelMatr", false]], "toggleorganelmesh() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.toggleOrganelMesh", false]], "toggleorganelsurf() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.toggleOrganelSurf", false]], "togglexray() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.toggleXray", false]], "tomat() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.ToMat", false]], "tovec() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.ToVec", false]], "tovec() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.ToVec", false]], "traj_type (cellpack.autopack.trajectory.dcdtrajectory attribute)": [[2, "cellpack.autopack.trajectory.dcdTrajectory.traj_type", false]], "traj_type (cellpack.autopack.trajectory.molbtrajectory attribute)": [[2, "cellpack.autopack.trajectory.molbTrajectory.traj_type", false]], "traj_type (cellpack.autopack.trajectory.trajectory attribute)": [[2, "cellpack.autopack.trajectory.Trajectory.traj_type", false]], "traj_type (cellpack.autopack.trajectory.xyztrajectory attribute)": [[2, "cellpack.autopack.trajectory.xyzTrajectory.traj_type", false]], "trajectory (class in cellpack.autopack.trajectory)": [[2, "cellpack.autopack.trajectory.Trajectory", false]], "transformmesh() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.transformMesh", false]], "transformnode() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.transformNode", false]], "transformpoints() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.transformPoints", false]], "transformpoints2d() (cellpack.autopack.plotly_result.plotlyanalysis method)": [[2, "cellpack.autopack.plotly_result.PlotlyAnalysis.transformPoints2D", false]], "transformpoints_mult() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.transformPoints_mult", false]], "translateobj() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.translateObj", false]], "translateobj() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.translateObj", false]], "transpose_image_for_projection() (cellpack.autopack.writers.imagewriter.imagewriter static method)": [[8, "cellpack.autopack.writers.ImageWriter.ImageWriter.transpose_image_for_projection", false]], "transposematrix() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.transposeMatrix", false]], "triangulate() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.triangulate", false]], "triangulateface() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.triangulateFace", false]], "triangulatefacearray() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.triangulateFaceArray", false]], "trimesh (cellpack.autopack.loaders.config_loader.inner_grid_methods attribute)": [[5, "cellpack.autopack.loaders.config_loader.Inner_Grid_Methods.TRIMESH", false]], "twocolorramp() (in module cellpack.autopack.upy.colors)": [[6, "cellpack.autopack.upy.colors.TwoColorRamp", false]], "undspmesh() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.undspMesh", false]], "undspsph() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.undspSph", false]], "uniform (cellpack.autopack.ingredient.ingredient.distributiontypes attribute)": [[3, "cellpack.autopack.ingredient.Ingredient.DistributionTypes.UNIFORM", false]], "unit_vector() (cellpack.autopack.upy.hosthelper.helper class method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.unit_vector", false]], "unlinktraj() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.unlinkTraj", false]], "unpack_curve() (cellpack.bin.simularium_converter.converttosimularium method)": [[9, "cellpack.bin.simularium_converter.ConvertToSimularium.unpack_curve", false]], "unpack_positions() (cellpack.bin.simularium_converter.converttosimularium method)": [[9, "cellpack.bin.simularium_converter.ConvertToSimularium.unpack_positions", false]], "update() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.update", false]], "update() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.update", false]], "update_after_place() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.update_after_place", false]], "update_data_tree() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.update_data_tree", false]], "update_display_rt() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.update_display_rt", false]], "update_distance_distribution_dictionaries() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.update_distance_distribution_dictionaries", false]], "update_doc() (cellpack.autopack.firebasehandler.firebasehandler method)": [[2, "cellpack.autopack.FirebaseHandler.FirebaseHandler.update_doc", false]], "update_elements_in_array() (cellpack.autopack.firebasehandler.firebasehandler static method)": [[2, "cellpack.autopack.FirebaseHandler.FirebaseHandler.update_elements_in_array", false]], "update_ingredient_size() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.update_ingredient_size", false]], "update_instance_positions_and_rotations() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.update_instance_positions_and_rotations", false]], "update_largest_smallest_size() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.update_largest_smallest_size", false]], "update_or_create() (cellpack.autopack.firebasehandler.firebasehandler method)": [[2, "cellpack.autopack.FirebaseHandler.FirebaseHandler.update_or_create", false]], "update_pairwise_distances() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.update_pairwise_distances", false]], "update_reference() (cellpack.autopack.dbrecipehandler.compositiondoc static method)": [[2, "cellpack.autopack.DBRecipeHandler.CompositionDoc.update_reference", false]], "update_reference_on_doc() (cellpack.autopack.firebasehandler.firebasehandler static method)": [[2, "cellpack.autopack.FirebaseHandler.FirebaseHandler.update_reference_on_doc", false]], "update_spline() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.update_spline", false]], "update_spline() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.update_spline", false]], "update_title() (cellpack.autopack.plotly_result.plotlyanalysis method)": [[2, "cellpack.autopack.plotly_result.PlotlyAnalysis.update_title", false]], "update_variable_ingredient_attributes() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.update_variable_ingredient_attributes", false]], "updateappli() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.updateAppli", false]], "updatearmature() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.updateArmature", false]], "updatebox() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.updateBox", false]], "updatebox() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.updateBox", false]], "updatedistances() (cellpack.autopack.basegrid.basegrid static method)": [[2, "cellpack.autopack.BaseGrid.BaseGrid.updateDistances", false]], "updatefrombb() (cellpack.autopack.ingredient.grow.actiningredient method)": [[3, "cellpack.autopack.ingredient.grow.ActinIngredient.updateFromBB", false]], "updategrid() (cellpack.autopack.ingredient.grow.growingredient method)": [[3, "cellpack.autopack.ingredient.grow.GrowIngredient.updateGrid", false]], "updatemasterinstance() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.updateMasterInstance", false]], "updatemasterinstance() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.updateMasterInstance", false]], "updatemesh() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.updateMesh", false]], "updateparticles() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.updateParticles", false]], "updatepath() (in module cellpack.autopack)": [[2, "cellpack.autopack.updatePath", false]], "updatepathdeform() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.updatePathDeform", false]], "updatepathdeform() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.updatePathDeform", false]], "updatepathjson() (in module cellpack.autopack)": [[2, "cellpack.autopack.updatePathJSON", false]], "updatepoly() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.updatePoly", false]], "updatepositionsradii() (in module cellpack.autopack.ioutils)": [[2, "cellpack.autopack.IOutils.updatePositionsRadii", false]], "updatepositionsradii() (in module cellpack.autopack.writers)": [[8, "cellpack.autopack.writers.updatePositionsRadii", false]], "updaterecipavailablexml() (in module cellpack.autopack)": [[2, "cellpack.autopack.updateRecipAvailableXML", false]], "updatereplacepath() (in module cellpack.autopack)": [[2, "cellpack.autopack.updateReplacePath", false]], "updatespring() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.updateSpring", false]], "updatetubemesh() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.updateTubeMesh", false]], "updatetubeobjs() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.updateTubeObjs", false]], "upload() (in module cellpack.bin.upload)": [[9, "cellpack.bin.upload.upload", false]], "upload_collections() (cellpack.autopack.dbrecipehandler.dbuploader method)": [[2, "cellpack.autopack.DBRecipeHandler.DBUploader.upload_collections", false]], "upload_compositions() (cellpack.autopack.dbrecipehandler.dbuploader method)": [[2, "cellpack.autopack.DBRecipeHandler.DBUploader.upload_compositions", false]], "upload_data() (cellpack.autopack.dbrecipehandler.dbuploader method)": [[2, "cellpack.autopack.DBRecipeHandler.DBUploader.upload_data", false]], "upload_doc() (cellpack.autopack.firebasehandler.firebasehandler method)": [[2, "cellpack.autopack.FirebaseHandler.FirebaseHandler.upload_doc", false]], "upload_file() (cellpack.autopack.awshandler.awshandler method)": [[2, "cellpack.autopack.AWSHandler.AWSHandler.upload_file", false]], "upload_gradients() (cellpack.autopack.dbrecipehandler.dbuploader method)": [[2, "cellpack.autopack.DBRecipeHandler.DBUploader.upload_gradients", false]], "upload_objects() (cellpack.autopack.dbrecipehandler.dbuploader method)": [[2, "cellpack.autopack.DBRecipeHandler.DBUploader.upload_objects", false]], "upload_recipe() (cellpack.autopack.dbrecipehandler.dbuploader method)": [[2, "cellpack.autopack.DBRecipeHandler.DBUploader.upload_recipe", false]], "upload_result_metadata() (cellpack.autopack.dbrecipehandler.dbuploader method)": [[2, "cellpack.autopack.DBRecipeHandler.DBUploader.upload_result_metadata", false]], "upload_single_object() (cellpack.autopack.dbrecipehandler.dbuploader method)": [[2, "cellpack.autopack.DBRecipeHandler.DBUploader.upload_single_object", false]], "uppercirclefunction() (cellpack.autopack.geometrytools.geometrytools method)": [[2, "cellpack.autopack.GeometryTools.GeometryTools.UpperCircleFunction", false]], "upperrectanglefunction() (cellpack.autopack.geometrytools.geometrytools method)": [[2, "cellpack.autopack.GeometryTools.GeometryTools.UpperRectangleFunction", false]], "url_exists() (in module cellpack.autopack)": [[2, "cellpack.autopack.url_exists", false]], "use_mesh() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.use_mesh", false]], "use_pdb() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.use_pdb", false]], "validate_distribution_options() (cellpack.autopack.ingredient.ingredient.ingredient static method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.validate_distribution_options", false]], "validate_existence() (cellpack.autopack.dbrecipehandler.resultdoc method)": [[2, "cellpack.autopack.DBRecipeHandler.ResultDoc.validate_existence", false]], "validate_gradient_data() (cellpack.autopack.interface_objects.gradient_data.gradientdata method)": [[4, "cellpack.autopack.interface_objects.gradient_data.GradientData.validate_gradient_data", false]], "validate_ingredient_info() (cellpack.autopack.ingredient.ingredient.ingredient static method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.validate_ingredient_info", false]], "validate_input_recipe_path() (cellpack.autopack.dbrecipehandler.dbrecipeloader method)": [[2, "cellpack.autopack.DBRecipeHandler.DBRecipeLoader.validate_input_recipe_path", false]], "validate_invert_settings() (cellpack.autopack.interface_objects.gradient_data.gradientdata method)": [[4, "cellpack.autopack.interface_objects.gradient_data.GradientData.validate_invert_settings", false]], "validate_mode_settings() (cellpack.autopack.interface_objects.gradient_data.gradientdata method)": [[4, "cellpack.autopack.interface_objects.gradient_data.GradientData.validate_mode_settings", false]], "validate_weight_mode_settings() (cellpack.autopack.interface_objects.gradient_data.gradientdata method)": [[4, "cellpack.autopack.interface_objects.gradient_data.GradientData.validate_weight_mode_settings", false]], "values() (cellpack.autopack.interface_objects.meta_enum.metaenum class method)": [[4, "cellpack.autopack.interface_objects.meta_enum.MetaEnum.values", false]], "vcross() (in module cellpack.autopack.ray)": [[2, "cellpack.autopack.ray.vcross", false]], "vcross() (in module cellpack.autopack.upy.hosthelper)": [[6, "cellpack.autopack.upy.hostHelper.vcross", false]], "vdiff() (in module cellpack.autopack.ray)": [[2, "cellpack.autopack.ray.vdiff", false]], "vdiff() (in module cellpack.autopack.upy.hosthelper)": [[6, "cellpack.autopack.upy.hostHelper.vdiff", false]], "vdistance() (in module cellpack.autopack.upy.hosthelper)": [[6, "cellpack.autopack.upy.hostHelper.vdistance", false]], "vector (cellpack.autopack.interface_objects.gradient_data.gradientmodes attribute)": [[4, "cellpack.autopack.interface_objects.gradient_data.GradientModes.VECTOR", false]], "vector_norm() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.vector_norm", false]], "verbose (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper attribute)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.VERBOSE", false]], "viewer (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper attribute)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.viewer", false]], "vlen() (in module cellpack.autopack.ray)": [[2, "cellpack.autopack.ray.vlen", false]], "vlen() (in module cellpack.autopack.upy.hosthelper)": [[6, "cellpack.autopack.upy.hostHelper.vlen", false]], "vnorm() (in module cellpack.autopack.ray)": [[2, "cellpack.autopack.ray.vnorm", false]], "vnorm() (in module cellpack.autopack.upy.hosthelper)": [[6, "cellpack.autopack.upy.hostHelper.vnorm", false]], "voxels (class in cellpack.autopack.binvox_rw)": [[2, "cellpack.autopack.binvox_rw.Voxels", false]], "walklattice() (cellpack.autopack.ingredient.grow.growingredient method)": [[3, "cellpack.autopack.ingredient.grow.GrowIngredient.walkLattice", false]], "walklatticesurface() (cellpack.autopack.ingredient.grow.growingredient method)": [[3, "cellpack.autopack.ingredient.grow.GrowIngredient.walkLatticeSurface", false]], "walksphere() (cellpack.autopack.ingredient.grow.growingredient method)": [[3, "cellpack.autopack.ingredient.grow.GrowIngredient.walkSphere", false]], "weight (cellpack.autopack.interface_objects.gradient_data.invertoptions attribute)": [[4, "cellpack.autopack.interface_objects.gradient_data.InvertOptions.weight", false]], "weightmodeoptions (class in cellpack.autopack.interface_objects.gradient_data)": [[4, "cellpack.autopack.interface_objects.gradient_data.WeightModeOptions", false]], "weightmodes (class in cellpack.autopack.interface_objects.gradient_data)": [[4, "cellpack.autopack.interface_objects.gradient_data.WeightModes", false]], "which_db() (cellpack.autopack.firebasehandler.firebasehandler static method)": [[2, "cellpack.autopack.FirebaseHandler.FirebaseHandler.which_db", false]], "with_colon() (cellpack.autopack.interface_objects.database_ids.database_ids class method)": [[4, "cellpack.autopack.interface_objects.database_ids.DATABASE_IDS.with_colon", false]], "write() (cellpack.autopack.binvox_rw.voxels method)": [[2, "cellpack.autopack.binvox_rw.Voxels.write", false]], "write() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.write", false]], "write() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.write", false]], "write() (cellpack.autopack.writers.ioingredienttool method)": [[8, "cellpack.autopack.writers.IOingredientTool.write", false]], "write() (in module cellpack.autopack.binvox_rw)": [[2, "cellpack.autopack.binvox_rw.write", false]], "write_creds_path() (cellpack.autopack.firebasehandler.firebasehandler static method)": [[2, "cellpack.autopack.FirebaseHandler.FirebaseHandler.write_creds_path", false]], "write_json_file() (in module cellpack.autopack.loaders.utils)": [[5, "cellpack.autopack.loaders.utils.write_json_file", false]], "write_username_to_creds() (in module cellpack.autopack)": [[2, "cellpack.autopack.write_username_to_creds", false]], "writearraystofile() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.writeArraysToFile", false]], "writedx() (cellpack.autopack.upy.hosthelper.helper class method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.writeDX", false]], "writejson() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.writeJSON", false]], "writemeshtofile() (cellpack.autopack.upy.hosthelper.helper class method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.writeMeshToFile", false]], "writer (class in cellpack.autopack.writers)": [[8, "cellpack.autopack.writers.Writer", false]], "writetofile() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.writeToFile", false]], "writetofile() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.writeToFile", false]], "x (cellpack.autopack.interface_objects.gradient_data.gradientmodes attribute)": [[4, "cellpack.autopack.interface_objects.gradient_data.GradientModes.X", false]], "xyztoijk() (cellpack.autopack.binvox_rw.voxels method)": [[2, "cellpack.autopack.binvox_rw.Voxels.xyzToijk", false]], "xyztrajectory (class in cellpack.autopack.trajectory)": [[2, "cellpack.autopack.trajectory.xyzTrajectory", false]], "y (cellpack.autopack.interface_objects.gradient_data.gradientmodes attribute)": [[4, "cellpack.autopack.interface_objects.gradient_data.GradientModes.Y", false]], "z (cellpack.autopack.interface_objects.gradient_data.gradientmodes attribute)": [[4, "cellpack.autopack.interface_objects.gradient_data.GradientModes.Z", false]]}, "objects": {"": [[1, 0, 0, "-", "cellpack"]], "cellpack": [[2, 0, 0, "-", "autopack"], [9, 0, 0, "-", "bin"], [1, 4, 1, "", "get_module_version"]], "cellpack.autopack": [[2, 0, 0, "-", "AWSHandler"], [2, 0, 0, "-", "Analysis"], [2, 0, 0, "-", "BaseGrid"], [2, 0, 0, "-", "Compartment"], [2, 0, 0, "-", "DBRecipeHandler"], [2, 0, 0, "-", "Environment"], [2, 0, 0, "-", "FirebaseHandler"], [2, 0, 0, "-", "GeometryTools"], [2, 0, 0, "-", "Gradient"], [2, 0, 0, "-", "Graphics"], [2, 0, 0, "-", "Grid"], [2, 0, 0, "-", "IOutils"], [2, 0, 0, "-", "MeshStore"], [2, 0, 0, "-", "Recipe"], [2, 0, 0, "-", "Serializable"], [2, 0, 0, "-", "binvox_rw"], [2, 4, 1, "", "checkErrorInPath"], [2, 4, 1, "", "checkPath"], [2, 4, 1, "", "checkRecipeAvailable"], [2, 4, 1, "", "clearCaches"], [2, 4, 1, "", "convert_db_shortname_to_url"], [2, 4, 1, "", "download_file"], [2, 4, 1, "", "fixOnePath"], [2, 4, 1, "", "fixPath"], [2, 4, 1, "", "get_cache_location"], [2, 4, 1, "", "get_local_file_location"], [3, 0, 0, "-", "ingredient"], [4, 0, 0, "-", "interface_objects"], [2, 4, 1, "", "is_full_url"], [2, 4, 1, "", "is_remote_path"], [2, 4, 1, "", "is_s3_url"], [2, 0, 0, "-", "ldSequence"], [2, 4, 1, "", "load_file"], [5, 0, 0, "-", "loaders"], [2, 4, 1, "", "make_directory_if_needed"], [2, 0, 0, "-", "octree"], [2, 4, 1, "", "parse_s3_uri"], [2, 0, 0, "-", "plotly_result"], [2, 0, 0, "-", "randomRot"], [2, 0, 0, "-", "ray"], [2, 4, 1, "", "read_text_file"], [2, 4, 1, "", "resetDefault"], [2, 4, 1, "", "saveRecipeAvailable"], [2, 4, 1, "", "saveRecipeAvailableJSON"], [2, 0, 0, "-", "trajectory"], [2, 0, 0, "-", "transformation"], [2, 4, 1, "", "updatePath"], [2, 4, 1, "", "updatePathJSON"], [2, 4, 1, "", "updateRecipAvailableXML"], [2, 4, 1, "", "updateReplacePath"], [6, 0, 0, "-", "upy"], [2, 4, 1, "", "url_exists"], [2, 0, 0, "-", "utils"], [2, 4, 1, "", "write_username_to_creds"], [8, 0, 0, "-", "writers"]], "cellpack.autopack.AWSHandler": [[2, 1, 1, "", "AWSHandler"]], "cellpack.autopack.AWSHandler.AWSHandler": [[2, 2, 1, "", "create_presigned_url"], [2, 2, 1, "", "download_file"], [2, 2, 1, "", "get_aws_object_key"], [2, 2, 1, "", "is_url_valid"], [2, 2, 1, "", "save_file_and_get_url"], [2, 2, 1, "", "upload_file"]], "cellpack.autopack.Analysis": [[2, 1, 1, "", "Analysis"]], "cellpack.autopack.Analysis.Analysis": [[2, 2, 1, "", "add_ingredient_positions_to_plot"], [2, 2, 1, "", "build_grid"], [2, 2, 1, "", "cartesian_to_sph"], [2, 2, 1, "", "combine_results_from_ingredients"], [2, 2, 1, "", "combine_results_from_seeds"], [2, 2, 1, "", "create_report"], [2, 2, 1, "", "doloop"], [2, 2, 1, "", "getHaltonUnique"], [2, 2, 1, "", "get_ingredient_key_from_object_or_comp_name"], [2, 2, 1, "", "get_ingredient_radii"], [2, 2, 1, "", "get_list_of_dims"], [2, 2, 1, "", "get_minimum_expected_distance_from_recipe"], [2, 2, 1, "", "get_number_of_ingredients_packed"], [2, 2, 1, "", "get_obj_dict"], [2, 2, 1, "", "get_packed_minimum_distance"], [2, 2, 1, "", "get_partner_pair_dict"], [2, 2, 1, "", "histogram"], [2, 2, 1, "", "loadJSON"], [2, 2, 1, "", "pack"], [2, 2, 1, "", "pack_one_seed"], [2, 2, 1, "", "plot"], [2, 2, 1, "", "plot_distance_distribution"], [2, 2, 1, "", "plot_occurence_distribution"], [2, 2, 1, "", "plot_position_distribution"], [2, 2, 1, "", "plot_position_distribution_total"], [2, 2, 1, "", "process_ingredients_in_recipe"], [2, 2, 1, "", "read_dict_from_glob_file"], [2, 2, 1, "", "run_analysis_workflow"], [2, 2, 1, "", "run_distance_analysis"], [2, 2, 1, "", "run_partner_analysis"], [2, 2, 1, "", "set_ingredient_color"], [2, 2, 1, "", "simpleplot"], [2, 2, 1, "", "update_distance_distribution_dictionaries"], [2, 2, 1, "", "update_pairwise_distances"], [2, 2, 1, "", "writeJSON"]], "cellpack.autopack.BaseGrid": [[2, 1, 1, "", "BaseGrid"], [2, 1, 1, "", "HaltonGrid"], [2, 1, 1, "", "gridPoint"]], "cellpack.autopack.BaseGrid.BaseGrid": [[2, 2, 1, "", "cartesian"], [2, 2, 1, "", "computeExteriorVolume"], [2, 2, 1, "", "computeGridNumberOfPoint"], [2, 2, 1, "", "computeVolume"], [2, 2, 1, "", "create_grid_point_positions"], [2, 2, 1, "", "getCenter"], [2, 2, 1, "", "getClosestFreeGridPoint"], [2, 2, 1, "", "getClosestGridPoint"], [2, 2, 1, "", "getDiagonal"], [2, 2, 1, "", "getIJK"], [2, 2, 1, "", "getPointFrom3D"], [2, 2, 1, "", "getPointsInCube"], [2, 2, 1, "", "getPointsInCubeFillBB"], [2, 2, 1, "", "getPointsInSphere"], [2, 2, 1, "", "getPositionPeridocity"], [2, 2, 1, "", "getRadius"], [2, 2, 1, "", "is_point_inside_bb"], [2, 2, 1, "", "removeFreePoint"], [2, 2, 1, "", "reorder_free_points"], [2, 2, 1, "", "reset"], [2, 2, 1, "", "restore"], [2, 2, 1, "", "save"], [2, 2, 1, "", "set_surfPtsBht"], [2, 2, 1, "", "set_surfPtscht"], [2, 2, 1, "", "setup"], [2, 2, 1, "", "setupBoundaryPeriodicity"], [2, 2, 1, "", "slow_box_fill"], [2, 2, 1, "", "test_points_in_bb"], [2, 2, 1, "", "updateDistances"]], "cellpack.autopack.BaseGrid.HaltonGrid": [[2, 2, 1, "", "create3DPointLookup"], [2, 2, 1, "", "getNBgridPoints"], [2, 2, 1, "", "getPointFrom3D"], [2, 2, 1, "", "getScale"]], "cellpack.autopack.Compartment": [[2, 1, 1, "", "Compartment"], [2, 1, 1, "", "CompartmentList"]], "cellpack.autopack.Compartment.Compartment": [[2, 2, 1, "", "BuildGrid"], [2, 2, 1, "", "BuildGridEnviroOnly"], [2, 2, 1, "", "BuildGrid_bhtree"], [2, 2, 1, "", "BuildGrid_binvox"], [2, 2, 1, "", "BuildGrid_box"], [2, 2, 1, "", "BuildGrid_kevin"], [2, 2, 1, "", "BuildGrid_multisdf"], [2, 2, 1, "", "BuildGrid_pyray"], [2, 2, 1, "", "BuildGrid_ray"], [2, 2, 1, "", "BuildGrid_scanline"], [2, 2, 1, "", "BuildGrid_trimesh"], [2, 2, 1, "", "BuildGrid_utsdf"], [2, 2, 1, "", "buildMesh"], [2, 2, 1, "", "buildSphere"], [2, 2, 1, "", "build_grid_sphere"], [2, 2, 1, "", "checkPointInsideBB"], [2, 2, 1, "", "compute_volume_and_set_count"], [2, 2, 1, "", "create3DPointLookup"], [2, 2, 1, "", "createSurfacePoints"], [2, 2, 1, "", "create_rbnode"], [2, 2, 1, "", "create_voxelization"], [2, 2, 1, "", "create_voxelized_mask"], [2, 2, 1, "", "extendGridArrays"], [2, 2, 1, "", "filter_surface_pts_to_fill_box"], [2, 2, 1, "", "find_nearest"], [2, 2, 1, "", "getBoundingBox"], [2, 2, 1, "", "getCenter"], [2, 2, 1, "", "getFaceNormals"], [2, 2, 1, "", "getFacesNfromV"], [2, 2, 1, "", "getInterpolatedNormal"], [2, 2, 1, "", "getMesh"], [2, 2, 1, "", "getMinMaxProteinSize"], [2, 2, 1, "", "getRadius"], [2, 2, 1, "", "getSizeXYZ"], [2, 2, 1, "", "getSurfaceInnerPoints"], [2, 2, 1, "", "getSurfaceInnerPoints_kevin"], [2, 2, 1, "", "getSurfaceInnerPoints_sdf"], [2, 2, 1, "", "getSurfaceInnerPoints_sdf_interpolate"], [2, 2, 1, "", "getSurfacePoint"], [2, 2, 1, "", "getVNfromF"], [2, 2, 1, "", "getVertexNormals"], [2, 2, 1, "", "get_bbox"], [2, 2, 1, "", "get_normal_for_point"], [2, 2, 1, "", "get_rb_model"], [2, 2, 1, "", "inBox"], [2, 2, 1, "", "inGrid"], [2, 2, 1, "", "initialize_shape"], [2, 2, 1, "", "is_point_inside_mesh"], [2, 2, 1, "", "prepare_buildgrid_box"], [2, 2, 1, "", "printFillInfo"], [2, 2, 1, "", "readGridFromFile"], [2, 2, 1, "", "reset"], [2, 2, 1, "", "saveGridToFile"], [2, 2, 1, "", "setCount"], [2, 2, 1, "", "setGeomFaces"], [2, 2, 1, "", "setInnerRecipe"], [2, 2, 1, "", "setMesh"], [2, 2, 1, "", "setNumber"], [2, 2, 1, "", "setSurfaceRecipe"], [2, 2, 1, "", "set_surface_distances"], [2, 2, 1, "", "store_packed_object"], [2, 2, 1, "", "transformMesh"]], "cellpack.autopack.Compartment.CompartmentList": [[2, 2, 1, "", "add_compartment"]], "cellpack.autopack.DBRecipeHandler": [[2, 1, 1, "", "CompositionDoc"], [2, 1, 1, "", "DBMaintenance"], [2, 1, 1, "", "DBRecipeLoader"], [2, 1, 1, "", "DBUploader"], [2, 1, 1, "", "DataDoc"], [2, 1, 1, "", "GradientDoc"], [2, 1, 1, "", "ObjectDoc"], [2, 1, 1, "", "ResultDoc"]], "cellpack.autopack.DBRecipeHandler.CompositionDoc": [[2, 3, 1, "", "DEFAULT_VALUES"], [2, 3, 1, "", "KEY_TO_DICT_MAPPING"], [2, 3, 1, "", "SHALLOW_MATCH"], [2, 2, 1, "", "as_dict"], [2, 2, 1, "", "check_and_replace_references"], [2, 2, 1, "", "get_reference_data"], [2, 2, 1, "", "get_reference_in_obj"], [2, 2, 1, "", "gradient_list_to_dict"], [2, 2, 1, "", "resolve_db_regions"], [2, 2, 1, "", "resolve_local_regions"], [2, 2, 1, "", "resolve_object_data"], [2, 2, 1, "", "should_write"], [2, 2, 1, "", "update_reference"]], "cellpack.autopack.DBRecipeHandler.DBMaintenance": [[2, 2, 1, "", "cleanup_results"], [2, 2, 1, "", "readme_url"]], "cellpack.autopack.DBRecipeHandler.DBRecipeLoader": [[2, 2, 1, "", "collect_and_sort_data"], [2, 2, 1, "", "collect_docs_by_id"], [2, 2, 1, "", "compile_db_recipe_data"], [2, 2, 1, "", "prep_db_doc_for_download"], [2, 2, 1, "", "validate_input_recipe_path"]], "cellpack.autopack.DBRecipeHandler.DBUploader": [[2, 2, 1, "", "prep_data_for_db"], [2, 2, 1, "", "upload_collections"], [2, 2, 1, "", "upload_compositions"], [2, 2, 1, "", "upload_data"], [2, 2, 1, "", "upload_gradients"], [2, 2, 1, "", "upload_objects"], [2, 2, 1, "", "upload_recipe"], [2, 2, 1, "", "upload_result_metadata"], [2, 2, 1, "", "upload_single_object"]], "cellpack.autopack.DBRecipeHandler.DataDoc": [[2, 2, 1, "", "as_dict"], [2, 2, 1, "", "is_db_dict"], [2, 2, 1, "", "is_key"], [2, 2, 1, "", "is_nested_list"], [2, 2, 1, "", "is_obj"], [2, 2, 1, "", "should_write"]], "cellpack.autopack.DBRecipeHandler.GradientDoc": [[2, 2, 1, "", "should_write"]], "cellpack.autopack.DBRecipeHandler.ObjectDoc": [[2, 2, 1, "", "as_dict"], [2, 2, 1, "", "convert_positions_in_representation"], [2, 2, 1, "", "convert_representation"], [2, 2, 1, "", "should_write"]], "cellpack.autopack.DBRecipeHandler.ResultDoc": [[2, 2, 1, "", "handle_expired_results"], [2, 2, 1, "", "validate_existence"]], "cellpack.autopack.Environment": [[2, 1, 1, "", "Environment"], [2, 4, 1, "", "random"]], "cellpack.autopack.Environment.Environment": [[2, 2, 1, "", "BuildCompartmentsGrids"], [2, 2, 1, "", "SetRBOptions"], [2, 2, 1, "", "SetSpringOptions"], [2, 2, 1, "", "addMeshRBOrganelle"], [2, 2, 1, "", "addRB"], [2, 2, 1, "", "add_seed_number_to_base_name"], [2, 2, 1, "", "applyStep"], [2, 2, 1, "", "buildGrid"], [2, 2, 1, "", "build_compartment_grids"], [2, 2, 1, "", "calc_pairwise_distances"], [2, 2, 1, "", "callFunction"], [2, 2, 1, "", "check_new_placement"], [2, 2, 1, "", "clean_grid_cache"], [2, 2, 1, "", "clear"], [2, 2, 1, "", "clearRBingredient"], [2, 2, 1, "", "collectResultPerIngredient"], [2, 2, 1, "", "compartment_id_for_nearest_grid_point"], [2, 2, 1, "", "convertPickleToText"], [2, 2, 1, "", "create_compartment"], [2, 2, 1, "", "create_ingredient"], [2, 2, 1, "", "create_objects"], [2, 2, 1, "", "create_voxelization"], [2, 2, 1, "", "delRB"], [2, 2, 1, "", "distance_check_failed"], [2, 2, 1, "", "dropOneIngr"], [2, 2, 1, "", "dropOneIngrJson"], [2, 2, 1, "", "exportToBD_BOX"], [2, 2, 1, "", "exportToReaDDy"], [2, 2, 1, "", "exportToTEM"], [2, 2, 1, "", "exportToTEM_SIM"], [2, 2, 1, "", "extend_bounding_box_for_compartments"], [2, 2, 1, "", "extractMeshComponent"], [2, 2, 1, "", "finishWithWater"], [2, 2, 1, "", "getActiveIng"], [2, 2, 1, "", "getIngrFromNameInRecipe"], [2, 2, 1, "", "getOneIngr"], [2, 2, 1, "", "getOneIngrJson"], [2, 2, 1, "", "getPointToDrop"], [2, 2, 1, "", "getRotTransRB"], [2, 2, 1, "", "getSortedActiveIngredients"], [2, 2, 1, "", "getTotalNbObject"], [2, 2, 1, "", "get_all_distances"], [2, 2, 1, "", "get_attributes_to_update"], [2, 2, 1, "", "get_bounding_box_limits"], [2, 2, 1, "", "get_closest_ingredients"], [2, 2, 1, "", "get_compartment_object_by_name"], [2, 2, 1, "", "get_distances"], [2, 2, 1, "", "get_distances_and_angles"], [2, 2, 1, "", "get_dpad"], [2, 2, 1, "", "get_ingredient_angles"], [2, 2, 1, "", "get_ingredient_by_name"], [2, 2, 1, "", "get_ingredients_in_tree"], [2, 2, 1, "", "get_size_of_bounding_box"], [2, 2, 1, "", "includeIngrRecipe"], [2, 2, 1, "", "includeIngrRecipes"], [2, 2, 1, "", "includeIngredientRecipe"], [2, 2, 1, "", "is_two_d"], [2, 2, 1, "", "linkTraj"], [2, 2, 1, "", "loadFreePoint"], [2, 2, 1, "", "loadResult"], [2, 2, 1, "", "load_asJson"], [2, 2, 1, "", "load_asTxt"], [2, 2, 1, "", "loopThroughIngr"], [2, 2, 1, "", "moveRBnode"], [2, 2, 1, "", "onePrevIngredient"], [2, 2, 1, "", "pack_grid"], [2, 2, 1, "", "pickIngredient"], [2, 2, 1, "", "prep_molecules_for_save"], [2, 2, 1, "", "printFillInfo"], [2, 2, 1, "", "readArraysFromFile"], [2, 2, 1, "", "removeOnePoint"], [2, 2, 1, "", "reportprogress"], [2, 2, 1, "", "reset"], [2, 2, 1, "", "resetIngrRecip"], [2, 2, 1, "", "resolve_gradient_data_objects"], [2, 2, 1, "", "restore"], [2, 2, 1, "", "restoreFreePoints"], [2, 2, 1, "", "restoreGridFromFile"], [2, 2, 1, "", "restore_grids_from_pickle"], [2, 2, 1, "", "restore_molecules_array"], [2, 2, 1, "", "runBullet"], [2, 2, 1, "", "saveGridLogsAsJson"], [2, 2, 1, "", "saveGridToFile"], [2, 2, 1, "", "save_grids_to_pickle"], [2, 2, 1, "", "save_result"], [2, 2, 1, "", "setExteriorRecipe"], [2, 2, 1, "", "setGeomFaces"], [2, 2, 1, "", "setSeed"], [2, 2, 1, "", "set_gradient"], [2, 2, 1, "", "set_partners_ingredient"], [2, 2, 1, "", "set_result_file_name"], [2, 2, 1, "", "setupOctree"], [2, 2, 1, "", "setupRBOptions"], [2, 2, 1, "", "sortIngredient"], [2, 2, 1, "", "store"], [2, 2, 1, "", "store_asJson"], [2, 2, 1, "", "timeFunction"], [2, 2, 1, "", "unlinkTraj"], [2, 2, 1, "", "update_after_place"], [2, 2, 1, "", "update_largest_smallest_size"], [2, 2, 1, "", "update_variable_ingredient_attributes"], [2, 2, 1, "", "writeArraysToFile"]], "cellpack.autopack.FirebaseHandler": [[2, 1, 1, "", "FirebaseHandler"]], "cellpack.autopack.FirebaseHandler.FirebaseHandler": [[2, 2, 1, "", "create_path"], [2, 2, 1, "", "create_timestamp"], [2, 2, 1, "", "db_name"], [2, 2, 1, "", "delete_doc"], [2, 2, 1, "", "doc_id"], [2, 2, 1, "", "doc_to_dict"], [2, 2, 1, "", "get_all_docs"], [2, 2, 1, "", "get_collection_id_from_path"], [2, 2, 1, "", "get_creds"], [2, 2, 1, "", "get_dev_creds"], [2, 2, 1, "", "get_doc_by_id"], [2, 2, 1, "", "get_doc_by_name"], [2, 2, 1, "", "get_doc_by_ref"], [2, 2, 1, "", "get_path_from_ref"], [2, 2, 1, "", "get_staging_creds"], [2, 2, 1, "", "get_username"], [2, 2, 1, "", "get_value"], [2, 2, 1, "", "is_firebase_obj"], [2, 2, 1, "", "is_reference"], [2, 2, 1, "", "set_doc"], [2, 2, 1, "", "update_doc"], [2, 2, 1, "", "update_elements_in_array"], [2, 2, 1, "", "update_or_create"], [2, 2, 1, "", "update_reference_on_doc"], [2, 2, 1, "", "upload_doc"], [2, 2, 1, "", "which_db"], [2, 2, 1, "", "write_creds_path"]], "cellpack.autopack.GeometryTools": [[2, 1, 1, "", "GeometryTools"], [2, 1, 1, "", "Rectangle"]], "cellpack.autopack.GeometryTools.GeometryTools": [[2, 2, 1, "", "GetDistance"], [2, 2, 1, "", "LowerCircleFunction"], [2, 2, 1, "", "LowerRectangleFunction"], [2, 3, 1, "", "Resolution"], [2, 2, 1, "", "UpperCircleFunction"], [2, 2, 1, "", "UpperRectangleFunction"], [2, 2, 1, "", "calc_volume"], [2, 2, 1, "", "check_rectangle_oustide"], [2, 2, 1, "", "check_sphere_inside"], [2, 2, 1, "", "getBoundary"], [2, 2, 1, "", "get_rectangle_cercle_area"], [2, 2, 1, "", "region_1"], [2, 2, 1, "", "region_1_2_theta"], [2, 2, 1, "", "region_2"], [2, 2, 1, "", "region_2_integrand"], [2, 2, 1, "", "region_3"], [2, 2, 1, "", "region_3_integrand"]], "cellpack.autopack.Gradient": [[2, 1, 1, "", "Gradient"], [2, 4, 1, "", "random"]], "cellpack.autopack.Gradient.Gradient": [[2, 2, 1, "", "build_axis_weight_map"], [2, 2, 1, "", "build_directional_weight_map"], [2, 2, 1, "", "build_radial_weight_map"], [2, 2, 1, "", "build_surface_distance_weight_map"], [2, 2, 1, "", "build_weight_map"], [2, 2, 1, "", "create_voxelization"], [2, 2, 1, "", "defaultFunction"], [2, 2, 1, "", "getBinaryWeighted"], [2, 2, 1, "", "getForwWeight"], [2, 2, 1, "", "getLinearWeighted"], [2, 2, 1, "", "getMaxWeight"], [2, 2, 1, "", "getMinWeight"], [2, 2, 1, "", "getRndWeighted"], [2, 2, 1, "", "getSubWeighted"], [2, 2, 1, "", "get_center"], [2, 2, 1, "", "get_gauss_weights"], [2, 2, 1, "", "get_normalized_values"], [2, 2, 1, "", "normalize_vector"], [2, 2, 1, "", "pickPoint"], [2, 2, 1, "", "set_weights_by_mode"]], "cellpack.autopack.Graphics": [[2, 1, 1, "", "AutopackViewer"], [2, 1, 1, "", "ColladaExporter"]], "cellpack.autopack.Graphics.AutopackViewer": [[2, 2, 1, "", "SetHistoVol"], [2, 2, 1, "", "addCompartmentFromGeom"], [2, 2, 1, "", "addIngredientFromGeom"], [2, 2, 1, "", "addMasterIngr"], [2, 2, 1, "", "appendIngrInstance"], [2, 2, 1, "", "buildIngrPrimitive"], [2, 2, 1, "", "callFunction"], [2, 2, 1, "", "checkCreateEmpty"], [2, 2, 1, "", "checkIngrPartnerProperties"], [2, 2, 1, "", "checkIngrSpheres"], [2, 2, 1, "", "clearAll"], [2, 2, 1, "", "clearFill"], [2, 2, 1, "", "clearIngr"], [2, 2, 1, "", "clearRecipe"], [2, 2, 1, "", "collectResult"], [2, 2, 1, "", "color"], [2, 2, 1, "", "colorByDistanceFrom"], [2, 2, 1, "", "colorByOrder"], [2, 2, 1, "", "colorPT"], [2, 2, 1, "", "createIngrMesh"], [2, 2, 1, "", "createOrganelMesh"], [2, 2, 1, "", "createTemplate"], [2, 2, 1, "", "createTemplateCompartment"], [2, 2, 1, "", "delIngr"], [2, 2, 1, "", "delIngredientGrow"], [2, 2, 1, "", "displayCompartment"], [2, 2, 1, "", "displayCompartmentPoints"], [2, 2, 1, "", "displayCompartments"], [2, 2, 1, "", "displayCompartmentsIngredients"], [2, 2, 1, "", "displayCompartmentsPoints"], [2, 2, 1, "", "displayCytoplasmIngredients"], [2, 2, 1, "", "displayDistance"], [2, 2, 1, "", "displayEnv"], [2, 2, 1, "", "displayFill"], [2, 2, 1, "", "displayFillBox"], [2, 2, 1, "", "displayFreePoints"], [2, 2, 1, "", "displayFreePointsAsPS"], [2, 2, 1, "", "displayGradient"], [2, 2, 1, "", "displayIngrCylinders"], [2, 2, 1, "", "displayIngrGrow"], [2, 2, 1, "", "displayIngrGrows"], [2, 2, 1, "", "displayIngrMesh"], [2, 2, 1, "", "displayIngrResults"], [2, 2, 1, "", "displayIngrSpheres"], [2, 2, 1, "", "displayIngredients"], [2, 2, 1, "", "displayInstancesIngredient"], [2, 2, 1, "", "displayLeafOctree"], [2, 2, 1, "", "displayOctree"], [2, 2, 1, "", "displayOctreeLeaf"], [2, 2, 1, "", "displayOneNodeOctree"], [2, 2, 1, "", "displayParticleVolumeDistance"], [2, 2, 1, "", "displayPoints"], [2, 2, 1, "", "displayPreFill"], [2, 2, 1, "", "displayRoot"], [2, 2, 1, "", "displaysubnode"], [2, 2, 1, "", "dspMesh"], [2, 2, 1, "", "dspSph"], [2, 2, 1, "", "exportAsIndexedMeshs"], [2, 2, 1, "", "exportIngredient"], [2, 2, 1, "", "exportRecipeIngredients"], [2, 2, 1, "", "hideIngrPrimitive"], [2, 2, 1, "", "prepareDynamic"], [2, 2, 1, "", "prepareIngredient"], [2, 2, 1, "", "prepareMaster"], [2, 2, 1, "", "printIngredients"], [2, 2, 1, "", "printOneIngr"], [2, 2, 1, "", "replaceIngrMesh"], [2, 2, 1, "", "showHide"], [2, 2, 1, "", "showIngrPrimitive"], [2, 2, 1, "", "timeFunction"], [2, 2, 1, "", "toggleOrganelMatr"], [2, 2, 1, "", "toggleOrganelMesh"], [2, 2, 1, "", "toggleOrganelSurf"], [2, 2, 1, "", "undspMesh"], [2, 2, 1, "", "undspSph"]], "cellpack.autopack.Grid": [[2, 1, 1, "", "Grid"]], "cellpack.autopack.Grid.Grid": [[2, 2, 1, "", "create3DPointLookup"], [2, 2, 1, "", "getIJK"], [2, 2, 1, "", "reset"], [2, 2, 1, "", "restore"], [2, 2, 1, "", "save"]], "cellpack.autopack.IOutils": [[2, 1, 1, "", "ExportCollada"], [2, 1, 1, "", "GrabResult"], [2, 1, 1, "", "IOingredientTool"], [2, 4, 1, "", "addCompartments"], [2, 4, 1, "", "checkRotFormat"], [2, 4, 1, "", "gatherResult"], [2, 4, 1, "", "getAllPosRot"], [2, 4, 1, "", "getStringValueOptions"], [2, 4, 1, "", "load_Json"], [2, 4, 1, "", "load_JsonString"], [2, 4, 1, "", "load_MixedasJson"], [2, 4, 1, "", "saveResultBinary"], [2, 4, 1, "", "saveResultBinaryDic"], [2, 4, 1, "", "save_asPython"], [2, 4, 1, "", "serializedFromResult"], [2, 4, 1, "", "serializedRecipe"], [2, 4, 1, "", "serializedRecipe_group"], [2, 4, 1, "", "serializedRecipe_group_dic"], [2, 4, 1, "", "setValueToPythonStr"], [2, 4, 1, "", "setupFromJsonDic"], [2, 4, 1, "", "toBinary"], [2, 4, 1, "", "updatePositionsRadii"]], "cellpack.autopack.IOutils.GrabResult": [[2, 2, 1, "", "grab"], [2, 2, 1, "", "reset"]], "cellpack.autopack.IOutils.IOingredientTool": [[2, 2, 1, "", "clean_arguments"], [2, 2, 1, "", "ingrJsonNode"], [2, 2, 1, "", "ingrPythonNode"], [2, 2, 1, "", "makeIngredient"], [2, 2, 1, "", "makeIngredientFromJson"], [2, 2, 1, "", "read"], [2, 2, 1, "", "set_recipe_ingredient"]], "cellpack.autopack.MeshStore": [[2, 1, 1, "", "MeshStore"]], "cellpack.autopack.MeshStore.MeshStore": [[2, 2, 1, "", "add_mesh_to_scene"], [2, 2, 1, "", "build_mesh"], [2, 2, 1, "", "calc_scaled_distances_for_positions"], [2, 2, 1, "", "contains_point"], [2, 2, 1, "", "contains_points_mesh"], [2, 2, 1, "", "create_mesh"], [2, 2, 1, "", "create_sphere"], [2, 2, 1, "", "create_sphere_data"], [2, 2, 1, "", "decompose_mesh"], [2, 2, 1, "", "get_centroid"], [2, 2, 1, "", "get_collada_material"], [2, 2, 1, "", "get_mesh"], [2, 2, 1, "", "get_mesh_filepath_and_extension"], [2, 2, 1, "", "get_midpoint"], [2, 2, 1, "", "get_normal"], [2, 2, 1, "", "get_nsphere"], [2, 2, 1, "", "get_object"], [2, 2, 1, "", "get_scaled_distances_between_surfaces"], [2, 2, 1, "", "get_smallest_radius"], [2, 2, 1, "", "norm"], [2, 2, 1, "", "normal_array"], [2, 2, 1, "", "normalize"], [2, 2, 1, "", "normalize_v3"], [2, 2, 1, "", "read_mesh_file"]], "cellpack.autopack.Recipe": [[2, 1, 1, "", "Recipe"], [2, 4, 1, "", "random"]], "cellpack.autopack.Recipe.Recipe": [[2, 2, 1, "", "addIngredient"], [2, 2, 1, "", "delIngredient"], [2, 2, 1, "", "getMinMaxProteinSize"], [2, 2, 1, "", "is_key"], [2, 2, 1, "", "printFillInfo"], [2, 2, 1, "", "resetIngrs"], [2, 2, 1, "", "resolve_composition"], [2, 2, 1, "", "setCount"], [2, 2, 1, "", "sort"]], "cellpack.autopack.Serializable": [[2, 1, 1, "", "sCompartment"], [2, 1, 1, "", "sIngredient"], [2, 1, 1, "", "sIngredientFiber"], [2, 1, 1, "", "sIngredientGroup"]], "cellpack.autopack.Serializable.sCompartment": [[2, 2, 1, "", "addCompartment"], [2, 2, 1, "", "addIngredientGroup"], [2, 3, 1, "", "static_id"], [2, 2, 1, "", "to_JSON"]], "cellpack.autopack.Serializable.sIngredient": [[2, 3, 1, "", "static_id"], [2, 2, 1, "", "to_JSON"]], "cellpack.autopack.Serializable.sIngredientFiber": [[2, 3, 1, "", "static_id"], [2, 2, 1, "", "to_JSON"]], "cellpack.autopack.Serializable.sIngredientGroup": [[2, 2, 1, "", "addIngredient"], [2, 3, 1, "", "static_id"], [2, 2, 1, "", "to_JSON"]], "cellpack.autopack.binvox_rw": [[2, 1, 1, "", "Voxels"], [2, 4, 1, "", "dense_to_sparse"], [2, 4, 1, "", "read"], [2, 4, 1, "", "read_as_3d_array"], [2, 4, 1, "", "read_as_coord_array"], [2, 4, 1, "", "read_header"], [2, 4, 1, "", "sparse_to_dense"], [2, 4, 1, "", "write"]], "cellpack.autopack.binvox_rw.Voxels": [[2, 2, 1, "", "cartesian"], [2, 2, 1, "", "clone"], [2, 2, 1, "", "getIndex"], [2, 2, 1, "", "getIndexData"], [2, 2, 1, "", "ijkToIndex"], [2, 2, 1, "", "ijkToxyz"], [2, 2, 1, "", "write"], [2, 2, 1, "", "xyzToijk"]], "cellpack.autopack.ingredient": [[3, 0, 0, "-", "Ingredient"], [3, 0, 0, "-", "agent"], [3, 0, 0, "-", "grow"], [3, 0, 0, "-", "multi_cylinder"], [3, 0, 0, "-", "multi_sphere"], [3, 0, 0, "-", "single_cube"], [3, 0, 0, "-", "single_cylinder"], [3, 0, 0, "-", "single_sphere"], [3, 0, 0, "-", "utils"]], "cellpack.autopack.ingredient.Ingredient": [[3, 1, 1, "", "DistributionOptions"], [3, 1, 1, "", "DistributionTypes"], [3, 1, 1, "", "Ingredient"], [3, 1, 1, "", "IngredientInstanceDrop"], [3, 4, 1, "", "random"]], "cellpack.autopack.ingredient.Ingredient.DistributionOptions": [[3, 3, 1, "", "LIST_VALUES"], [3, 3, 1, "", "MAX"], [3, 3, 1, "", "MEAN"], [3, 3, 1, "", "MIN"], [3, 3, 1, "", "STD"]], "cellpack.autopack.ingredient.Ingredient.DistributionTypes": [[3, 3, 1, "", "LIST"], [3, 3, 1, "", "NORMAL"], [3, 3, 1, "", "UNIFORM"]], "cellpack.autopack.ingredient.Ingredient.Ingredient": [[3, 3, 1, "", "ARGUMENTS"], [3, 2, 1, "", "DecomposeMesh"], [3, 2, 1, "", "alignRotation"], [3, 2, 1, "", "apply_rotation"], [3, 2, 1, "", "attempt_to_pack_at_grid_location"], [3, 2, 1, "", "buildMesh"], [3, 2, 1, "", "checkDistance"], [3, 2, 1, "", "checkIfUpdate"], [3, 2, 1, "", "check_against_one_packed_ingr"], [3, 2, 1, "", "close_partner_check"], [3, 2, 1, "", "correctBB"], [3, 2, 1, "", "deleteblist"], [3, 2, 1, "", "far_enough_from_surfaces"], [3, 2, 1, "", "getAxisRotation"], [3, 2, 1, "", "getBiasedRotation"], [3, 2, 1, "", "getData"], [3, 2, 1, "", "getEncapsulatingRadius"], [3, 2, 1, "", "getIngredientsInBox"], [3, 2, 1, "", "getListCompFromMask"], [3, 2, 1, "", "getMaxJitter"], [3, 2, 1, "", "getMesh"], [3, 2, 1, "", "get_all_positions_to_check"], [3, 2, 1, "", "get_compartment"], [3, 2, 1, "", "get_cuttoff_value"], [3, 2, 1, "", "get_list_of_free_indices"], [3, 2, 1, "", "get_new_distances_and_inside_points"], [3, 2, 1, "", "get_new_jitter_location_and_rotation"], [3, 2, 1, "", "get_new_pos"], [3, 2, 1, "", "get_partners"], [3, 2, 1, "", "get_rbNodes"], [3, 2, 1, "", "get_rb_model"], [3, 2, 1, "", "get_rotation"], [3, 2, 1, "", "handle_real_time_visualization"], [3, 2, 1, "", "has_mesh"], [3, 2, 1, "", "has_pdb"], [3, 2, 1, "", "initialize_mesh"], [3, 2, 1, "", "is_point_in_correct_region"], [3, 2, 1, "", "jitterPosition"], [3, 2, 1, "", "jitter_place"], [3, 2, 1, "", "lookForNeighbours"], [3, 2, 1, "", "merge_place_results"], [3, 2, 1, "", "np_check_collision"], [3, 2, 1, "", "oneJitter"], [3, 2, 1, "", "pack_at_grid_pt_location"], [3, 2, 1, "", "perturbAxis"], [3, 2, 1, "", "place"], [3, 2, 1, "", "point_is_available"], [3, 2, 1, "", "randomize_rotation"], [3, 2, 1, "", "randomize_translation"], [3, 2, 1, "", "reject"], [3, 2, 1, "", "remove_from_realtime_display"], [3, 2, 1, "", "reset"], [3, 2, 1, "", "rigid_place"], [3, 2, 1, "", "setTilling"], [3, 2, 1, "", "spheres_SST_place"], [3, 3, 1, "", "static_id"], [3, 2, 1, "", "store_packed_object"], [3, 2, 1, "", "swap"], [3, 2, 1, "", "transformPoints"], [3, 2, 1, "", "transformPoints_mult"], [3, 2, 1, "", "update_data_tree"], [3, 2, 1, "", "update_display_rt"], [3, 2, 1, "", "update_ingredient_size"], [3, 2, 1, "", "use_mesh"], [3, 2, 1, "", "use_pdb"], [3, 2, 1, "", "validate_distribution_options"], [3, 2, 1, "", "validate_ingredient_info"]], "cellpack.autopack.ingredient.agent": [[3, 1, 1, "", "Agent"], [3, 4, 1, "", "random"]], "cellpack.autopack.ingredient.agent.Agent": [[3, 2, 1, "", "getSubWeighted"], [3, 2, 1, "", "get_weights_by_distance"], [3, 2, 1, "", "pick_partner_grid_index"]], "cellpack.autopack.ingredient.grow": [[3, 1, 1, "", "ActinIngredient"], [3, 1, 1, "", "GrowIngredient"], [3, 4, 1, "", "random"]], "cellpack.autopack.ingredient.grow.ActinIngredient": [[3, 2, 1, "", "updateFromBB"]], "cellpack.autopack.ingredient.grow.GrowIngredient": [[3, 3, 1, "", "ARGUMENTS"], [3, 2, 1, "", "getFirstPoint"], [3, 2, 1, "", "getInterpolatedSphere"], [3, 2, 1, "", "getJtransRot"], [3, 2, 1, "", "getJtransRot_r"], [3, 2, 1, "", "getNextPoint"], [3, 2, 1, "", "getNextPtIndCyl"], [3, 2, 1, "", "getV3"], [3, 2, 1, "", "get_alternate_position"], [3, 2, 1, "", "get_alternate_position_p"], [3, 2, 1, "", "get_new_distance_values"], [3, 2, 1, "", "get_signed_distance"], [3, 2, 1, "", "grow"], [3, 2, 1, "", "grow_place"], [3, 2, 1, "", "mask_sphere_points"], [3, 2, 1, "", "mask_sphere_points_angle"], [3, 2, 1, "", "mask_sphere_points_boundary"], [3, 2, 1, "", "mask_sphere_points_dihedral"], [3, 2, 1, "", "mask_sphere_points_ingredients"], [3, 2, 1, "", "mask_sphere_points_vector"], [3, 2, 1, "", "pickAlternateHalton"], [3, 2, 1, "", "pickHalton"], [3, 2, 1, "", "pickRandomSphere"], [3, 2, 1, "", "pick_alternate"], [3, 2, 1, "", "pick_random_alternate"], [3, 2, 1, "", "place_alternate"], [3, 2, 1, "", "place_alternate_p"], [3, 2, 1, "", "prepare_alternates"], [3, 2, 1, "", "prepare_alternates_proba"], [3, 2, 1, "", "reset"], [3, 2, 1, "", "resetLastPoint"], [3, 2, 1, "", "resetSphereDistribution"], [3, 2, 1, "", "updateGrid"], [3, 2, 1, "", "walkLattice"], [3, 2, 1, "", "walkLatticeSurface"], [3, 2, 1, "", "walkSphere"]], "cellpack.autopack.ingredient.multi_cylinder": [[3, 1, 1, "", "MultiCylindersIngr"]], "cellpack.autopack.ingredient.multi_cylinder.MultiCylindersIngr": [[3, 2, 1, "", "checkCylCollisions"], [3, 2, 1, "", "collides_with_compartment"], [3, 2, 1, "", "collision_jitter"], [3, 2, 1, "", "getBigBB"], [3, 2, 1, "", "get_cuttoff_value"], [3, 2, 1, "", "initialize_mesh"]], "cellpack.autopack.ingredient.multi_sphere": [[3, 1, 1, "", "MultiSphereIngr"]], "cellpack.autopack.ingredient.multi_sphere.MultiSphereIngr": [[3, 2, 1, "", "collides_with_compartment"], [3, 2, 1, "", "collision_jitter"], [3, 2, 1, "", "get_new_distance_values"], [3, 2, 1, "", "get_radius"], [3, 2, 1, "", "get_signed_distance"], [3, 2, 1, "", "pack_at_grid_pt_location"]], "cellpack.autopack.ingredient.single_cube": [[3, 1, 1, "", "SingleCubeIngr"]], "cellpack.autopack.ingredient.single_cube.SingleCubeIngr": [[3, 2, 1, "", "collides_with_compartment"], [3, 2, 1, "", "collision_jitter"], [3, 2, 1, "", "cube_surface_distance"], [3, 2, 1, "", "get_new_distance_values"], [3, 2, 1, "", "get_signed_distance"]], "cellpack.autopack.ingredient.single_cylinder": [[3, 1, 1, "", "SingleCylinderIngr"]], "cellpack.autopack.ingredient.single_cylinder.SingleCylinderIngr": [[3, 2, 1, "", "checkCylCollisions"], [3, 2, 1, "", "collides_with_compartment"], [3, 2, 1, "", "collision_jitter"], [3, 2, 1, "", "getBigBB"], [3, 2, 1, "", "get_cuttoff_value"], [3, 2, 1, "", "get_signed_distance"], [3, 2, 1, "", "initialize_mesh"]], "cellpack.autopack.ingredient.single_sphere": [[3, 1, 1, "", "SingleSphereIngr"]], "cellpack.autopack.ingredient.single_sphere.SingleSphereIngr": [[3, 2, 1, "", "collides_with_compartment"], [3, 2, 1, "", "collision_jitter"], [3, 2, 1, "", "create_circular_mask"], [3, 2, 1, "", "create_voxelization"], [3, 2, 1, "", "get_new_distance_values"], [3, 2, 1, "", "get_radius"], [3, 2, 1, "", "get_signed_distance"], [3, 2, 1, "", "initialize_mesh"]], "cellpack.autopack.ingredient.utils": [[3, 4, 1, "", "ApplyMatrix"], [3, 4, 1, "", "bullet_checkCollision_mp"], [3, 4, 1, "", "getDihedral"], [3, 4, 1, "", "getNormedVector"], [3, 4, 1, "", "getNormedVectorOnes"], [3, 4, 1, "", "getNormedVectorU"], [3, 4, 1, "", "get_reflected_point"], [3, 4, 1, "", "rotVectToVect"], [3, 4, 1, "", "rotax"]], "cellpack.autopack.interface_objects": [[4, 0, 0, "-", "database_ids"], [4, 0, 0, "-", "default_values"], [4, 0, 0, "-", "gradient_data"], [4, 0, 0, "-", "ingredient_types"], [4, 0, 0, "-", "meta_enum"], [4, 0, 0, "-", "packed_objects"], [4, 0, 0, "-", "partners"], [4, 0, 0, "-", "representations"]], "cellpack.autopack.interface_objects.database_ids": [[4, 1, 1, "", "DATABASE_IDS"]], "cellpack.autopack.interface_objects.database_ids.DATABASE_IDS": [[4, 3, 1, "", "AWS"], [4, 3, 1, "", "FIREBASE"], [4, 3, 1, "", "GITHUB"], [4, 2, 1, "", "handlers"], [4, 2, 1, "", "with_colon"]], "cellpack.autopack.interface_objects.gradient_data": [[4, 1, 1, "", "GradientData"], [4, 1, 1, "", "GradientModes"], [4, 1, 1, "", "InvertOptions"], [4, 1, 1, "", "ModeOptions"], [4, 1, 1, "", "PickModes"], [4, 1, 1, "", "WeightModeOptions"], [4, 1, 1, "", "WeightModes"]], "cellpack.autopack.interface_objects.gradient_data.GradientData": [[4, 3, 1, "", "default_values"], [4, 2, 1, "", "set_mode_properties"], [4, 2, 1, "", "validate_gradient_data"], [4, 2, 1, "", "validate_invert_settings"], [4, 2, 1, "", "validate_mode_settings"], [4, 2, 1, "", "validate_weight_mode_settings"]], "cellpack.autopack.interface_objects.gradient_data.GradientModes": [[4, 3, 1, "", "RADIAL"], [4, 3, 1, "", "SURFACE"], [4, 3, 1, "", "VECTOR"], [4, 3, 1, "", "X"], [4, 3, 1, "", "Y"], [4, 3, 1, "", "Z"]], "cellpack.autopack.interface_objects.gradient_data.InvertOptions": [[4, 3, 1, "", "distance"], [4, 3, 1, "", "weight"]], "cellpack.autopack.interface_objects.gradient_data.ModeOptions": [[4, 3, 1, "", "center"], [4, 3, 1, "", "direction"], [4, 3, 1, "", "gblob"], [4, 3, 1, "", "object"], [4, 3, 1, "", "radius"], [4, 3, 1, "", "scale_distance_between"]], "cellpack.autopack.interface_objects.gradient_data.PickModes": [[4, 3, 1, "", "BINARY"], [4, 3, 1, "", "LINEAR"], [4, 3, 1, "", "MAX"], [4, 3, 1, "", "MIN"], [4, 3, 1, "", "REG"], [4, 3, 1, "", "RND"], [4, 3, 1, "", "SUB"]], "cellpack.autopack.interface_objects.gradient_data.WeightModeOptions": [[4, 3, 1, "", "decay_length"], [4, 3, 1, "", "power"]], "cellpack.autopack.interface_objects.gradient_data.WeightModes": [[4, 3, 1, "", "CUBE"], [4, 3, 1, "", "EXPONENTIAL"], [4, 3, 1, "", "LINEAR"], [4, 3, 1, "", "POWER"], [4, 3, 1, "", "SQUARE"]], "cellpack.autopack.interface_objects.ingredient_types": [[4, 1, 1, "", "INGREDIENT_TYPE"]], "cellpack.autopack.interface_objects.ingredient_types.INGREDIENT_TYPE": [[4, 3, 1, "", "GROW"], [4, 3, 1, "", "MESH"], [4, 3, 1, "", "MULTI_CYLINDER"], [4, 3, 1, "", "MULTI_SPHERE"], [4, 3, 1, "", "SINGLE_CUBE"], [4, 3, 1, "", "SINGLE_CYLINDER"], [4, 3, 1, "", "SINGLE_SPHERE"]], "cellpack.autopack.interface_objects.meta_enum": [[4, 1, 1, "", "MetaEnum"]], "cellpack.autopack.interface_objects.meta_enum.MetaEnum": [[4, 2, 1, "", "is_member"], [4, 2, 1, "", "values"]], "cellpack.autopack.interface_objects.packed_objects": [[4, 1, 1, "", "PackedObject"], [4, 1, 1, "", "PackedObjects"]], "cellpack.autopack.interface_objects.packed_objects.PackedObjects": [[4, 2, 1, "", "add"], [4, 2, 1, "", "get_all"], [4, 2, 1, "", "get_compartment"], [4, 2, 1, "", "get_encapsulating_radii"], [4, 2, 1, "", "get_ingredients"], [4, 2, 1, "", "get_positions"], [4, 2, 1, "", "get_positions_for_ingredient"], [4, 2, 1, "", "get_radii"], [4, 2, 1, "", "get_rotations_for_ingredient"]], "cellpack.autopack.interface_objects.partners": [[4, 1, 1, "", "Partner"], [4, 1, 1, "", "Partners"]], "cellpack.autopack.interface_objects.partners.Partner": [[4, 2, 1, "", "distanceFunction"], [4, 2, 1, "", "get_point"], [4, 2, 1, "", "set_ingredient"]], "cellpack.autopack.interface_objects.partners.Partners": [[4, 2, 1, "", "add_partner"], [4, 2, 1, "", "get_partner_by_ingr_name"], [4, 2, 1, "", "is_partner"]], "cellpack.autopack.interface_objects.representations": [[4, 1, 1, "", "Representations"]], "cellpack.autopack.interface_objects.representations.Representations": [[4, 3, 1, "", "DATABASE"], [4, 2, 1, "", "get_active"], [4, 2, 1, "", "get_active_data"], [4, 2, 1, "", "get_adjusted_position"], [4, 2, 1, "", "get_deepest_level"], [4, 2, 1, "", "get_mesh_format"], [4, 2, 1, "", "get_mesh_name"], [4, 2, 1, "", "get_mesh_path"], [4, 2, 1, "", "get_min_max_radius"], [4, 2, 1, "", "get_pdb_path"], [4, 2, 1, "", "get_positions"], [4, 2, 1, "", "get_radii"], [4, 2, 1, "", "has_mesh"], [4, 2, 1, "", "has_pdb"], [4, 2, 1, "", "set_active"], [4, 2, 1, "", "set_sphere_positions"]], "cellpack.autopack.ldSequence": [[2, 1, 1, "", "HaltonSequence"], [2, 4, 1, "", "SphereHalton"], [2, 1, 1, "", "cHaltonSequence3"], [2, 4, 1, "", "halton"], [2, 4, 1, "", "halton2"], [2, 4, 1, "", "halton3"], [2, 4, 1, "", "halton_sequence"], [2, 4, 1, "", "haltonterm"]], "cellpack.autopack.ldSequence.cHaltonSequence3": [[2, 2, 1, "", "inc"], [2, 2, 1, "", "reset"]], "cellpack.autopack.loaders": [[5, 0, 0, "-", "analysis_config_loader"], [5, 0, 0, "-", "config_loader"], [5, 0, 0, "-", "migrate_v1_to_v2"], [5, 0, 0, "-", "migrate_v2_to_v2_1"], [5, 0, 0, "-", "recipe_loader"], [5, 0, 0, "-", "utils"], [5, 0, 0, "-", "v1_v2_attribute_changes"]], "cellpack.autopack.loaders.analysis_config_loader": [[5, 1, 1, "", "AnalysisConfigLoader"]], "cellpack.autopack.loaders.analysis_config_loader.AnalysisConfigLoader": [[5, 3, 1, "", "default_values"]], "cellpack.autopack.loaders.config_loader": [[5, 1, 1, "", "ConfigLoader"], [5, 1, 1, "", "Inner_Grid_Methods"], [5, 1, 1, "", "Place_Methods"]], "cellpack.autopack.loaders.config_loader.ConfigLoader": [[5, 3, 1, "", "default_values"]], "cellpack.autopack.loaders.config_loader.Inner_Grid_Methods": [[5, 3, 1, "", "RAYTRACE"], [5, 3, 1, "", "SCANLINE"], [5, 3, 1, "", "TRIMESH"]], "cellpack.autopack.loaders.config_loader.Place_Methods": [[5, 3, 1, "", "JITTER"], [5, 3, 1, "", "SPHERES_SST"]], "cellpack.autopack.loaders.migrate_v1_to_v2": [[5, 4, 1, "", "check_required_attributes"], [5, 4, 1, "", "convert"], [5, 4, 1, "", "convert_rotation_range"], [5, 4, 1, "", "get_and_store_v2_object"], [5, 4, 1, "", "get_representations"], [5, 4, 1, "", "migrate_ingredient"], [5, 4, 1, "", "split_ingredient_data"]], "cellpack.autopack.loaders.migrate_v2_to_v2_1": [[5, 4, 1, "", "convert"], [5, 4, 1, "", "convert_gradients"], [5, 4, 1, "", "convert_partners"]], "cellpack.autopack.loaders.recipe_loader": [[5, 1, 1, "", "RecipeLoader"]], "cellpack.autopack.loaders.recipe_loader.RecipeLoader": [[5, 3, 1, "", "default_values"], [5, 2, 1, "", "get_all_ingredients"], [5, 2, 1, "", "resolve_inheritance"]], "cellpack.autopack.loaders.utils": [[5, 4, 1, "", "create_file_info_object_from_full_path"], [5, 4, 1, "", "create_output_dir"], [5, 4, 1, "", "read_json_file"], [5, 4, 1, "", "write_json_file"]], "cellpack.autopack.octree": [[2, 1, 1, "", "OctNode"], [2, 1, 1, "", "Octree"]], "cellpack.autopack.octree.Octree": [[2, 2, 1, "", "addNode"], [2, 2, 1, "", "findBranch"], [2, 2, 1, "", "findPosition"], [2, 2, 1, "", "insertNode"]], "cellpack.autopack.plotly_result": [[2, 1, 1, "", "PlotlyAnalysis"]], "cellpack.autopack.plotly_result.PlotlyAnalysis": [[2, 2, 1, "", "add_circle"], [2, 2, 1, "", "add_ingredient_positions"], [2, 2, 1, "", "add_square"], [2, 2, 1, "", "format_color"], [2, 2, 1, "", "make_and_show_heatmap"], [2, 2, 1, "", "make_grid_heatmap"], [2, 2, 1, "", "show"], [2, 2, 1, "", "transformPoints2D"], [2, 2, 1, "", "update_title"]], "cellpack.autopack.randomRot": [[2, 1, 1, "", "RandomRot"]], "cellpack.autopack.randomRot.RandomRot": [[2, 2, 1, "", "get"], [2, 2, 1, "", "getOld"], [2, 2, 1, "", "quaternion_matrix"], [2, 2, 1, "", "random_quaternion"], [2, 2, 1, "", "random_rotation_matrix"], [2, 2, 1, "", "setSeed"]], "cellpack.autopack.ray": [[2, 4, 1, "", "dot"], [2, 4, 1, "", "f_dot_product"], [2, 4, 1, "", "f_ray_intersect_polyhedron"], [2, 4, 1, "", "findPointsCenter"], [2, 4, 1, "", "makeMarchingCube"], [2, 4, 1, "", "ray_intersect_polygon"], [2, 4, 1, "", "ray_intersect_polyhedron"], [2, 4, 1, "", "vcross"], [2, 4, 1, "", "vdiff"], [2, 4, 1, "", "vlen"], [2, 4, 1, "", "vnorm"]], "cellpack.autopack.trajectory": [[2, 1, 1, "", "Trajectory"], [2, 1, 1, "", "dcdTrajectory"], [2, 1, 1, "", "molbTrajectory"], [2, 1, 1, "", "xyzTrajectory"]], "cellpack.autopack.trajectory.Trajectory": [[2, 2, 1, "", "applyState"], [2, 2, 1, "", "applyState_cb"], [2, 2, 1, "", "applyState_name"], [2, 2, 1, "", "applyState_primitive_name"], [2, 2, 1, "", "completeMapping"], [2, 2, 1, "", "generalApply"], [2, 2, 1, "", "getIngredientInstancePos"], [2, 2, 1, "", "makeIngrMapping"], [2, 3, 1, "", "reg"], [2, 3, 1, "", "traj_type"]], "cellpack.autopack.trajectory.dcdTrajectory": [[2, 3, 1, "", "dcd"], [2, 2, 1, "", "getPosAt"], [2, 2, 1, "", "parse"], [2, 3, 1, "", "traj_type"]], "cellpack.autopack.trajectory.molbTrajectory": [[2, 2, 1, "", "applyState_name"], [2, 2, 1, "", "applyState_primitive_name"], [2, 2, 1, "", "getPosAt"], [2, 2, 1, "", "parse"], [2, 2, 1, "", "parse_one_mol"], [2, 3, 1, "", "traj_type"]], "cellpack.autopack.trajectory.xyzTrajectory": [[2, 2, 1, "", "getPosAt"], [2, 2, 1, "", "getPosLine"], [2, 2, 1, "", "parse"], [2, 3, 1, "", "traj_type"]], "cellpack.autopack.upy": [[6, 0, 0, "-", "colors"], [6, 4, 1, "", "getHClass"], [6, 4, 1, "", "getHelperClass"], [6, 0, 0, "-", "hostHelper"], [6, 4, 1, "", "retrieveHost"], [7, 0, 0, "-", "simularium"]], "cellpack.autopack.upy.colors": [[6, 4, 1, "", "RedWhiteBlueRamp"], [6, 4, 1, "", "ThreeColorRamp"], [6, 4, 1, "", "TwoColorRamp"], [6, 4, 1, "", "create_divergent_color_map_with_scaled_values"], [6, 4, 1, "", "getRamp"], [6, 4, 1, "", "hexToRgb"], [6, 4, 1, "", "map_colors"]], "cellpack.autopack.upy.hostHelper": [[6, 1, 1, "", "Helper"], [6, 4, 1, "", "dot"], [6, 4, 1, "", "vcross"], [6, 4, 1, "", "vdiff"], [6, 4, 1, "", "vdistance"], [6, 4, 1, "", "vlen"], [6, 4, 1, "", "vnorm"]], "cellpack.autopack.upy.hostHelper.Helper": [[6, 2, 1, "", "AddObject"], [6, 2, 1, "", "ApplyMatrix"], [6, 3, 1, "", "BONES"], [6, 3, 1, "", "CAM_OPTIONS"], [6, 2, 1, "", "Circle"], [6, 2, 1, "", "Cylinder"], [6, 2, 1, "", "CylinderHeadTails"], [6, 2, 1, "", "Decompose4x4"], [6, 2, 1, "", "Dodecahedron"], [6, 2, 1, "", "FixNormals"], [6, 2, 1, "", "Hexahedron"], [6, 3, 1, "", "IK"], [6, 2, 1, "", "Icosahedron"], [6, 2, 1, "", "IndexedPolgonsToTriPoints"], [6, 2, 1, "", "JoinsObjects"], [6, 3, 1, "", "LIGHT_OPTIONS"], [6, 2, 1, "", "MidPoint"], [6, 2, 1, "", "ObjectsSelection"], [6, 2, 1, "", "Octahedron"], [6, 2, 1, "", "Platonic"], [6, 2, 1, "", "PointCloudObject"], [6, 2, 1, "", "Sphere"], [6, 2, 1, "", "Tetrahedron"], [6, 2, 1, "", "Text"], [6, 2, 1, "", "ToMat"], [6, 2, 1, "", "ToVec"], [6, 2, 1, "", "addBone"], [6, 2, 1, "", "addCameraToScene"], [6, 2, 1, "", "addConstraint"], [6, 2, 1, "", "addLampToScene"], [6, 2, 1, "", "addMaterial"], [6, 2, 1, "", "addMaterialFromDic"], [6, 2, 1, "", "addMeshEdge"], [6, 2, 1, "", "addMeshEdges"], [6, 2, 1, "", "addMeshFace"], [6, 2, 1, "", "addMeshFaces"], [6, 2, 1, "", "addMeshVertice"], [6, 2, 1, "", "addMeshVertices"], [6, 2, 1, "", "addObjectToScene"], [6, 2, 1, "", "advance_randpoint_onsphere"], [6, 2, 1, "", "angle_between_vectors"], [6, 2, 1, "", "animationStart"], [6, 2, 1, "", "animationStop"], [6, 2, 1, "", "armature"], [6, 2, 1, "", "assignMaterial"], [6, 2, 1, "", "assignNewMaterial"], [6, 2, 1, "", "box"], [6, 2, 1, "", "changeColor"], [6, 2, 1, "", "changeMaterialProperty"], [6, 2, 1, "", "changeObjColorMat"], [6, 2, 1, "", "checkIsMesh"], [6, 2, 1, "", "checkName"], [6, 2, 1, "", "colorMaterial"], [6, 2, 1, "", "colorObject"], [6, 2, 1, "", "combineDaeMeshData"], [6, 2, 1, "", "concatObjectMatrix"], [6, 2, 1, "", "constraintLookAt"], [6, 2, 1, "", "convertColor"], [6, 2, 1, "", "createColorsMat"], [6, 2, 1, "", "createMaterial"], [6, 2, 1, "", "createSpring"], [6, 2, 1, "", "createsNmesh"], [6, 2, 1, "", "deleteChildrens"], [6, 2, 1, "", "deleteMeshEdges"], [6, 2, 1, "", "deleteMeshFaces"], [6, 2, 1, "", "deleteMeshVertices"], [6, 2, 1, "", "dihedral"], [6, 2, 1, "", "dodecahedron"], [6, 2, 1, "", "drawGradientLine"], [6, 2, 1, "", "drawPtCol"], [6, 3, 1, "", "dupliVert"], [6, 2, 1, "", "eulerToMatrix"], [6, 2, 1, "", "fillTriangleColor"], [6, 2, 1, "", "findClosestPoint"], [6, 2, 1, "", "fit_view3D"], [6, 2, 1, "", "frameAdvanced"], [6, 2, 1, "", "getA"], [6, 2, 1, "", "getAllMaterials"], [6, 2, 1, "", "getAngleAxis"], [6, 2, 1, "", "getBoxSize"], [6, 2, 1, "", "getCenter"], [6, 2, 1, "", "getCornerPointCube"], [6, 2, 1, "", "getCurrentScene"], [6, 2, 1, "", "getCurrentSceneName"], [6, 2, 1, "", "getCurrentSelection"], [6, 2, 1, "", "getFace"], [6, 2, 1, "", "getFaceEdges"], [6, 2, 1, "", "getFaceNormalsArea"], [6, 2, 1, "", "getFaces"], [6, 2, 1, "", "getFacesfromV"], [6, 2, 1, "", "getImage"], [6, 2, 1, "", "getLayers"], [6, 2, 1, "", "getMasterInstance"], [6, 2, 1, "", "getMaterial"], [6, 2, 1, "", "getMaterialProperty"], [6, 2, 1, "", "getMesh"], [6, 2, 1, "", "getMeshEdge"], [6, 2, 1, "", "getMeshEdges"], [6, 2, 1, "", "getMeshFaces"], [6, 2, 1, "", "getMeshNormales"], [6, 2, 1, "", "getMeshVertice"], [6, 2, 1, "", "getMeshVertices"], [6, 2, 1, "", "getName"], [6, 2, 1, "", "getObject"], [6, 2, 1, "", "getObjectName"], [6, 2, 1, "", "getOrder"], [6, 2, 1, "", "getParticles"], [6, 2, 1, "", "getParticulesPosition"], [6, 2, 1, "", "getPosUntilRoot"], [6, 2, 1, "", "getProperty"], [6, 2, 1, "", "getPropertyObject"], [6, 2, 1, "", "getScale"], [6, 2, 1, "", "getSize"], [6, 2, 1, "", "getTranslation"], [6, 2, 1, "", "getTubeProperties"], [6, 2, 1, "", "getTubePropertiesMatrix"], [6, 2, 1, "", "getUV"], [6, 2, 1, "", "getUVs"], [6, 2, 1, "", "getVisibility"], [6, 2, 1, "", "get_noise"], [6, 2, 1, "", "hexahedron"], [6, 2, 1, "", "icosahedron"], [6, 2, 1, "", "instancesToCollada"], [6, 2, 1, "", "isSphere"], [6, 2, 1, "", "makeTexture"], [6, 2, 1, "", "matrixToFacesMesh"], [6, 2, 1, "", "matrixToVNMesh"], [6, 2, 1, "", "measure_distance"], [6, 2, 1, "", "metaballs"], [6, 2, 1, "", "newEmpty"], [6, 2, 1, "", "newInstance"], [6, 2, 1, "", "norm"], [6, 2, 1, "", "normal_array"], [6, 2, 1, "", "normalize"], [6, 2, 1, "", "normalize_v3"], [6, 2, 1, "", "octahedron"], [6, 2, 1, "", "oneMetaBall"], [6, 2, 1, "", "particle"], [6, 2, 1, "", "pathDeform"], [6, 2, 1, "", "plane"], [6, 2, 1, "", "progressBar"], [6, 2, 1, "", "randpoint_onsphere"], [6, 2, 1, "", "raycast"], [6, 2, 1, "", "reParent"], [6, 2, 1, "", "read"], [6, 2, 1, "", "readMeshFromFile"], [6, 2, 1, "", "recalc_normals"], [6, 2, 1, "", "reporthook"], [6, 2, 1, "", "rerieveAxis"], [6, 2, 1, "", "resetProgressBar"], [6, 2, 1, "", "resetTransformation"], [6, 2, 1, "", "restoreEditMode"], [6, 2, 1, "", "retrieveColorMat"], [6, 2, 1, "", "rotVectToVect"], [6, 2, 1, "", "rotateObj"], [6, 2, 1, "", "rotatePoint"], [6, 2, 1, "", "rotate_about_axis"], [6, 2, 1, "", "rotation_matrix"], [6, 2, 1, "", "saveDejaVuMesh"], [6, 2, 1, "", "saveObjMesh"], [6, 2, 1, "", "scalar"], [6, 2, 1, "", "scaleObj"], [6, 2, 1, "", "selectEdge"], [6, 2, 1, "", "selectEdges"], [6, 2, 1, "", "selectFace"], [6, 2, 1, "", "selectFaces"], [6, 2, 1, "", "selectVertice"], [6, 2, 1, "", "selectVertices"], [6, 2, 1, "", "setCurrentSelection"], [6, 2, 1, "", "setFrame"], [6, 2, 1, "", "setKeyFrame"], [6, 2, 1, "", "setLayers"], [6, 2, 1, "", "setMeshEdge"], [6, 2, 1, "", "setMeshEdges"], [6, 2, 1, "", "setMeshFace"], [6, 2, 1, "", "setMeshFaces"], [6, 2, 1, "", "setMeshVertice"], [6, 2, 1, "", "setMeshVertices"], [6, 2, 1, "", "setName"], [6, 2, 1, "", "setObjectMatrix"], [6, 2, 1, "", "setParticulesPosition"], [6, 2, 1, "", "setProperty"], [6, 2, 1, "", "setPropertyObject"], [6, 2, 1, "", "setRigidBody"], [6, 2, 1, "", "setSoftBody"], [6, 2, 1, "", "setTransformation"], [6, 2, 1, "", "setTranslation"], [6, 2, 1, "", "setUV"], [6, 2, 1, "", "setUVs"], [6, 2, 1, "", "setViewport"], [6, 2, 1, "", "spline"], [6, 2, 1, "", "testForEscape"], [6, 2, 1, "", "tetrahedron"], [6, 2, 1, "", "toggle"], [6, 2, 1, "", "toggleDisplay"], [6, 2, 1, "", "toggleEditMode"], [6, 2, 1, "", "toggleXray"], [6, 2, 1, "", "translateObj"], [6, 2, 1, "", "transposeMatrix"], [6, 2, 1, "", "triangulate"], [6, 2, 1, "", "triangulateFace"], [6, 2, 1, "", "triangulateFaceArray"], [6, 2, 1, "", "unit_vector"], [6, 2, 1, "", "update"], [6, 2, 1, "", "updateArmature"], [6, 2, 1, "", "updateBox"], [6, 2, 1, "", "updateMasterInstance"], [6, 2, 1, "", "updateParticles"], [6, 2, 1, "", "updatePathDeform"], [6, 2, 1, "", "updateSpring"], [6, 2, 1, "", "updateTubeObjs"], [6, 2, 1, "", "update_spline"], [6, 2, 1, "", "vector_norm"], [6, 2, 1, "", "write"], [6, 2, 1, "", "writeDX"], [6, 2, 1, "", "writeMeshToFile"], [6, 2, 1, "", "writeToFile"]], "cellpack.autopack.upy.simularium": [[7, 0, 0, "-", "plots"], [7, 0, 0, "-", "simularium_helper"]], "cellpack.autopack.upy.simularium.plots": [[7, 1, 1, "", "PlotData"]], "cellpack.autopack.upy.simularium.plots.PlotData": [[7, 2, 1, "", "add_histogram"], [7, 2, 1, "", "add_scatter"]], "cellpack.autopack.upy.simularium.simularium_helper": [[7, 1, 1, "", "Instance"], [7, 1, 1, "", "simulariumHelper"]], "cellpack.autopack.upy.simularium.simularium_helper.Instance": [[7, 2, 1, "", "increment_static"], [7, 2, 1, "", "move"], [7, 2, 1, "", "set_static"]], "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper": [[7, 2, 1, "", "Box"], [7, 2, 1, "", "Cube"], [7, 2, 1, "", "Cylinders"], [7, 3, 1, "", "DATABASE"], [7, 3, 1, "", "DEBUG"], [7, 2, 1, "", "DecomposeMesh"], [7, 3, 1, "", "EMPTY"], [7, 2, 1, "", "FromVec"], [7, 2, 1, "", "Geom"], [7, 2, 1, "", "GetAbsPosUntilRoot"], [7, 3, 1, "", "INSTANCE"], [7, 2, 1, "", "IndexedPolygons"], [7, 2, 1, "", "Labels"], [7, 2, 1, "", "ObjectsSelection"], [7, 3, 1, "", "POLYGON"], [7, 2, 1, "", "Points"], [7, 2, 1, "", "Polylines"], [7, 3, 1, "", "SPHERE"], [7, 3, 1, "", "SPLINE"], [7, 2, 1, "", "Spheres"], [7, 2, 1, "", "TextureFaceCoordintesToVertexCoordinates"], [7, 2, 1, "", "ToVec"], [7, 3, 1, "", "VERBOSE"], [7, 2, 1, "", "addCameraToScene"], [7, 2, 1, "", "addLampToScene"], [7, 2, 1, "", "addMaterial"], [7, 2, 1, "", "add_compartment_to_scene"], [7, 2, 1, "", "add_grid_data_to_scene"], [7, 2, 1, "", "add_instance"], [7, 2, 1, "", "add_new_instance_and_update_time"], [7, 2, 1, "", "add_object_to_scene"], [7, 2, 1, "", "assignMaterial"], [7, 2, 1, "", "box"], [7, 2, 1, "", "changeColor"], [7, 2, 1, "", "changeColorO"], [7, 2, 1, "", "changeObjColorMat"], [7, 2, 1, "", "clear"], [7, 2, 1, "", "concatObjectMatrix"], [7, 2, 1, "", "createTexturedMaterial"], [7, 2, 1, "", "cylinder"], [7, 2, 1, "", "decomposeColladaGeom"], [7, 2, 1, "", "deleteInstance"], [7, 2, 1, "", "deleteObject"], [7, 2, 1, "", "format_rgb_color"], [7, 2, 1, "", "getAllMaterials"], [7, 2, 1, "", "getChilds"], [7, 2, 1, "", "getColladaMaterial"], [7, 2, 1, "", "getCornerPointCube"], [7, 2, 1, "", "getCurrentScene"], [7, 2, 1, "", "getCurrentSelection"], [7, 2, 1, "", "getFace"], [7, 2, 1, "", "getMaterial"], [7, 2, 1, "", "getMaterialName"], [7, 2, 1, "", "getMaterialObject"], [7, 2, 1, "", "getMesh"], [7, 2, 1, "", "getMeshEdges"], [7, 2, 1, "", "getMeshFaces"], [7, 2, 1, "", "getMeshNormales"], [7, 2, 1, "", "getMeshVertices"], [7, 2, 1, "", "getName"], [7, 2, 1, "", "getNormals"], [7, 2, 1, "", "getObject"], [7, 2, 1, "", "getTransformation"], [7, 2, 1, "", "getTranslation"], [7, 2, 1, "", "getType"], [7, 2, 1, "", "getVisibility"], [7, 2, 1, "", "get_display_data"], [7, 3, 1, "", "host"], [7, 2, 1, "", "increment_static_objects"], [7, 2, 1, "", "increment_time"], [7, 2, 1, "", "init_scene_with_objects"], [7, 2, 1, "", "instancePolygon"], [7, 2, 1, "", "instancesCylinder"], [7, 2, 1, "", "instancesSphere"], [7, 2, 1, "", "isIndexedPolyon"], [7, 2, 1, "", "is_fiber"], [7, 2, 1, "", "move_object"], [7, 2, 1, "", "newEmpty"], [7, 2, 1, "", "nodeToGeom"], [7, 2, 1, "", "oneColladaGeom"], [7, 2, 1, "", "oneCylinder"], [7, 2, 1, "", "open_in_simularium"], [7, 2, 1, "", "pathDeform"], [7, 3, 1, "", "pb"], [7, 2, 1, "", "place_object"], [7, 2, 1, "", "plane"], [7, 2, 1, "", "post_and_open_file"], [7, 2, 1, "", "progressBar"], [7, 2, 1, "", "raycast"], [7, 2, 1, "", "raycast_test"], [7, 2, 1, "", "reParent"], [7, 2, 1, "", "remove_nans"], [7, 2, 1, "", "resetProgressBar"], [7, 2, 1, "", "rotateObj"], [7, 2, 1, "", "scaleObj"], [7, 2, 1, "", "setInstance"], [7, 2, 1, "", "setObjectMatrix"], [7, 2, 1, "", "setRigidBody"], [7, 2, 1, "", "setTranslation"], [7, 2, 1, "", "setViewer"], [7, 2, 1, "", "set_object_static"], [7, 2, 1, "", "sort_values"], [7, 2, 1, "", "sphere"], [7, 2, 1, "", "spline"], [7, 2, 1, "", "store_metadata"], [7, 2, 1, "", "store_result_file"], [7, 2, 1, "", "toggleDisplay"], [7, 2, 1, "", "transformNode"], [7, 2, 1, "", "translateObj"], [7, 2, 1, "", "update"], [7, 2, 1, "", "updateAppli"], [7, 2, 1, "", "updateBox"], [7, 2, 1, "", "updateMasterInstance"], [7, 2, 1, "", "updateMesh"], [7, 2, 1, "", "updatePathDeform"], [7, 2, 1, "", "updatePoly"], [7, 2, 1, "", "updateTubeMesh"], [7, 2, 1, "", "update_instance_positions_and_rotations"], [7, 2, 1, "", "update_spline"], [7, 3, 1, "", "viewer"], [7, 2, 1, "", "write"], [7, 2, 1, "", "writeToFile"]], "cellpack.autopack.utils": [[2, 4, 1, "", "check_paired_key"], [2, 4, 1, "", "cmp_to_key"], [2, 4, 1, "", "deep_merge"], [2, 4, 1, "", "expand_object_using_key"], [2, 4, 1, "", "get_distance"], [2, 4, 1, "", "get_distances_from_point"], [2, 4, 1, "", "get_max_value_from_distribution"], [2, 4, 1, "", "get_min_value_from_distribution"], [2, 4, 1, "", "get_paired_key"], [2, 4, 1, "", "get_seed_list"], [2, 4, 1, "", "get_value_from_distribution"], [2, 4, 1, "", "ingredient_compare0"], [2, 4, 1, "", "ingredient_compare1"], [2, 4, 1, "", "ingredient_compare2"], [2, 4, 1, "", "load_object_from_pickle"]], "cellpack.autopack.writers": [[8, 1, 1, "", "IOingredientTool"], [8, 0, 0, "-", "ImageWriter"], [8, 1, 1, "", "NumpyArrayEncoder"], [8, 1, 1, "", "Writer"], [8, 4, 1, "", "updatePositionsRadii"]], "cellpack.autopack.writers.IOingredientTool": [[8, 2, 1, "", "ingrJsonNode"], [8, 2, 1, "", "write"]], "cellpack.autopack.writers.ImageWriter": [[8, 1, 1, "", "ImageWriter"]], "cellpack.autopack.writers.ImageWriter.ImageWriter": [[8, 2, 1, "", "concatenate_image_data"], [8, 2, 1, "", "convolve_channel"], [8, 2, 1, "", "convolve_image"], [8, 2, 1, "", "create_box_psf"], [8, 2, 1, "", "create_gaussian_psf"], [8, 2, 1, "", "export_image"], [8, 2, 1, "", "transpose_image_for_projection"]], "cellpack.autopack.writers.NumpyArrayEncoder": [[8, 2, 1, "", "default"]], "cellpack.autopack.writers.Writer": [[8, 2, 1, "", "return_object_value"], [8, 2, 1, "", "save"], [8, 2, 1, "", "save_Mixed_asJson"], [8, 2, 1, "", "save_as_simularium"], [8, 2, 1, "", "setValueToJsonNode"]], "cellpack.bin": [[9, 0, 0, "-", "analyze"], [9, 0, 0, "-", "clean"], [9, 0, 0, "-", "cleanup_tasks"], [9, 0, 0, "-", "pack"], [9, 0, 0, "-", "simularium_converter"], [9, 0, 0, "-", "upload"]], "cellpack.bin.analyze": [[9, 4, 1, "", "analyze"], [9, 4, 1, "", "main"]], "cellpack.bin.clean": [[9, 4, 1, "", "clean"], [9, 4, 1, "", "main"]], "cellpack.bin.cleanup_tasks": [[9, 4, 1, "", "run_cleanup"]], "cellpack.bin.pack": [[9, 4, 1, "", "main"], [9, 4, 1, "", "pack"]], "cellpack.bin.simularium_converter": [[9, 1, 1, "", "ConvertToSimularium"], [9, 4, 1, "", "main"]], "cellpack.bin.simularium_converter.ConvertToSimularium": [[9, 3, 1, "", "DEFAULT_GEO_TYPE"], [9, 3, 1, "", "DEFAULT_INPUT_RECIPE"], [9, 3, 1, "", "DEFAULT_OUTPUT_DIRECTORY"], [9, 3, 1, "", "DEFAULT_PACKING_RESULT"], [9, 3, 1, "", "DEFAULT_SCALE_FACTOR"], [9, 2, 1, "", "fill_in_empty_fiber_data"], [9, 2, 1, "", "get_bounding_box"], [9, 2, 1, "", "get_euler"], [9, 2, 1, "", "get_euler_from_matrix"], [9, 2, 1, "", "get_euler_from_quat"], [9, 2, 1, "", "get_ingredient_data"], [9, 2, 1, "", "get_ingredient_display_data"], [9, 2, 1, "", "get_mesh_data"], [9, 2, 1, "", "get_positions_per_ingredient"], [9, 2, 1, "", "is_matrix"], [9, 2, 1, "", "process_one_ingredient"], [9, 2, 1, "", "unpack_curve"], [9, 2, 1, "", "unpack_positions"]], "cellpack.bin.upload": [[9, 4, 1, "", "get_recipe_metadata"], [9, 4, 1, "", "main"], [9, 4, 1, "", "upload"]]}, "objnames": {"0": ["py", "module", "Python module"], "1": ["py", "class", "Python class"], "2": ["py", "method", "Python method"], "3": ["py", "attribute", "Python attribute"], "4": ["py", "function", "Python function"]}, "objtypes": {"0": "py:module", "1": "py:class", "2": "py:method", "3": "py:attribute", "4": "py:function"}, "terms": {"": [0, 2, 6, 10, 14], "0": [2, 3, 4, 5, 6, 7, 8, 9, 11], "00": 1, "0006022": 2, "0015926529164868282": 6, "01": [2, 3, 9], "01_04": 2, "022e23": 2, "022x10": 2, "04": 2, "06": 2, "06146124": 2, "09": 2, "0list": 2, "0x1e4fc4b0": [6, 7], "0x1e4fd3a0": 6, "0x1e4fd3d0": 6, "0x246c01a0": [6, 7], "1": [1, 3, 4, 5, 6, 7, 8, 9], "10": [0, 2, 3, 6, 7, 14], "100": [0, 2, 3, 5, 14], "1000": [0, 14], "10000": 2, "1000\u00e5": 2, "1024": 2, "1085": 2, "1087": 2, "10cm": 2, "10x": 2, "11": 2, "12": [6, 7], "1208118": 2, "123": 2, "124": 2, "130": 2, "132": 2, "133000000000003": 2, "14": 6, "141592653589793": [3, 6], "1415927": [0, 14], "15": [0, 2, 6, 7, 14], "16": [2, 6], "1660\u00e5": 2, "175": 2, "18": 2, "18nm": 2, "19": 2, "192": 2, "1978": 2, "1987": 2, "1990": 2, "1991": 2, "1992": 2, "1994": 2, "1cm": 2, "1d": 2, "1ing": 2, "1l": 2, "1m": 2, "1nm": 2, "1sphere": 6, "1\u00e5": 2, "2": [0, 2, 3, 6, 7, 14], "20": [1, 3, 6, 7], "200": [0, 2, 14], "2000": [2, 6], "2004": 2, "2005": 2, "2006": 2, "2009": 2, "2010": [2, 3, 6, 7], "2011": 2, "2012": 1, "2013": 2, "2014": 2, "2016": 2, "22": [2, 3], "222": [2, 6], "229": 2, "23": 1, "234": 2, "24": 2, "25": [2, 6], "255": [2, 6, 7], "256": [2, 6], "27": 2, "2831": [0, 3, 14], "29": 2, "29097116474265428": 6, "293748": 2, "29751650059422086": 6, "2d": [0, 2, 3, 6, 14], "2nd": 2, "2x": 2, "2x3": [6, 7], "3": [0, 2, 3, 6, 7, 11, 14], "30": [0, 3, 6, 7, 14], "32": 2, "320": 2, "323": 2, "324": 2, "32x32x32": 2, "331": 2, "345": 2, "35": [2, 3], "360": 6, "3600": 2, "3d": [2, 3, 6, 7], "4": [2, 6], "40": [6, 7], "41": 2, "41614630875957009": 6, "44": 2, "4492935982947064e": 6, "472": 2, "475": 2, "480": 6, "498": [0, 14], "49b": [6, 7], "4d": 6, "4x4": [2, 3, 6], "4x4arrai": [3, 6], "5": [0, 2, 3, 4, 6, 7, 8, 14], "50": [1, 3], "52": 2, "53": 1, "55": 2, "5708": 6, "58": 2, "595": 2, "6": [0, 2, 3, 6, 7, 14], "60": [0, 2, 14], "604": 2, "629": 2, "6330381706044601": 6, "642": 2, "65275180908484898": 6, "69670582573323303": 6, "6nm": 2, "7": [2, 11], "71735518109654839": 6, "7853981633974483": 2, "8": [2, 3, 6, 11], "827": 2, "828": 2, "8\u00e5": 2, "9": [2, 11], "90": [2, 3], "90929627358879683": 6, "95532": 6, "99810947": 2, "999": 3, "A": [0, 2, 6, 7, 10, 14], "AND": 2, "AS": 2, "As": [0, 14], "BE": 2, "BUT": 2, "BY": 2, "By": 2, "FOR": [2, 6, 7], "For": [2, 6, 8, 11], "IF": 2, "IN": 2, "IT": 11, "If": [0, 2, 3, 6, 7, 8, 11, 12, 14], "In": [0, 2, 6, 14], "It": [0, 2, 8, 10, 11, 14], "NO": 2, "NOT": 2, "No": 2, "OF": 2, "ON": 2, "OR": [2, 6], "One": [0, 6, 14], "Or": 12, "SUCH": 2, "THE": 2, "TO": [2, 6, 7], "The": [0, 3, 8, 9, 12, 14], "Then": 10, "These": 4, "To": [2, 6, 8, 11, 12], "Will": [0, 14], "__init__": [2, 7], "_also_": 2, "_analysi": 2, "_distance_dict": 2, "_not_": 3, "a34": 2, "a_norm": [2, 6], "ab": 2, "about": [2, 3, 6], "abov": 2, "absolu": [6, 7], "absolut": [2, 6, 7], "accept": [0, 14], "access": [2, 6, 7], "accompani": 2, "accord": [2, 6, 7], "according": 6, "account": [6, 11], "accum_result": 3, "accur": [0, 14], "across": [2, 3], "acta": 2, "actin": 3, "actiningredi": [2, 3], "action": 11, "activ": [2, 6, 7, 11], "activeingredi": 2, "actual": 2, "ad": [2, 3, 6, 7], "add": [2, 4, 6, 7, 10], "add_circl": [1, 2], "add_compart": [1, 2], "add_compartment_to_scen": [6, 7], "add_grid_data_to_scen": [6, 7], "add_histogram": [6, 7], "add_ingredient_posit": [1, 2], "add_ingredient_positions_to_plot": [1, 2], "add_inst": [6, 7], "add_mesh_to_scen": [1, 2], "add_new_instance_and_update_tim": [6, 7], "add_object_to_scen": [6, 7], "add_partn": [2, 4], "add_scatt": [6, 7], "add_seed_number_to_base_nam": [1, 2], "add_squar": [1, 2], "add_to_result": 2, "addbon": [2, 6], "addcameratoscen": [2, 6, 7], "addcompart": [1, 2], "addcompartmentfromgeom": [1, 2], "addconstraint": [2, 6], "addingredi": [1, 2], "addingredientfromgeom": [1, 2], "addingredientgroup": [1, 2], "addit": [0, 2, 6, 7, 14], "addlamptoscen": [2, 6, 7], "addmasteringr": [1, 2], "addmateri": [2, 6, 7], "addmaterialfromd": [2, 6], "addmeshedg": [2, 6], "addmeshfac": [2, 6], "addmeshrborganel": [1, 2], "addmeshvertic": [2, 6], "addnod": [1, 2], "addobject": [2, 6], "addobjecttoscen": [2, 6], "addrb": [1, 2], "addsp": 2, "adict": 2, "adjust": 3, "advance_randpoint_onspher": [2, 6], "advis": 2, "aeroplan": 6, "af": 2, "affili": 2, "afgui": 2, "after": [2, 3, 6, 7], "afvi": 3, "afview": 2, "against": [0, 2, 14], "agent": [1, 2], "agent_id": 9, "aic": 11, "al": 2, "algo": [0, 2, 14], "algorithm": [0, 2, 3, 11, 14], "alia": 6, "align": [3, 6], "alignrot": [2, 3], "all": [0, 2, 3, 4, 6, 7, 8, 10, 11, 14], "all_ingredi": 9, "all_ingredient_dist": 2, "all_object": 2, "all_po": 2, "all_pos_list": 2, "all_posit": 2, "all_rot": 2, "allclos": [2, 6], "allen": 9, "allencel": 11, "allingredi": 2, "allow": [0, 2, 14], "allow_nan": 8, "almost": 2, "along": [2, 6, 7], "alpha": [2, 6], "alreadi": 2, "also": [0, 2, 3, 10, 11, 14], "alt": 3, "altern": 3, "although": [2, 3], "alti": 3, "alusi": 2, "alwai": [0, 10, 12, 14], "am": 2, "amount": [0, 14], "amplitud": 3, "an": [0, 2, 3, 5, 6, 7, 8, 9, 11, 14], "anaconda": 10, "analys": [2, 9], "analyseap": 2, "analysi": [1, 9, 13], "analysis_config": 2, "analysis_config_load": [1, 2], "analysis_config_path": 9, "analysisconfigload": [2, 5], "analyz": [1, 2, 13], "andrew": 2, "angl": [2, 3, 6], "angle_between_vector": [2, 6], "ani": [2, 3, 6, 7, 11], "anim": 6, "animationstart": [2, 6], "animationstop": [2, 6], "anoth": [2, 3, 6], "anyth": 2, "apart": 2, "api": 2, "append": [2, 3], "appendingrinst": [1, 2], "applcabl": 6, "appli": [2, 3, 6, 7], "applic": [2, 6], "apply_rot": [2, 3], "applymatrix": [2, 3, 6], "applyst": [1, 2], "applystate_cb": [1, 2], "applystate_nam": [1, 2], "applystate_primitive_nam": [1, 2], "applystep": [1, 2], "appreci": 10, "approach": [2, 3], "appropri": 6, "apr": [0, 14], "april": 2, "ar": [0, 2, 3, 4, 6, 8, 10, 11, 14], "arai": 6, "arbitrari": [2, 8], "arcbal": 2, "area": [2, 6], "arg": [2, 6, 7, 9], "arguement": 6, "arguemt": 6, "argument": [2, 3, 6, 7, 9], "arguments_to_includ": 2, "aris": 2, "armatur": [2, 6], "armdata": 6, "around": [2, 6], "arr": [2, 6], "arrai": [0, 2, 3, 6, 7, 8, 14], "arrang": 2, "arthur": 2, "articl": 2, "as_dict": [1, 2], "ascii": 8, "asin": 6, "asmo": 2, "assign": [2, 3, 6, 7], "assignmateri": [2, 6, 7], "assignnewmateri": [2, 6], "assist": 2, "associ": 3, "assum": 2, "astr": 2, "atmost": 2, "atom": [4, 5, 11], "attempt": [0, 2, 3, 8, 14], "attempt_to_pack_at_grid_loc": [2, 3], "attenu": [6, 7], "attitud": [2, 6], "attractor": [0, 14], "attribut": [2, 3], "attrnam": [2, 8], "author": 2, "autin": [2, 6, 7], "auto": 6, "autofil": 2, "automat": 6, "autopack": [1, 9, 11, 13], "autopackserv": [0, 14], "autopackview": [1, 2], "avail": [2, 3, 4, 6, 7], "available_region": 3, "averag": 2, "avg_num_pack": 2, "avoid": [2, 6], "aw": [2, 4], "awai": [2, 3], "aws_access_key_id": 11, "aws_secret_access_kei": 11, "aws_url": 7, "awshandl": [1, 13], "ax": [2, 6], "axi": [2, 3, 6, 7], "axis_ord": 2, "az": 6, "azimuth": 6, "b": [2, 3, 6, 7, 10], "back": 2, "backward": 2, "bake": 6, "ball": [2, 6], "bank": 6, "bar": [2, 6, 7], "barycent": 2, "base": [0, 2, 3, 4, 5, 6, 7, 8, 9, 14], "base1": 2, "base2": 2, "base3": 2, "basedocu": [6, 7], "basegrid": [1, 13], "basenam": [2, 6], "baseobject": [6, 7], "basi": 8, "basic": [6, 7], "bb": [2, 3, 7], "bb_scale": 2, "bd_type": 2, "becam": 2, "becaus": [0, 2, 6, 14], "been": [2, 3], "befor": [0, 2, 3, 14], "begin": [2, 3], "behavior": [6, 8], "being": [0, 2, 6, 14], "believ": [0, 14], "belong": 3, "best": 2, "beta": 2, "better": 2, "between": [0, 2, 6, 14], "bezier": [6, 7], "bhtree": [0, 14], "bi": 2, "bia": 6, "bias": [3, 6], "bin": [1, 13], "binari": [2, 3, 4], "binding_prob": [2, 4], "binvox": [0, 2, 14], "binvox_rw": [1, 13], "biologi": 2, "bionumb": 2, "bisect": 2, "bit": 10, "bkp": 2, "blender": [2, 6, 7], "block": 2, "blockid_": 2, "blocksiz": 6, "blogspot": 2, "bodi": [2, 6, 7], "bond": 6, "bone": [2, 6], "bonepar": 6, "booelan": [6, 7], "book": 2, "bool": [2, 6, 7], "boolean": [0, 2, 3, 6, 7, 14], "both": [2, 11], "boto3": 11, "bottom": [2, 3, 6, 7], "bound": [0, 2, 3, 14], "bounding_box": [2, 3, 5], "boundingbox": [2, 3], "box": [0, 2, 3, 6, 7, 8, 14], "bpy_strct": [6, 7], "br": 10, "branch": [10, 11], "break": 11, "brep": 2, "brian": 3, "broadcast": 2, "browser": 11, "bucket": 2, "bucket_nam": 2, "buffer": 2, "bugfix": 10, "build": [0, 2, 3, 6, 10, 11, 14], "build_axis_weight_map": [1, 2], "build_compartment_grid": [1, 2], "build_directional_weight_map": [1, 2], "build_grid": [1, 2], "build_grid_spher": [1, 2], "build_mesh": [1, 2], "build_radial_weight_map": [1, 2], "build_surface_distance_weight_map": [1, 2], "build_weight_map": [1, 2], "buildcompartmentsgrid": [1, 2], "buildgrid": [1, 2], "buildgrid_bhtre": [1, 2], "buildgrid_binvox": [1, 2], "buildgrid_box": [1, 2], "buildgrid_kevin": [1, 2], "buildgrid_multisdf": [1, 2], "buildgrid_pyrai": [1, 2], "buildgrid_rai": [1, 2], "buildgrid_scanlin": [1, 2], "buildgrid_trimesh": [1, 2], "buildgrid_utsdf": [1, 2], "buildgridenviroonli": [1, 2], "buildingrprimit": [1, 2], "buildmesh": [1, 2, 3], "buildspher": [1, 2], "built": [0, 2, 14], "bullet_checkcollision_mp": [2, 3], "bump2vers": 10, "bumpvers": 11, "busi": 2, "byte": 2, "c": [2, 3, 6, 7, 11], "c0": 6, "c1": 6, "c4d": [2, 6, 7], "ca": 2, "cach": [2, 9], "calc_distance_between_surfac": 2, "calc_pairwise_dist": [1, 2], "calc_scaled_distances_for_posit": [1, 2], "calc_volum": [1, 2], "calcul": [0, 2, 3, 6, 14], "california": 2, "call": [2, 3, 6, 7, 8], "callbac": 6, "callback": [2, 6], "callfunct": [1, 2], "cam": [6, 7], "cam1": [6, 7], "cam_opt": [2, 6], "cambridg": 2, "came": 6, "camera": [6, 7], "cameratyp": [6, 7], "can": [0, 2, 3, 6, 7, 8, 10, 11, 12, 14], "cant": 6, "caract": 6, "card": 2, "carri": 2, "cartesian": [1, 2], "cartesian_to_sph": [1, 2], "carv": 2, "case": [0, 2, 6, 14], "caus": [2, 8], "cb": [2, 6], "cb_function": 2, "ccw": 2, "cd": [2, 10], "cellpack": [10, 12], "cellpack_data": [4, 7], "cellpack_database_1": [4, 7], "center": [2, 3, 4, 6, 7], "center_distance_dict": 2, "centerroot": 6, "centers1": 3, "centers2": 3, "cff": 2, "cgindex": 2, "chair": 2, "chair_out": 2, "chaltonsequence3": [1, 2], "chanc": 2, "chang": [2, 3, 6, 7, 10, 11], "changecolor": [2, 6, 7], "changecoloro": [6, 7], "changematerialproperti": [2, 6], "changeobjcolormat": [2, 6, 7], "channel": 8, "chapter": 2, "charact": [2, 8], "check": [0, 2, 3, 6, 8, 10, 14], "check_against_one_packed_ingr": [2, 3], "check_and_replace_refer": [1, 2], "check_circular": 8, "check_new_plac": [1, 2], "check_paired_kei": [1, 2], "check_rectangle_oustid": [1, 2], "check_required_attribut": [2, 5], "check_sphere_insid": [1, 2], "checkcollis": 3, "checkcreateempti": [1, 2], "checkcylcollis": [2, 3], "checkdist": [2, 3], "checkerrorinpath": [1, 2], "checkifupd": [2, 3], "checkingrpartnerproperti": [1, 2], "checkingrspher": [1, 2], "checkismesh": [2, 6], "checknam": [2, 6], "checkout": 10, "checkpath": [1, 2], "checkpointinsidebb": [1, 2], "checkrecipeavail": [1, 2], "checkrotformat": [1, 2], "child": 6, "children": [6, 7], "choic": 2, "chosen": 2, "christoph": 2, "chunk": [2, 3], "cid": 3, "ciff": 4, "cinema4d": [2, 6, 7], "circl": [2, 6], "circlespher": 2, "circular": [3, 8], "ckdtree": 2, "class": [3, 4, 5, 6, 8, 9], "classmethod": [2, 4, 6], "clean": [1, 2, 11, 13], "clean_argu": [1, 2], "clean_grid_cach": [1, 2, 5], "cleanup": 9, "cleanup_result": [1, 2], "cleanup_task": [1, 13], "clear": [1, 2, 6, 7], "clearal": [1, 2], "clearcach": [1, 2], "clearfil": [1, 2], "clearingr": [1, 2], "clearrbingredi": [1, 2], "clearrecip": [1, 2], "cli": 11, "clockwis": 3, "clone": [1, 2, 10, 12], "cloner": 6, "close": [0, 2, 3, 6, 7, 14], "close_indic": 3, "close_partner_check": [2, 3], "closepartn": [0, 14], "closest": [2, 6], "closest_ingredi": 2, "cloud": 2, "cmp": 2, "cmp_to_kei": [1, 2], "cmpt461": 2, "co": 6, "code": [2, 6, 9], "coffe": 2, "col": [2, 6, 7], "col1": 6, "col2": 6, "col3": 6, "colis": 2, "collada_xml": 6, "colladaexport": [1, 2], "collect": [2, 3], "collect_and_sort_data": [1, 2], "collect_docs_by_id": [1, 2], "collectresult": [1, 2], "collectresultperingredi": [1, 2], "collid": [0, 14], "collides_with_compart": [2, 3], "collinear": 6, "collis": [0, 3, 14], "collision_jitt": [2, 3], "collision_poss": 3, "collisiontre": 2, "color": [1, 2, 3, 7], "color_list": 6, "colorbydistancefrom": [1, 2], "colorbyord": [1, 2], "colormap": 6, "colormateri": [2, 6], "colorobject": [2, 6], "colorpt": [1, 2], "column": [2, 6], "com": [2, 4, 6, 7, 10, 11, 12], "combin": [2, 3], "combine_results_from_ingredi": [1, 2], "combine_results_from_se": [1, 2], "combined_pairwise_distance_dict": 2, "combinedaemeshdata": [2, 6], "come": 2, "command": [9, 12], "commen": 6, "commit": [10, 11], "common": 2, "comp": [2, 3], "comp_data": 2, "comp_dict": 2, "comp_id": [3, 9], "comp_or_obj": 2, "compact": 8, "compar": [2, 8], "compart": [0, 1, 3, 6, 7, 13, 14], "compartment_id": [2, 3], "compartment_id_for_nearest_grid_point": [1, 2], "compartment_kei": 2, "compartment_nam": 2, "compartmentlist": 1, "compdic": 2, "compid": 2, "compil": 2, "compile_db_recipe_data": [1, 2], "complet": [0, 2, 3, 14], "completemap": [1, 2], "completli": 2, "complex": [2, 3], "compliant": 8, "compmask": 3, "compon": [2, 6], "compose_matrix": 2, "composit": 2, "composition_dict": 2, "composition_id": 2, "compositiondoc": [1, 2], "comput": [2, 3, 6], "compute_volume_and_set_count": [1, 2], "computeexteriorvolum": [1, 2], "computegridnumberofpoint": [1, 2], "computevolum": [1, 2], "concaten": 2, "concatenate_image_data": [2, 8], "concatenate_matric": 2, "concatobjectmatrix": [2, 6, 7], "concentr": [0, 3, 14], "concept": [6, 7], "concert": 2, "conda": 11, "condit": 2, "config": [2, 9, 11], "config_load": [1, 2], "config_path": 9, "configload": [2, 5], "configur": [2, 11], "consequenti": 2, "consid": [0, 14], "consist": [3, 8], "constraint": 6, "constraintlookat": [2, 6], "constraintmarg": 3, "construct": 2, "constructor": [2, 8], "contact": 11, "contain": [2, 6, 8], "contains_point": [1, 2], "contains_points_mesh": [1, 2], "content": 13, "contigu": 2, "contr": 2, "contract": 2, "contributor": 2, "control": [2, 6], "control_point": 7, "convent": [2, 6], "conver": 6, "convers": [2, 6], "convert": [2, 5, 6, 7, 11], "convert_db_shortname_to_url": [1, 2], "convert_gradi": [2, 5], "convert_partn": [2, 5], "convert_positions_in_represent": [1, 2], "convert_represent": [1, 2], "convert_rotation_rang": [2, 5], "convertcolor": [2, 6], "convertpickletotext": [1, 2], "converttosimularium": [1, 9], "convolution_opt": 8, "convolv": 8, "convolve_channel": [2, 8], "convolve_imag": [2, 8], "coord": [3, 6, 7], "coord1": 6, "coord2": 6, "coordiant": 3, "coordin": [2, 6, 7], "copi": [2, 3, 6, 7, 12], "copyinggnugpl": 2, "copyright": [2, 6, 7], "corner": [0, 2, 3, 6, 7, 14], "cornerpoint": [3, 6, 7], "correct": [2, 6], "correctbb": [2, 3], "corrected_nam": 6, "correspond": [2, 6], "cosntraint": 6, "could": [2, 8], "count": [2, 3, 6], "count_opt": 3, "counter": 3, "cpython": 2, "cradiu": 7, "creat": [1, 3, 4, 6, 7, 8, 10, 11], "create3dpointlookup": [1, 2], "create_box_psf": [2, 8], "create_circular_mask": [2, 3], "create_compart": [1, 2], "create_divergent_color_map_with_scaled_valu": [2, 6], "create_file_info_object_from_full_path": [2, 5], "create_gaussian_psf": [2, 8], "create_grid_point_posit": [1, 2], "create_ingredi": [1, 2], "create_mesh": [1, 2], "create_object": [1, 2], "create_output_dir": [2, 5], "create_path": [1, 2], "create_presigned_url": [1, 2], "create_rbnod": [1, 2], "create_report": [1, 2], "create_spher": [1, 2], "create_sphere_data": [1, 2], "create_timestamp": [1, 2], "create_voxel": [1, 2, 3], "create_voxelized_mask": [1, 2], "createcolorsmat": [2, 6], "createingrmesh": [1, 2], "createmateri": [2, 6], "createorganelmesh": [1, 2], "createsnmesh": [2, 6], "createspr": [2, 6], "createsurfacepoint": [1, 2], "createtempl": [1, 2], "createtemplatecompart": [1, 2], "createtexturedmateri": [6, 7], "creation": [6, 7], "credenti": 11, "credit": 10, "crete": 6, "cron": 11, "cross": 2, "crowsandcat": 2, "cryst": 2, "csource2": 2, "ctree": 2, "cube": [2, 3, 4, 6, 7], "cube_surface_dist": [2, 3], "cubic": [2, 6, 7], "cumul": 6, "curl": 12, "curren": [6, 7], "current": [2, 6, 7, 8], "current_grid_dist": 3, "current_inst": 3, "current_object": 2, "current_packing_posit": 3, "currentpt": 3, "curret": 6, "curv": [6, 7], "custom": 8, "cutoff": [2, 3], "cutoff_boundari": 3, "cutoff_surfac": 3, "cw": 2, "cylind": [0, 2, 3, 6, 7, 14], "cylinderheadtail": [2, 6], "cytoplasm": [2, 3, 9], "d": [2, 3, 4], "dai": [8, 11], "damag": 2, "damp": 6, "dashboard": 11, "data": [2, 5, 6, 7, 8, 9], "data_d": 2, "data_in": 9, "data_sd": 2, "databas": [0, 2, 4, 6, 7, 9, 14], "database_id": [1, 2, 9], "database_nam": 2, "datadoc": [1, 2], "date": 11, "david": 2, "db": [2, 7], "db_choic": 2, "db_data": 2, "db_doc": 2, "db_handler": 2, "db_id": 9, "db_name": [1, 2], "db_recipe_data": 2, "dbmainten": [1, 2], "dbrecipehandl": [1, 13], "dbrecipeload": [1, 2], "dbupload": [1, 2], "dc": 2, "dcd": [1, 2], "dcdtrajectori": [1, 2], "dct": 2, "ddist": 6, "de": 2, "debug": [6, 7], "decay_length": [2, 4], "decid": 2, "declar": 2, "decod": 8, "decompos": [2, 6], "decompose4x4": [2, 6], "decompose_matrix": 2, "decompose_mesh": [1, 2], "decomposecolladageom": [6, 7], "decomposemesh": [2, 3, 6, 7], "decomposit": 6, "decreas": 2, "decres": 2, "deep_merg": [1, 2], "deepcopi": 2, "def": 8, "default": [0, 2, 3, 4, 5, 6, 8, 14], "default_db": 2, "default_geo_typ": [1, 9], "default_input_recip": [1, 9], "default_output_directori": [1, 9], "default_packing_result": [1, 9], "default_scale_factor": [1, 9], "default_valu": [1, 2, 5], "defaultfunct": [1, 2], "defin": [0, 2, 6, 9, 11, 14], "degre": 2, "deir": [6, 7], "dejavu": [2, 3, 6], "dejavutk": 7, "delet": [2, 6], "delete_doc": [1, 2], "deleteblist": [2, 3], "deletechildren": [2, 6], "deleteinst": [6, 7], "deletemeshedg": [2, 6], "deletemeshfac": [2, 6], "deletemeshvertic": [2, 6], "deleteobject": [6, 7], "delimit": 2, "delingr": [1, 2], "delingredi": [1, 2], "delingredientgrow": [1, 2], "delrb": [1, 2], "dens": 2, "dense_to_spars": [1, 2], "densiti": 3, "densityinmolar": 2, "depend": 11, "depnd": [6, 7], "deposit": 2, "deprec": [2, 6, 7], "deriv": [2, 6], "descend": [2, 3], "describ": [2, 6, 7], "descript": [4, 10], "design": 6, "desir": [6, 7], "destin": 2, "destinaon": 6, "detail": [2, 6, 7, 10], "detect": [0, 3, 14], "determin": [0, 2, 14], "dev": [2, 9, 10, 11], "develop": [0, 2, 10, 14], "diag": 2, "dic": 6, "dicgeom": 7, "dict": [2, 6, 8], "dictionari": [2, 3, 4, 6, 7, 8], "did": 2, "didnt": 6, "diebel": 2, "differ": [2, 6], "diffus": [6, 7], "dihedr": [2, 6], "dihedralgeometryerror": 6, "dilat": 2, "dim": 2, "dimens": [2, 6], "dimension": [2, 6], "direc": 6, "direct": [0, 2, 4, 6, 7, 14], "directli": [0, 11, 14], "directori": [2, 9], "diret": 3, "disclaim": 2, "discuss": 2, "displai": [0, 2, 6, 7, 14], "displaycompart": [1, 2], "displaycompartmentpoint": [1, 2], "displaycompartmentsingredi": [1, 2], "displaycompartmentspoint": [1, 2], "displaycytoplasmingredi": [1, 2], "displaydist": [1, 2], "displayenv": [1, 2], "displayfil": [1, 2], "displayfillbox": [1, 2], "displayfreepoint": [1, 2], "displayfreepointsasp": [1, 2], "displaygradi": [1, 2], "displayingrcylind": [1, 2], "displayingredi": [1, 2], "displayingrgrow": [1, 2], "displayingrmesh": [1, 2], "displayingrresult": [1, 2], "displayingrspher": [1, 2], "displayinstancesingredi": [1, 2], "displayleafoctre": [1, 2], "displayoctre": [1, 2], "displayoctreeleaf": [1, 2], "displayonenodeoctre": [1, 2], "displayparticlevolumedist": [1, 2], "displaypoint": [1, 2], "displayprefil": [1, 2], "displayroot": [1, 2], "displaysubnod": [1, 2], "dist": [2, 6, 7], "distanc": [0, 2, 3, 4, 6, 7, 14], "distance_check_fail": [1, 2], "distance_express": 3, "distance_funct": 3, "distancefunct": [2, 4], "distinct": 6, "distribut": [2, 3, 6, 7], "distribution_opt": [2, 3], "distributionopt": [2, 3], "distributiontyp": [2, 3], "disttoclosestsurf": 2, "distu": 6, "diverg": 6, "dmin": 2, "do": [0, 2, 3, 6, 7, 14], "doc": [2, 6, 7, 11], "doc_id": [1, 2], "doc_ref": 2, "doc_to_dict": [1, 2], "document": [2, 6, 7], "dodeca": 6, "dodecahedron": [2, 6], "doe": [0, 2, 6, 7, 14], "doesn": 2, "doesnt": [6, 7], "doloop": [1, 2], "domesh": 2, "don": [11, 12], "done": [2, 10], "dospher": 2, "dot": [1, 2, 6], "doubl": [2, 6], "down": [2, 6], "download": [2, 11, 12], "download_fil": [1, 2], "downloaded_data": 2, "downsampl": 2, "dpad": 3, "drastic": 6, "draw": [3, 6, 7], "drawgradientlin": [2, 6], "drawptcol": [2, 6], "drop": [0, 2, 3, 14], "dropbox": 9, "droponeingr": [1, 2], "droponeingrjson": [1, 2], "dropped_posit": 3, "dropped_rot": 3, "dspmesh": [1, 2], "dspsph": [1, 2], "dtype": [2, 6], "due": [2, 6], "duplic": 2, "duplifac": 6, "duplivert": [2, 6], "durat": 6, "dure": [3, 8], "dxf": 2, "dynam": 2, "dynamicsangulardamp": 6, "dynamicsbodi": 6, "dynamicslineardamp": 6, "e": [0, 2, 3, 6, 7, 10, 11, 14], "each": [0, 2, 3, 6, 7, 11, 14], "ed": 2, "edg": [0, 2, 3, 6, 7, 14], "edge_vertices_indic": 6, "edgeindc": 6, "edges_vertices_indic": 6, "edit": [2, 3, 6, 7, 10, 11], "editmod": 6, "editor": [6, 7], "edu": [2, 6], "eex": 2, "effect": 11, "effici": [0, 14], "egd": 6, "either": [2, 3, 6, 7, 12], "el": 6, "element": [2, 8], "elementari": 6, "elev": 6, "eli": [2, 3], "elimin": [3, 8], "els": [2, 6, 7, 8], "emanuel": 2, "emat": 6, "embed": 6, "emploi": 2, "empti": [2, 6, 7], "empty_child": [6, 7], "en": [6, 11], "encapsul": 2, "encapsulating_radiu": 2, "encod": [2, 8], "encourag": 11, "end": [2, 7], "endors": 2, "energi": [6, 7], "eng": 2, "enhanc": 2, "ensur": [8, 11], "ensure_ascii": 8, "enter": 11, "entir": [0, 2, 14], "entri": 9, "enum": [0, 4, 14], "enumer": [3, 4, 5], "env": [2, 3, 8, 11], "enviro": [0, 14], "environ": [1, 8, 10, 11, 13], "envum": 2, "epmv": [2, 6, 7], "epydoc": 2, "equal": 2, "error": 2, "esc": 6, "escap": 8, "essenti": 9, "establish": 4, "etc": [2, 6, 7], "eucledian": 6, "euclideanspac": 6, "euler": [2, 6], "euler_from_matrix": 2, "euler_matrix": 2, "eulertomatrix": [2, 6], "evalu": [0, 14], "even": [0, 2, 3, 6, 7, 11, 14], "event": 2, "everi": [2, 6, 10, 11], "everyth": 2, "ex": 10, "exact": 2, "exampl": [2, 6, 8, 9, 11], "except": [2, 8], "exclud": 2, "execut": [2, 6, 9], "exemplari": 2, "exist": [2, 11], "expand_dim": 6, "expand_object_using_kei": [1, 2], "expand_on": 2, "expect": [0, 2, 6, 14], "experi": 6, "expir": [2, 9], "exponenti": [2, 4], "export": [6, 8], "export_imag": [2, 8], "exportasindexedmesh": [1, 2], "exportcollada": [1, 2], "exportingredi": [1, 2], "exportrecipeingredi": [1, 2], "exporttobd_box": [1, 2], "exporttoreaddi": [1, 2], "exporttotem": [1, 2], "exporttotem_sim": [1, 2], "express": [2, 4], "ext": 2, "extend": 2, "extend_bounding_box_for_compart": [1, 2], "extendgridarrai": [1, 2], "exterior": 2, "extract": [2, 9], "extractmeshcompon": [1, 2], "extrem": [0, 2, 14], "f": [2, 6, 7], "f_dot_product": [1, 2], "f_ray_intersect_polyhedron": [1, 2], "face": [0, 2, 3, 6, 7, 14], "face_vertices_indic": 6, "faceindc": 6, "faceindex": 6, "faceindic": 6, "facemateri": [6, 7], "faces_vertices_indic": 6, "facesselect": [6, 7], "facilit": 2, "factor": 2, "fail": 3, "fals": [0, 2, 3, 4, 5, 6, 7, 8, 9, 14], "far_enough_from_surfac": [2, 3], "fast": [0, 2, 3, 14], "faster": [2, 3], "fbox_bb": 2, "featur": [6, 10], "field": [0, 2, 14], "figur": [2, 6], "figure_path": 2, "file": [0, 2, 3, 4, 6, 7, 8, 9, 10, 11, 14], "file_loc": 2, "file_nam": [2, 7], "file_path": [2, 7], "filenam": [2, 3, 6, 7, 8], "filepath": 6, "filespec": 2, "fill": [0, 2, 3, 14], "fill_in_empty_fiber_data": [1, 9], "fillbb": 2, "fillboxpseudocod": 2, "filltrianglecolor": [2, 6], "filter_surface_pts_to_fill_box": [1, 2], "final": 2, "find": [0, 2, 6, 14], "find_nearest": [1, 2], "findbranch": [1, 2], "findclosestpoint": [2, 6], "findpointscent": [1, 2], "findposit": [1, 2], "finishwithwat": [1, 2], "firebas": [2, 4, 9], "firebase_admin": 11, "firebasehandl": [1, 13], "first": [0, 2, 3, 6, 14], "fit": [2, 6, 7], "fit_view3d": [2, 6], "fix": 2, "fix_coord": 2, "fixnorm": [2, 6], "fixonepath": [1, 2], "fixpath": [1, 2], "flag": 2, "flex": 2, "float": [2, 3, 6, 7, 8], "float64": [2, 6], "flood": [0, 2, 14], "floodfil": [0, 14], "fluoresc": 2, "fn": 6, "fnorm": 6, "focal": [6, 7], "foce": 2, "folder": 2, "follow": [2, 3], "font": 6, "forc": [0, 2, 14], "force_random": 3, "foreach": 6, "forev": 2, "fork": 10, "form": [2, 3, 6], "format": [2, 5, 6, 7, 8], "format_color": [1, 2], "format_rgb_color": [6, 7], "format_vers": 5, "fortran": 3, "forward": 6, "forwhich": [6, 7], "found": [6, 10], "foundat": [2, 6, 7], "four": [2, 6], "fp": 2, "frame": [2, 6], "frameadvanc": [2, 6], "free": [0, 2, 3, 6, 7, 14], "free_point": [2, 3], "freepoint": 2, "fri": 1, "from": [0, 2, 3, 4, 6, 7, 9, 11, 14], "fromvec": [6, 7], "ftype": 2, "full": 11, "full_ingredient_nam": 4, "full_path": 5, "full_path_to_input_recipe_fil": 11, "full_path_to_packing_result": 11, "fulli": 2, "func": 2, "function": [0, 2, 3, 4, 6, 7, 8, 9, 14], "functon": 6, "futur": [6, 7], "g": [0, 2, 6, 7, 14], "ga": 2, "gain": 6, "gamma": 2, "gatherresult": [1, 2], "gauss": [2, 3], "gaussian": [2, 8], "gblob": [2, 4], "gem": 2, "gener": [2, 3, 6, 7, 11], "generalappli": [1, 2], "geom": [2, 6, 7], "geometri": [0, 2, 3, 6, 14], "geometrytool": [1, 13], "geomnam": [2, 3], "get": [0, 1, 2, 3, 6, 7, 8, 13, 14], "get_act": [2, 4], "get_active_data": [2, 4], "get_adjusted_posit": [2, 4], "get_al": [2, 4], "get_all_dist": [1, 2], "get_all_doc": [1, 2], "get_all_ingredi": [2, 5], "get_all_positions_to_check": [2, 3], "get_alternate_posit": [2, 3], "get_alternate_position_p": [2, 3], "get_and_store_v2_object": [2, 5], "get_angl": 2, "get_attributes_to_upd": [1, 2], "get_aws_object_kei": [1, 2], "get_bbox": [1, 2], "get_bounding_box": [1, 9], "get_bounding_box_limit": [1, 2], "get_cache_loc": [1, 2], "get_cent": [1, 2], "get_centroid": [1, 2], "get_closest_ingredi": [1, 2], "get_collada_materi": [1, 2], "get_collection_id_from_path": [1, 2], "get_compart": [2, 3, 4], "get_compartment_object_by_nam": [1, 2], "get_cr": [1, 2], "get_cuttoff_valu": [2, 3], "get_deepest_level": [2, 4], "get_dev_cr": [1, 2], "get_display_data": [6, 7], "get_dist": [1, 2], "get_distance_distribut": 2, "get_distances_and_angl": [1, 2], "get_distances_from_point": [1, 2], "get_doc_by_id": [1, 2], "get_doc_by_nam": [1, 2], "get_doc_by_ref": [1, 2], "get_dpad": [1, 2], "get_encapsulating_radii": [2, 4], "get_eul": [1, 9], "get_euler_from_matrix": [1, 9], "get_euler_from_quat": [1, 9], "get_gauss_weight": [1, 2], "get_ingredi": [2, 4], "get_ingredient_angl": [1, 2], "get_ingredient_by_nam": [1, 2], "get_ingredient_data": [1, 9], "get_ingredient_display_data": [1, 9], "get_ingredient_key_from_object_or_comp_nam": [1, 2], "get_ingredient_radii": [1, 2], "get_ingredients_in_tre": [1, 2], "get_list_of_dim": [1, 2], "get_list_of_free_indic": [2, 3], "get_local_file_loc": [1, 2], "get_max_value_from_distribut": [1, 2], "get_mesh": [1, 2], "get_mesh_data": [1, 9], "get_mesh_filepath_and_extens": [1, 2], "get_mesh_format": [2, 4], "get_mesh_nam": [2, 4], "get_mesh_path": [2, 4], "get_midpoint": [1, 2], "get_min_max_radiu": [2, 4], "get_min_value_from_distribut": [1, 2], "get_minimum_expected_distance_from_recip": [1, 2], "get_module_vers": [1, 13], "get_new_distance_valu": [2, 3], "get_new_distances_and_inside_point": [2, 3], "get_new_jitter_location_and_rot": [2, 3], "get_new_po": [2, 3], "get_nois": [2, 6], "get_norm": [1, 2], "get_normal_for_point": [1, 2], "get_normalized_valu": [1, 2], "get_nspher": [1, 2], "get_number_of_ingredients_pack": [1, 2], "get_obj_dict": [1, 2], "get_object": [1, 2], "get_packed_minimum_dist": [1, 2], "get_paired_kei": [1, 2], "get_partn": [2, 3], "get_partner_by_ingr_nam": [2, 4], "get_partner_pair_dict": [1, 2], "get_path_from_ref": [1, 2], "get_pdb_path": [2, 4], "get_point": [2, 4], "get_posit": [2, 4], "get_positions_for_ingredi": [2, 4], "get_positions_per_ingredi": [1, 9], "get_radii": [2, 4], "get_radiu": [2, 3], "get_rb_model": [1, 2, 3], "get_rbnod": [2, 3], "get_recipe_metadata": [1, 9], "get_rectangle_cercle_area": [1, 2], "get_reference_data": [1, 2], "get_reference_in_obj": [1, 2], "get_reflected_point": [2, 3], "get_represent": [2, 5], "get_rot": [2, 3], "get_rotations_for_ingredi": [2, 4], "get_scaled_distances_between_surfac": [1, 2], "get_seed_list": [1, 2], "get_signed_dist": [2, 3], "get_size_of_bounding_box": [1, 2], "get_smallest_radiu": [1, 2], "get_staging_cr": [1, 2], "get_usernam": [1, 2], "get_valu": [1, 2], "get_value_from_distribut": [1, 2], "get_weights_by_dist": [2, 3], "geta": [2, 6], "getabsposuntilroot": [6, 7], "getact": [1, 2], "getallmateri": [2, 6, 7], "getallposrot": [1, 2], "getangleaxi": [2, 6], "getaxisrot": [2, 3], "getbiasedrot": [2, 3], "getbigbb": [2, 3], "getbinaryweight": [1, 2], "getboundari": [1, 2], "getboundingbox": [1, 2], "getboxs": [2, 6], "getcent": [1, 2, 6], "getchild": [6, 7], "getclosestfreegridpoint": [1, 2], "getclosestgridpoint": [1, 2], "getcolladamateri": [6, 7], "getcornerpointcub": [2, 6, 7], "getcurrentscen": [2, 6, 7], "getcurrentscenenam": [2, 6], "getcurrentselect": [2, 6, 7], "getdata": [2, 3], "getdiagon": [1, 2], "getdihedr": [2, 3], "getdist": [1, 2], "getencapsulatingradiu": [2, 3], "getfac": [2, 6, 7], "getfaceedg": [2, 6], "getfacenorm": [1, 2], "getfacenormalsarea": [2, 6], "getfacesfromv": [2, 6], "getfacesnfromv": [1, 2], "getfirstpoint": [2, 3], "getforwweight": [1, 2], "gethaltonuniqu": [1, 2], "gethclass": [2, 6], "gethelperclass": [2, 6], "getijk": [1, 2], "getimag": [2, 6], "getindex": [1, 2], "getindexdata": [1, 2], "getinfo": 3, "getingredientinstancepo": [1, 2], "getingredientsinbox": [2, 3], "getingrfromnameinrecip": [1, 2], "getinterpolatednorm": [1, 2], "getinterpolatedspher": [2, 3], "getjtransrot": [2, 3], "getjtransrot_r": [2, 3], "getlay": [2, 6], "getlinearweight": [1, 2], "getlistcompfrommask": [2, 3], "getmasterinst": [2, 6], "getmateri": [2, 6, 7], "getmaterialnam": [6, 7], "getmaterialobject": [6, 7], "getmaterialproperti": [2, 6], "getmaxjitt": [2, 3], "getmaxweight": [1, 2], "getmesh": [1, 2, 3, 6, 7], "getmeshedg": [2, 6, 7], "getmeshfac": [2, 6, 7], "getmeshnormal": [2, 6, 7], "getmeshvertic": [2, 6, 7], "getminmaxproteins": [1, 2], "getminweight": [1, 2], "getnam": [2, 6, 7], "getnbgridpoint": [1, 2], "getnextpoint": [2, 3], "getnextptindcyl": [2, 3], "getnorm": [6, 7], "getnormedvector": [2, 3], "getnormedvectoron": [2, 3], "getnormedvectoru": [2, 3], "getobjecnam": [6, 7], "getobject": [2, 6, 7], "getobjectnam": [2, 6, 7], "getold": [1, 2], "getoneingr": [1, 2], "getoneingrjson": [1, 2], "getord": [2, 6], "getparticl": [2, 6], "getparticulesposit": [2, 6], "getpointfrom3d": [1, 2], "getpointsincub": [1, 2], "getpointsincubefillbb": [1, 2], "getpointsinspher": [1, 2], "getpointtodrop": [1, 2], "getposat": [1, 2], "getpositionperidoc": [1, 2], "getposlin": [1, 2], "getposuntilroot": [2, 6], "getproperti": [2, 6], "getpropertyobject": [2, 6], "getradiu": [1, 2], "getramp": [2, 6], "getrndweight": [1, 2], "getrottransrb": [1, 2], "getscal": [1, 2, 6], "getsiz": [2, 6], "getsizexyz": [1, 2], "getsortedactiveingredi": [1, 2], "getstringvalueopt": [1, 2], "getsubweight": [1, 2, 3], "getsurfaceinnerpoint": [1, 2], "getsurfaceinnerpoints_kevin": [1, 2], "getsurfaceinnerpoints_sdf": [1, 2], "getsurfaceinnerpoints_sdf_interpol": [1, 2], "getsurfacepoint": [1, 2], "gettotalnbobject": [1, 2], "gettransform": [6, 7], "gettransl": [2, 6, 7], "gettubeproperti": [2, 6], "gettubepropertiesmatrix": [2, 6], "gettyp": [6, 7], "getuv": [2, 6], "getv3": [2, 3], "getvertexnorm": [1, 2], "getvis": [2, 6, 7], "getvnfromf": [1, 2], "gh": 10, "git": [10, 11, 12], "git_upi": [6, 7], "github": [2, 4, 9, 10, 11, 12], "githubusercont": [4, 7], "give": [2, 6, 7], "given": [2, 3, 6, 7, 10], "gj": [0, 14], "gl": [6, 7], "glmultmatrixd": 2, "glob_str": 2, "global": [2, 6, 7], "globalc": 2, "glowingpython": 2, "gnu": [2, 6, 7], "go": [2, 6], "gohlk": [2, 6], "goldman": 2, "good": 2, "googl": 11, "gov": 2, "gpl": [6, 7], "grab": [1, 2], "grabresult": [1, 2], "grad_dict": 2, "grad_nam": 2, "gradient": [1, 3, 4, 6, 13], "gradient_data": [1, 2], "gradient_list_to_dict": [1, 2], "gradient_nam": 4, "gradient_opt": 4, "gradientdata": [2, 4], "gradientdoc": [1, 2], "gradientmod": [2, 4], "graham": 2, "graph": 2, "graphic": [1, 13], "grd": 2, "grdaient": 2, "grdpo": 2, "greatest": 2, "greatli": 10, "grid": [0, 1, 3, 8, 13, 14], "grid_distance_valu": 3, "grid_file_nam": 2, "grid_file_path": 2, "grid_point_compartment_id": 7, "grid_point_dist": 3, "grid_point_index": [2, 3], "grid_point_loc": 3, "grid_point_posit": 7, "grid_pt_radiu": 7, "gridcent": 6, "gridfilenam": 2, "gridfileout": 2, "gridpoint": [1, 2], "gridpointscoord": 3, "gridspac": 2, "gridstep": 6, "gridvalu": 6, "grisiz": 6, "group": 3, "group_nam": 6, "grouptyp": 2, "grow": [0, 1, 2, 4, 14], "grow_plac": [2, 3], "growingredi": [2, 3], "guarante": 8, "guess": 6, "guid": [2, 11, 12], "h": 2, "ha": [0, 2, 3, 14], "hack": [2, 3], "halton": [1, 2], "halton2": [1, 2], "halton3": [1, 2], "halton_sequ": [1, 2], "haltongrid": [1, 2], "haltonsequ": [1, 2], "haltonterm": [1, 2], "ham": 3, "hand": [2, 6], "handl": [2, 6, 7, 10], "handle_expired_result": [1, 2], "handle_real_time_visu": [2, 3], "handler": [2, 4], "hartlei": 2, "has_mesh": [2, 3, 4], "has_pdb": [2, 3, 4], "have": [2, 6, 7, 12], "hclass": 6, "he": 6, "head": [6, 7, 11], "headcoord": 6, "header": 2, "height": 6, "help": [2, 10], "helper": [2, 3], "hemisph": 6, "here": [2, 3, 10], "hexa": 6, "hexahedron": [2, 6], "hexatil": [0, 14], "hextorgb": [2, 6], "hi": [2, 6, 7], "hide": [6, 7], "hideingrprimit": [1, 2], "hierarchi": [2, 6], "high": [0, 2, 3, 14], "hip": 2, "histo": 2, "histogram": [1, 2], "histovol": [2, 3], "histovolum": 2, "hold": 2, "holder": 2, "hollasch": 2, "hollow": [2, 8], "home": 6, "homogen": [2, 3], "hope": [2, 6, 7], "horn": 2, "host": [0, 2, 6, 7, 14], "hostap": 6, "hostapp": [2, 6, 7], "hostdo": 6, "hostedg": 6, "hostfac": [6, 7], "hosthelp": [1, 2], "hostmateri": [6, 7], "hostmatric": [6, 7], "hostmesh": [6, 7], "hostobj": [6, 7], "hostobjec": 3, "hostobject": [2, 6, 7], "hostscen": 6, "hosttyp": [6, 7], "how": [0, 3, 6, 10, 14], "howev": 2, "hr": 6, "htm": [2, 6], "html": [2, 6, 7, 10, 11], "http": [2, 3, 4, 6, 7, 11, 12], "hybrid": 2, "i": [0, 2, 3, 6, 7, 8, 9, 10, 11, 12, 14], "ico": 6, "icosahedron": [2, 6], "id": [0, 2, 3, 9, 14], "idarrai": 2, "ideal": 2, "ident": [2, 6], "identity_matrix": 2, "ie": [0, 2, 6, 7, 14], "ii": 2, "iii": 2, "ijk": 2, "ijktoindex": [1, 2], "ijktoxyz": [1, 2], "ik": [2, 6], "imag": [2, 6, 8], "image_data": [2, 3], "image_export_opt": 2, "image_s": [2, 3], "image_writ": 2, "imagewrit": [1, 2], "imdraw": 6, "img": 6, "implement": [2, 6, 8], "impli": [2, 6, 7], "import": [2, 6], "improv": 3, "inbox": [1, 2], "inc": [1, 2], "incident": 2, "includ": [0, 2, 10, 11, 14], "includeingredientrecip": [1, 2], "includeingrrecip": [1, 2], "incom": [3, 8], "incoming_nam": 7, "increas": 2, "increment": 6, "increment_stat": [6, 7], "increment_static_object": [6, 7], "increment_tim": [6, 7], "ind": 2, "indent": [2, 8], "independ": 2, "index": [2, 3, 4, 6, 9, 11], "indexedpolgonstotripoint": [2, 6], "indexedpolygon": [3, 6, 7], "indexpolygon": 6, "indic": [2, 6], "indicesinsid": 2, "indirect": 2, "individu": 4, "indpolfac": 6, "indpolvert": 6, "infin": 8, "infinit": [2, 8], "influenc": 2, "influencerad": 3, "info": [2, 3, 4], "inform": [2, 11], "ing": 2, "ingr": [2, 3, 8], "ingr1nam": 2, "ingr2nam": 2, "ingr_format": 8, "ingr_result": 2, "ingr_typ": 7, "ingrcompnum": 2, "ingrdic": 2, "ingred": 2, "ingredi": [1, 2, 7, 9], "ingredient_angle_dict": 2, "ingredient_compare0": [1, 2], "ingredient_compare1": [1, 2], "ingredient_compare2": [1, 2], "ingredient_data": [5, 9], "ingredient_info": 3, "ingredient_kei": [2, 5], "ingredient_key_dict": 2, "ingredient_nam": [2, 4, 9], "ingredient_occurence_dict": 2, "ingredient_posit": 2, "ingredient_position_dict": 2, "ingredient_radii": 2, "ingredient_typ": [1, 2], "ingredientinstancedrop": [2, 3], "ingrgroup": 2, "ingrid": [1, 2], "ingrjsonnod": [1, 2, 8], "ingrnam": 2, "ingrobj": 2, "ingrpythonnod": [1, 2], "inherit": [2, 6], "init_scene_with_object": [6, 7], "initi": [2, 9], "initialize_mesh": [2, 3], "initialize_shap": [1, 2], "inner": 2, "inner_grid_method": [2, 5], "inner_mesh": 2, "inner_mesh_nam": 2, "inod": 2, "input": [0, 2, 3, 6, 14], "input_dict": 2, "input_file_loc": 2, "input_file_path": 5, "insert": [2, 6, 8], "insertnod": [1, 2], "insid": [0, 2, 6, 14], "inside_point": 3, "insidepoint": 2, "inst": 9, "instal": [2, 10, 11], "instanc": [2, 4, 6, 7], "instance_id": [2, 7], "instance_nod": 6, "instance_sph": [6, 7], "instancepolygon": [6, 7], "instancescylind": [6, 7], "instancesspher": [6, 7], "instancestocollada": [2, 6], "instanci": 6, "instanti": 2, "instead": [0, 2, 6, 7, 14], "instruct": 11, "int": [2, 6, 7, 8], "intact": 2, "integ": [6, 8], "integr": 2, "intel": 2, "intens": [6, 7], "interest": [2, 3], "interfac": [2, 4], "interface_object": [1, 2], "interior": [2, 3], "intermedi": 6, "intern": 2, "interpol": [2, 6], "interpret": [2, 6, 7], "interrupt": 2, "intersect": 2, "interv": [2, 3], "inv": 2, "invalid": 6, "invert": [2, 4, 6], "invert_opt": 4, "invertopt": [2, 4], "involv": 2, "io": 11, "io_ingr": 2, "ioingredienttool": [1, 2, 8], "ioutil": [1, 13], "irvin": 2, "is_attractor": 3, "is_compart": 4, "is_db_dict": [1, 2], "is_fib": [6, 7], "is_firebase_obj": [1, 2], "is_full_url": [1, 2], "is_kei": [1, 2], "is_matrix": [1, 9], "is_memb": [2, 4], "is_nested_list": [1, 2], "is_obj": [1, 2], "is_partn": [2, 4], "is_point_in_correct_region": [2, 3], "is_point_inside_bb": [1, 2], "is_point_inside_mesh": [1, 2], "is_refer": [1, 2], "is_remote_path": [1, 2], "is_s3_url": [1, 2], "is_same_transform": [2, 6], "is_stat": 7, "is_two_d": [1, 2], "is_url_valid": [1, 2], "isindexedpolyon": [6, 7], "isn": [0, 3, 14], "isph1": [6, 7], "ispolyhedron": 2, "isspher": [2, 6], "item": [2, 4, 8], "item_separ": 8, "iter": [2, 8], "its": [2, 6], "itzhack": 2, "iv": 2, "ix": 2, "j": [2, 6, 7], "jame": 2, "jan": 2, "javascript": 8, "jitter": [0, 2, 3, 5, 14], "jitter_attempt": 3, "jitter_plac": [2, 3], "jitterposit": [2, 3], "jmp": 2, "johnson": 2, "join": [6, 7], "joinsobject": [2, 6], "jot": 2, "json": [0, 2, 8, 9, 11, 14], "jsonencod": 8, "jtran": 3, "jul": 1, "juli": 2, "jun": 2, "just": [2, 3, 11], "jwa3": 2, "jy": 2, "j\u00f6bstl": 2, "k": [2, 6, 7], "kabsch": 2, "karnei": 2, "kaufmann": 2, "keep": 2, "kei": [2, 6, 8, 11], "ken": 2, "kevin": [0, 2, 14], "key1": 2, "key2": 2, "key_from_pairwise_distance_dict": 2, "key_or_dict": 2, "key_separ": 8, "key_to_dict_map": [1, 2], "keyfram": 6, "keyword": [2, 6, 7], "known": [0, 2, 14], "knurbscurv": 7, "kw": [2, 3, 6, 7], "kwarg": [2, 3], "kwd": [2, 8], "kz": 2, "l": [2, 6, 7], "la": [0, 14], "lab": 2, "label": [2, 6, 7], "laboratori": 2, "lacunar": 6, "lai": 2, "larg": 2, "larger": [2, 3], "largest": [0, 2, 14], "last": 2, "later": [2, 6, 7], "latest": 11, "latitud": 6, "latter": 6, "launch": 11, "layer": 6, "ldsequenc": [1, 13], "leakag": [0, 2, 14], "leakproof": [0, 2, 14], "leas": 2, "leav": 2, "left": [0, 2, 3, 6, 7, 14], "left_hand": 9, "leftbound": 2, "lefthand": 2, "len": 2, "length": [3, 6, 7], "less": 2, "let": 8, "level": [0, 1, 3, 6, 8, 14], "lexic": 2, "lexsort": 2, "lfd": [2, 6], "liabil": 2, "liabl": 2, "librari": 2, "licens": [2, 6, 7, 11], "light": [6, 7], "light1": [6, 7], "light_opt": [2, 6], "like": [2, 8], "limit": 2, "linalg": [2, 6], "line": [2, 9], "linear": [2, 4, 6, 7], "link": 2, "linktraj": [1, 2], "lint": [10, 11], "linux": 6, "list": [2, 3, 6, 7, 8], "list_of_pt": 2, "list_valu": [2, 3], "liste_nod": 3, "liste_object": 6, "listeclosest": 3, "listeind": 6, "listenam": 6, "listeobj": 6, "listeobject": [6, 7], "listept": 6, "listeptcurv": 3, "listeptlinear": 3, "lister": 6, "listingredi": 2, "listobj": 7, "listorganel": 2, "listpt": 2, "littl": 10, "live_pack": 5, "load_asjson": [1, 2], "load_astxt": [1, 2], "load_fil": [1, 2], "load_from_grid_fil": 5, "load_json": [1, 2], "load_jsonstr": [1, 2], "load_mixedasjson": [1, 2], "load_object_from_pickl": [1, 2], "loader": [1, 2, 9], "loadfreepoint": [1, 2], "loadjson": [1, 2], "loadresult": [1, 2], "local": [2, 6, 7, 9, 10], "local_data": 2, "local_file_path": 2, "locat": [0, 2, 3, 6, 7, 14], "loevel": 6, "log": 2, "logic": 2, "long": 6, "longitud": 6, "look": [0, 2, 6, 14], "lookat": 6, "lookforneighbour": [2, 3], "lookup_dict": 2, "loop": 2, "loopthroughingr": [1, 2], "loss": 2, "lot": 2, "low": [0, 2, 3, 14], "lower": 3, "lowercirclefunct": [1, 2], "lowerrectanglefunct": [1, 2], "ludo": 2, "ludov": 2, "lue": 2, "m": [0, 2, 6, 7, 10, 14], "m0": 2, "m00": 6, "m01": 6, "m02": 6, "m1": 2, "m10": 6, "m11": 6, "m12": 6, "m2": 2, "m20": 6, "m21": 6, "m22": 6, "m2r": 10, "made": 2, "maerial": [6, 7], "mai": [2, 6], "main": [1, 2, 6, 9, 11, 12], "main_contain": 9, "mainli": 2, "maintain": 10, "mainten": 2, "major": [2, 3, 10], "make": [2, 6, 10, 11], "make_and_show_heatmap": [1, 2], "make_directory_if_need": [1, 2], "make_grid_heatmap": [1, 2], "makeingredi": [1, 2], "makeingredientfromjson": [1, 2], "makeingrmap": [1, 2], "makemarchingcub": [1, 2], "makenurbsphere1": 6, "maketextur": [2, 6], "manag": [2, 3], "mani": [0, 3, 14], "map": [2, 6], "map_color": [2, 6], "mar": 2, "march": 2, "marg": [2, 3, 6], "marge_diedr": 3, "marge_in": 3, "marge_out": 3, "markdown": 2, "marrai": 2, "mask": [0, 2, 3, 14], "mask_sphere_point": [2, 3], "mask_sphere_points_angl": [2, 3], "mask_sphere_points_boundari": [2, 3], "mask_sphere_points_dihedr": [2, 3], "mask_sphere_points_ingredi": [2, 3], "mask_sphere_points_vector": [2, 3], "mass": [2, 6], "massclamp": 6, "master": [2, 4, 7], "master_grid_posit": 2, "mat": [3, 6, 7], "mat1": 6, "mat2": 6, "mat_to_quat": 3, "match": 2, "matdic": 6, "mater": 6, "materi": [2, 6, 7], "math": [2, 6], "matnam": [6, 7], "matric": [2, 6, 7], "matrix": [2, 3, 6, 7], "matrixtofacesmesh": [2, 6], "matrixtovnmesh": [2, 6], "max": [2, 3, 4, 6], "max_jitt": 3, "max_radiu": 3, "max_valu": 6, "maxi": [2, 6], "maximum": [2, 6], "maxl": 2, "maxx": 2, "maxz": 2, "maya": [2, 6, 7], "mb": 2, "md": [2, 11], "mean": [2, 3], "meant": 2, "measur": [2, 6], "measure_dist": [2, 6], "meganriel": 9, "mehan": 9, "member": [2, 8], "memori": 2, "merchant": [2, 6, 7], "merg": [2, 6, 11], "merge_dct": 2, "merge_place_result": [2, 3], "mesh": [0, 2, 3, 4, 5, 6, 7, 14], "mesh_nam": 2, "mesh_stor": [2, 3], "meshfil": 3, "meshobject": 3, "meshspher": 7, "meshstor": [1, 13], "mesoscal": 2, "mesoscop": [4, 7, 11, 12], "messag": [6, 7], "mesur": 2, "met": 2, "meta_enum": [1, 2], "metab": 6, "metabal": [2, 6], "metadata": [2, 9], "metaenum": [2, 3, 4, 5], "meteri": 6, "method": [0, 2, 3, 6, 7, 8, 12, 14], "michel": 2, "midpoint": [2, 6], "might": 2, "migrate_ingredi": [2, 5], "migrate_v1_to_v2": [1, 2], "migrate_v2_to_v2_1": [1, 2], "min": [2, 3, 4, 6], "min_radiu": 2, "min_valu": 6, "mingr": 2, "mini": [2, 6], "minim": 6, "minimum": 2, "minor": [2, 10], "minx": 2, "minz": 2, "mira": 2, "miss": 2, "mit": 11, "mix": 2, "mod": 2, "mode": [2, 4, 6, 10, 11], "mode_nam": 4, "mode_set": 4, "mode_settings_dict": 4, "model": [2, 6], "model_typ": 3, "modeltyp": 3, "modeopt": [2, 4], "modif": [2, 6, 7], "modifi": [2, 6, 7], "modifierfor": [6, 7], "modul": [11, 13], "mol": 2, "molar": [2, 3], "molb": 2, "molbiol": 2, "molbtrajectori": [1, 2], "mole": 2, "molecul": [2, 6], "molecular": [2, 11], "mon": 2, "more": [2, 6, 7], "morgan": 2, "most": [6, 8, 11, 12], "mostafa": 2, "mostli": 2, "move": [0, 2, 3, 6, 7, 14], "move_object": [6, 7], "moverbnod": [1, 2], "msh": 2, "much": 3, "multi_bound": 3, "multi_cylind": [1, 2, 4], "multi_spher": [1, 2, 4], "multicylind": [0, 14], "multicylindersingr": [2, 3], "multipl": 2, "multisdf": 2, "multispher": [0, 3, 14], "multisphereingr": [2, 3], "must": [2, 3], "mutat": 2, "mx": 3, "mycmp": 2, "myspher": [6, 7], "myspinningspher": 6, "n": [2, 3, 6, 7, 11], "n_pick": 2, "na": 2, "name": [2, 3, 4, 5, 6, 7, 8], "namespac": 9, "nan": 8, "nasa": 6, "natur": 11, "navig": 11, "nbasi": 6, "nbfreepoint": [2, 3], "nbgridpoint": 2, "nbingredi": 2, "nbinstanc": 2, "nbr": 2, "ncbi": 2, "ndarrai": [2, 6, 8], "near_by_ingredi": 3, "nearbi": [0, 2, 14], "nearest": 2, "necessari": [0, 2, 6, 11, 14], "need": [2, 3, 6, 7], "neg": [0, 3, 6, 8, 14], "neglig": 2, "neighbor": [0, 14], "neither": 2, "nest": 2, "net": [2, 3], "never": [0, 14], "new": [2, 3, 6, 7, 10, 11], "new_dist": 2, "new_dist_point": 3, "new_inside_point": 3, "new_item_ref": 2, "new_object": 4, "new_point": 7, "new_posit": [2, 3], "new_result": 3, "newdistpoint": 2, "newempti": [2, 6, 7], "newinst": [2, 6, 7], "newli": 2, "newlin": 8, "newmesh": [2, 7], "newpath": 2, "newpo": 6, "newpt": 3, "next": 2, "ni": 7, "nih": 2, "nlm": 2, "nm_analysis_c_rapid": 9, "nm_analysis_figurea": [0, 14], "nm_analysis_figurea1": [0, 14], "nm_analysis_figureb1": 11, "nm_analysis_figurec1": 9, "node": [2, 7], "node1": 3, "node2": 3, "nodetogeom": [6, 7], "nodexml": 7, "non": [3, 6, 8], "none": [2, 3, 4, 5, 6, 7, 8, 9], "nonzero": 2, "nor": 2, "norga": 2, "norm": [1, 2, 6], "normal": [1, 2, 3, 6, 7], "normal_arrai": [1, 2, 6], "normalize_v3": [1, 2, 6], "normalize_vector": [1, 2], "normalizedprior": 2, "note": [2, 3, 6], "notic": 2, "novo": 2, "now": [2, 3, 10], "np": [2, 8], "np_array_of_pt": 2, "np_check_collis": [2, 3], "nr": 2, "ntype": 6, "null": [0, 6, 7, 14], "null1": [6, 7], "null2": [6, 7], "num": 2, "number": [0, 2, 3, 6, 14], "number_of_pack": 5, "number_of_point": 2, "numberingredientstopack": 2, "numer": 6, "numpi": [2, 6, 7, 8], "numpyarrayencod": [2, 8], "o": [2, 6, 7, 8, 11], "obj": [2, 4, 6, 7, 8], "obj1": 6, "obj2": 6, "obj_data": 2, "obj_dict": 2, "obj_id": 2, "obj_nam": 2, "objdata": 2, "objec": [6, 7], "object": [0, 2, 3, 5, 7, 8, 14], "object_data": [2, 5], "object_info": 2, "object_kei": [2, 5], "object_nam": [2, 3], "objectdoc": [1, 2], "objects_dict": 5, "objects_to_path_map": 2, "objectsselect": [2, 6, 7], "obtain": [6, 11], "ocata": 6, "occur": 2, "octahedron": [2, 6], "octav": 6, "octnod": [1, 2], "octre": [1, 13], "odd": 2, "off": [2, 6, 7], "off_grid_po": 2, "off_grid_surface_point": 2, "off_grid_surface_pt": 2, "offset": [1, 3, 6, 13], "ol": 12, "old_gradients_dict": 5, "old_ingredi": 5, "old_ingredient_data": 5, "old_recip": 5, "olson": 2, "omit": 3, "omni": [6, 7], "onam": [6, 7], "onc": [2, 3, 12], "one": [2, 3, 6, 7], "one_spher": 11, "onecolladageom": [6, 7], "onecylind": [6, 7], "onejitt": [2, 3], "onemetabal": [2, 6], "oneprevingredi": [1, 2], "ones": 2, "onli": [0, 2, 3, 6, 7, 8, 14], "opac": 2, "open": 2, "open_in_simularium": [6, 7], "open_results_in_brows": [5, 7], "opengl": [2, 3, 6], "openvdb": 2, "oper": [2, 9], "opposit": [0, 3, 14], "opt": 2, "optim": 2, "option": [2, 3, 4, 6, 7], "optionli": 6, "order": [0, 2, 3, 6, 7, 14], "ordered_pack": 5, "org": [2, 6, 7, 11], "orga": 2, "organ": 2, "organam": 2, "organel": [2, 3], "orgaresult": 2, "orient": [2, 3, 6], "orient_bias_rang": 3, "origin": [0, 2, 3, 10, 14], "ortho": 6, "orthogon": 2, "orthogonal": [6, 7], "otat": 2, "other": [0, 2, 10, 11, 14], "otherwis": [2, 8], "our": 2, "out": [2, 3, 5, 6, 8, 11], "out_base_fold": 5, "outer": 2, "outer_mesh": 2, "outer_mesh_nam": 2, "output": [2, 3, 5, 8], "output_image_loc": 2, "output_path": [2, 8, 9, 11], "outputsimularium": [1, 13], "outsid": [0, 2, 6, 14], "overal": [2, 3], "overrid": [0, 14], "overwrit": [0, 6, 7, 14], "overwrite_distance_funct": 3, "overwrite_place_method": 5, "overwriten": 6, "own": [6, 7], "owner": [2, 11], "p": [2, 6, 11], "p1": [2, 3, 6], "p2": [2, 3, 6], "pack": [0, 1, 2, 3, 4, 5, 13, 14], "pack_at_grid_pt_loc": [2, 3], "pack_grid": [1, 2], "pack_one_se": [1, 2], "packag": [0, 10, 11, 13, 14], "packed_object": [1, 2], "packed_posit": 3, "packed_rot": 3, "packedobject": [2, 4], "packignprior": 3, "packing_config_data": 2, "packing_loc": 3, "packing_mod": 3, "packing_opt": 8, "packing_result_path": 5, "packing_results_path": [2, 9], "packingradiu": [0, 14], "packingweight": [0, 14], "pad": 2, "pade": 2, "page": [6, 11], "pair": 2, "pairwis": 2, "pairwise_distance_dict": 2, "parallel": 5, "param": [2, 3, 6, 7, 9], "paramet": [0, 2, 6, 8, 14], "parent": [2, 6, 7], "parent_object": 6, "parentcent": [6, 7], "parentnod": 2, "parentxml": 7, "parentxmlnod": 7, "pariti": 2, "parrallelpip": 3, "pars": [1, 2, 6], "parse_one_mol": [1, 2], "parse_s3_uri": [1, 2], "part": [2, 3, 6, 7, 9], "particl": [2, 6], "particul": 6, "particular": [2, 6, 7], "partner": [0, 1, 2, 3, 14], "pass": [2, 3, 6, 7, 8, 10], "patch": 10, "path": [2, 5, 6, 7, 9], "pathdeform": [2, 6, 7], "paulbourk": 2, "pb": [6, 7], "pdb": [1, 3, 4, 13], "pdf": 2, "per": [0, 2, 3, 6, 7, 14], "perform": [0, 2, 9, 14], "period": [0, 2, 14], "permiss": 2, "permit": [2, 6], "persp": [2, 6, 7], "perspect": [2, 6, 7], "perturb_axis_amplitud": 3, "perturbaxi": [2, 3], "pervertex": [6, 7], "pervertic": 6, "pgridspac": 2, "phi": 6, "phong": 6, "php": 2, "physic": 6, "pi": [0, 6, 14], "pick": [0, 2, 4, 14], "pick_altern": [2, 3], "pick_mod": 4, "pick_partner_grid_index": [2, 3], "pick_random_altern": [2, 3], "pickalternatehalton": [2, 3], "pickhalton": [2, 3], "pickingredi": [1, 2], "pickl": 2, "pickle_file_object": 2, "pickmod": [2, 4], "pickpoint": [1, 2], "pickrandomspher": [2, 3], "pil": 6, "pip": [10, 11, 12], "piror": 2, "place": [0, 2, 3, 8, 14], "place_altern": [2, 3], "place_alternate_p": [2, 3], "place_method": [2, 3, 5], "place_object": [6, 7], "placed_partn": 3, "placer": 2, "plai": 6, "plane": [2, 6, 7], "platon": [2, 6], "pleas": 11, "plot": [1, 2, 6], "plot_distance_distribut": [1, 2], "plot_figur": 2, "plot_occurence_distribut": [1, 2], "plot_position_distribut": [1, 2], "plot_position_distribution_tot": [1, 2], "plotdata": [6, 7], "plotly_result": [1, 13], "plotlyanalysi": [1, 2], "plu": 3, "plug": 2, "ply": 2, "pmc": 2, "pmc3910158": 2, "png": 2, "po": [2, 3, 6, 7], "point": [0, 2, 3, 6, 7, 14], "point2": 6, "point_is_avail": [2, 3], "point_po": 2, "pointcloud": [2, 6], "pointcloudobject": [2, 6], "poli": [2, 3, 6, 7], "polygon": [2, 3, 6, 7], "polygone1": [6, 7], "polyhedr": 2, "polyhedron": [0, 2, 14], "polylin": [6, 7], "posit": [2, 3, 4, 6, 7], "position2": 3, "position_list": 2, "positions2": 3, "positions_to_adjust": 3, "possibl": [2, 10], "post_and_open_fil": [6, 7], "potenti": [0, 14], "pov": 2, "power": [2, 4], "pp": 2, "pquadranglepointlist": 2, "pquadranglepointposit": 2, "pr": 11, "prayendpo": 2, "praystartpo": 2, "pre": 11, "precis": 2, "precomput": 2, "prefer": 12, "prep_data_for_db": [1, 2], "prep_db_doc_for_download": [1, 2], "prep_molecules_for_sav": [1, 2], "prep_recipe_data": 2, "prepar": 2, "prepare_altern": [2, 3], "prepare_alternates_proba": [2, 3], "prepare_buildgrid_box": [1, 2], "preparedynam": [1, 2], "prepareingredi": [1, 2], "preparemast": [1, 2], "presign": 2, "press": [2, 6], "pretti": 8, "prevent": 8, "previous": 2, "previouspoint": 3, "prevpoint": 3, "prim": [0, 14], "primit": [0, 14], "princip": 3, "principal_vector": 3, "print": [2, 6, 7, 8], "printfillinfo": [1, 2], "printingredi": [1, 2], "printoneingr": [1, 2], "prior": 2, "priorit": [0, 14], "prioriti": [2, 3], "privat": 11, "probability_bind": 4, "probabl": 2, "process": [2, 12], "process_ingredients_in_recip": [1, 2], "process_one_ingredi": [1, 9], "procur": 2, "produc": [2, 6, 7], "product": [2, 6], "profit": 2, "progress": [2, 6, 7], "progressbar": [2, 6, 7], "project": [0, 2, 10, 11, 14], "projection_axi": 8, "promot": 2, "prompt": 11, "properti": [2, 3, 6], "protein": [0, 2, 14], "provid": [0, 2, 3, 6, 7, 14], "proxycol": 6, "proxyobject": [6, 7], "pseudo": 2, "psf": 8, "psf_paramet": 8, "pt": [2, 3, 6], "pt1": [2, 3, 6], "pt2": [2, 3, 6], "pt3d": 2, "pt_ind": 3, "pt_index": [3, 4], "pti": 2, "ptid": 3, "ptind": [2, 3], "ptruncatetoseg": 2, "ptsinspher": 3, "pub": 6, "public": [2, 6, 7, 12], "publicli": [0, 14], "publish": [2, 6, 7, 10], "pull": [10, 11], "purpos": [2, 6, 7], "push": [2, 10, 11], "put": [6, 7], "pv": 3, "px": [6, 7], "py": [2, 3, 6, 7, 11, 12], "pyembre": 2, "pypi": [10, 11], "pyrai": [0, 14], "python": [2, 3, 6, 7, 10, 11, 12], "pz": [6, 7], "q": 2, "quad": 6, "qualiti": [6, 7], "quaternion": [2, 8], "quaternion_about_axi": 2, "quaternion_matrix": [1, 2], "quaternion_multipli": 2, "quatut": 2, "queri": 2, "question": 2, "qx": 2, "qy": 2, "qz": 2, "r": [2, 3, 6, 7, 11], "r0": 6, "r1": 6, "rad": [2, 6], "radc": 3, "radial": [2, 4], "radian": [2, 3, 6], "radii": [2, 3, 7], "radiu": [0, 2, 3, 4, 6, 7, 14], "rai": [1, 13], "rais": [6, 8], "ramp": 2, "ramp_color1": 2, "ramp_color2": 2, "ramp_color3": 2, "rand": [2, 6], "random": [0, 1, 2, 3, 6, 14], "random_quaternion": [1, 2], "random_rotation_matrix": [1, 2], "random_vector": 2, "randomis": 6, "randomize_rot": [2, 3], "randomize_transl": [2, 3], "randomli": [0, 2, 14], "randomness_se": 5, "randompartn": [0, 14], "randomrot": [1, 13], "randpoint_onspher": [2, 6], "rang": [2, 6], "rare": 11, "rather": 2, "ratio": 3, "raw": [2, 4, 7, 10], "ray_intersect_polygon": [1, 2], "ray_intersect_polyhedron": [1, 2], "raycast": [0, 2, 6, 7, 14], "raycast_test": [6, 7], "raytrac": [0, 2, 5, 14], "rb": [2, 3], "rdf": 2, "rdic": 2, "re": [2, 6, 7, 10], "reach": [2, 6, 11], "read": [1, 2, 6, 10], "read_as_3d_arrai": [1, 2], "read_as_coord_arrai": [1, 2], "read_dict_from_glob_fil": [1, 2], "read_head": [1, 2], "read_json_fil": [2, 5], "read_mesh_fil": [1, 2], "read_text_fil": [1, 2], "readarraysfromfil": [1, 2], "readgridfromfil": [1, 2], "readi": [2, 10], "readm": 2, "readme_url": [1, 2], "readmeshfromfil": [2, 6], "realtim": [0, 14], "reativ": 2, "rebuild": 2, "recal": [0, 14], "recalc_norm": [2, 6], "recalcul": 6, "receiv": [2, 6, 7], "recent": [6, 12], "reciev": 2, "recip": [1, 3, 4, 8, 9, 11, 13], "recipe_data": [2, 9], "recipe_data_2_0": 5, "recipe_dictionari": 2, "recipe_load": [1, 2], "recipe_meta_data": 2, "recipe_nam": [5, 7], "recipe_path": 9, "recipe_to_sav": 2, "recipefil": 2, "recipeload": [2, 5], "recipesfil": 2, "recommend": [2, 10, 11], "recov": 2, "recreat": 2, "rect": 2, "rectangl": [1, 2, 6], "rectilinear": 6, "recurs": [2, 6, 8], "recursionerror": 8, "red": 6, "redistribut": [2, 6, 7], "redund": [6, 7], "redwhiteblueramp": [2, 6], "refer": [2, 6, 7, 8], "referenc": 2, "references_to_upd": 2, "referring_comp_id": 2, "reflect": 2, "reg": [1, 2, 4], "regent": 2, "region": 2, "region_1": [1, 2], "region_1_2_theta": [1, 2], "region_2": [1, 2], "region_2_integrand": [1, 2], "region_3": [1, 2], "region_3_integrand": [1, 2], "region_list": 5, "region_nam": 2, "regress": 8, "reject": [0, 2, 3, 14], "rejection_threshold": 3, "rejectioncount": 3, "rel": 3, "relat": [2, 11], "releas": [10, 11], "remain": 2, "remind": 10, "remov": [2, 6, 7], "remove_comp_nam": 2, "remove_from_realtime_displai": [2, 3], "remove_item": 2, "remove_nan": [6, 7], "removefreepoint": [1, 2], "removelast": 3, "removeonepoint": [1, 2], "renam": 6, "render": [2, 6, 7], "rendermod": [6, 7], "renedr": [6, 7], "reorder": 2, "reorder_free_point": [1, 2], "rep": 2, "repar": [2, 6, 7], "repetit": 2, "replac": 2, "replaceingrmesh": [1, 2], "repo": [6, 10, 12], "report": 2, "report_md": 2, "report_output_path": 2, "reporthook": [2, 6], "reportprogress": [1, 2], "repositori": [11, 12], "repres": [2, 3], "represent": [1, 2, 3, 5, 8], "reproduc": 2, "request": [6, 7, 10, 11], "requir": [0, 1, 3, 11, 14], "requisit": 11, "rerieveaxi": [2, 6], "res_filenam": 2, "reserv": 2, "reset": [1, 2, 3, 6, 7], "resetdefault": [1, 2], "resetingr": [1, 2], "resetingrrecip": [1, 2], "resetlastpoint": [2, 3], "resetprogressbar": [2, 6, 7], "resetspheredistribut": [2, 3], "resettransform": [2, 6], "resolut": [1, 2, 6], "resolution_dictionari": 3, "resolv": [2, 10], "resolve_composit": [1, 2], "resolve_db_region": [1, 2], "resolve_gradient_data_object": [1, 2], "resolve_inherit": [2, 5], "resolve_local_region": [1, 2], "resolve_object_data": [1, 2], "respect": [2, 6], "restor": [1, 2, 6], "restore_grid": 2, "restore_grids_from_pickl": [1, 2], "restore_molecules_arrai": [1, 2], "restoreeditmod": [2, 6], "restorefreepoint": [1, 2], "restoregridfromfil": [1, 2], "restructur": 2, "result": [0, 2, 3, 6, 7, 8, 9, 14], "resultdoc": [1, 2], "resultfilenam": 2, "results_data_in": [5, 9], "results_seed_0": 9, "retain": 2, "retriev": [2, 6, 7], "retrievecolormat": [2, 6], "retrievehost": [2, 6], "return": [0, 2, 3, 6, 7, 8, 9, 14], "return_int": 2, "return_object_valu": [2, 8], "revers": [4, 6, 7], "revis": 2, "rg": 3, "rgb": [6, 7], "rho": 2, "ri": 2, "rid": 2, "right": [0, 2, 6, 7, 14], "rightbound": 2, "rightmost": 2, "rigid": [2, 6, 7], "rigid_plac": [2, 3], "rlength": 6, "rnd": [2, 4], "roll": 6, "ronald": 2, "root": [2, 6], "rot": [2, 3, 6, 7], "rot_mat": 3, "rotat": [2, 3, 4, 6, 7], "rotate_about_axi": [2, 6], "rotateobj": [2, 6, 7], "rotatepoint": [2, 6], "rotatio_i": [6, 7], "rotation_axi": 3, "rotation_matrix": [2, 3, 6], "rotation_rang": 3, "rotation_x": [6, 7], "rotation_z": [6, 7], "rotax": [2, 3], "rotmassclamp": 6, "rotmat": [2, 3], "rotmatj": 3, "rotvecttovect": [2, 3, 6], "rotx": 2, "rotz": 2, "row": [2, 6], "rq": 2, "rsz": 6, "rtype": [2, 3, 6, 7], "ru": 2, "rule": 2, "run": [2, 3, 6, 9, 10, 12], "run_": 2, "run_analysis_workflow": [1, 2], "run_cleanup": [1, 9], "run_distance_analysi": [1, 2], "run_partner_analysi": [1, 2], "runbullet": [1, 2], "runtim": [2, 3], "runtimedisplai": 2, "rx": 2, "rxyz": 2, "ry": 2, "ryxi": 2, "rz": [2, 6], "s3": 2, "s3_uri": 2, "safeguard": [0, 2, 14], "sagenb": 6, "said": 2, "same": [2, 3], "sampl": 2, "sane": 2, "sanner": 2, "saturdai": 1, "save": [0, 1, 2, 8, 14], "save_analyze_result": 5, "save_as_simularium": [2, 8], "save_aspython": [1, 2], "save_converted_recip": 5, "save_file_and_get_url": [1, 2], "save_gradient_data_as_imag": [2, 5], "save_grid_log": 2, "save_grids_to_pickl": [1, 2], "save_mixed_asjson": [2, 8], "save_png": 2, "save_result": [1, 2], "save_result_as_fil": 2, "savedejavumesh": [2, 6], "savegridlogsasjson": [1, 2], "savegridtofil": [1, 2], "saveobjmesh": [2, 6], "saverecipeavail": [1, 2], "saverecipeavailablejson": [1, 2], "saveresultbinari": [1, 2], "saveresultbinaryd": [1, 2], "saw": 3, "sc": [6, 7], "scalar": [2, 6], "scale": [2, 6, 7], "scale_distance_between": [2, 4], "scale_matrix": 2, "scaleobj": [2, 6, 7], "scan": 6, "scanlin": [0, 2, 5, 14], "scene": [6, 7, 8], "schedul": 9, "schemat": 2, "scheme": 2, "scientif": 6, "scn": 6, "scname": 6, "scompart": [1, 2], "script": [2, 6, 9], "sdf": [0, 14], "sdk": 11, "search": [2, 3, 11], "search_nam": 2, "search_tre": 3, "second": [2, 6], "secondpoint": 3, "section": [2, 11], "see": [2, 6, 7, 11], "seed": [2, 3], "seed_basenam": 2, "seed_index": 2, "seed_list": 2, "seed_numb": 2, "seed_to_results_map": 8, "seednum": 2, "segment": 2, "sel": 2, "selecion": [6, 7], "select": [0, 2, 6, 7, 11, 14], "selectedg": [2, 6], "selectfac": [2, 6], "selectvertic": [2, 6], "self": [2, 3, 8], "sensibl": 8, "separ": [2, 8, 11], "sept": 2, "septemb": 1, "sequenc": [2, 3], "sequenti": 6, "serial": 8, "serializ": [1, 8, 13], "serializedfromresult": [1, 2], "serializedrecip": [1, 2], "serializedrecipe_group": [1, 2], "serializedrecipe_group_d": [1, 2], "servic": [2, 11], "set": [0, 2, 3, 6, 7, 10, 11, 14], "set_act": [2, 4], "set_doc": [1, 2], "set_gradi": [1, 2], "set_ingredi": [2, 4], "set_ingredient_color": [1, 2], "set_mode_properti": [2, 4], "set_object_stat": [6, 7], "set_partners_ingredi": [1, 2], "set_recipe_ingredi": [1, 2], "set_result_file_nam": [1, 2], "set_sphere_posit": [2, 4], "set_stat": [6, 7], "set_surface_dist": [1, 2], "set_surfptsbht": [1, 2], "set_surfptscht": [1, 2], "set_weights_by_mod": [1, 2], "setcount": [1, 2], "setcurrentselect": [2, 6], "setexteriorrecip": [1, 2], "setfram": [2, 6], "setgeomfac": [1, 2], "sethistovol": [1, 2], "setinnerrecip": [1, 2], "setinst": [6, 7], "setkeyfram": [2, 6], "setlay": [2, 6], "setmesh": [1, 2], "setmeshedg": [2, 6], "setmeshfac": [2, 6], "setmeshvertic": [2, 6], "setnam": [2, 6], "setnumb": [1, 2], "setobjectmatrix": [2, 6, 7], "setparticulesposit": [2, 6], "setproperti": [2, 6], "setpropertyobject": [2, 6], "setrbopt": [1, 2], "setrigidbodi": [2, 6, 7], "setse": [1, 2], "setsoftbodi": [2, 6], "setspringopt": [1, 2], "setsurfacerecip": [1, 2], "settil": [2, 3], "settransform": [2, 6], "settransl": [2, 6, 7], "setup": [0, 1, 2, 8, 12, 14], "setupboundaryperiod": [1, 2], "setupfil": 2, "setupfromjsond": [1, 2], "setupoctre": [1, 2], "setuprbopt": [1, 2], "setuv": [2, 6], "setvaluetojsonnod": [2, 8], "setvaluetopythonstr": [1, 2], "setview": [6, 7], "setviewport": [2, 6], "sfu": 2, "shadow": [6, 7], "shall": 2, "shallow_match": [1, 2], "shape": [2, 3, 6], "share": 2, "sharealik": 2, "shear": 2, "shear_matrix": 2, "shoemak": 2, "short": [2, 10], "shoud": 6, "should": [2, 3, 6, 7, 8, 11], "should_writ": [1, 2], "show": [1, 2], "show_grid": 2, "show_grid_plot": 5, "show_plotly_plot": 2, "show_progress_bar": 5, "show_sphere_tre": [5, 7], "showhid": [1, 2], "showingrprimit": [1, 2], "shown": 2, "side": [0, 3, 11, 14], "side_length": 2, "sigma": 8, "sign": [0, 2, 6, 14], "signed_distance_to_surfac": 3, "similar": 2, "simpl": [0, 2, 14], "simpleplot": [1, 2], "simpli": [0, 2, 6, 8, 14], "simularium": [2, 5, 6, 8, 11], "simularium_convert": [1, 13], "simularium_help": [2, 6], "simulariumhelp": [6, 7], "simulationtim": 2, "sin": 6, "sinc": [2, 3], "singl": [0, 3, 14], "single_cub": [1, 2, 4], "single_cylind": [1, 2, 4], "single_spher": [1, 2, 4], "singlecub": [0, 14], "singlecubeingr": [2, 3], "singlecylinderingr": [2, 3], "singlespher": [0, 14], "singlesphereingr": [2, 3], "singredi": [1, 2], "singredientfib": [1, 2], "singredientgroup": [1, 2], "size": [2, 3, 6, 7, 8], "size_opt": 3, "sizei": 6, "sizex": 6, "skip": [2, 3, 8], "skipkei": 8, "slow": [0, 14], "slow_box_fil": [1, 2], "small": 11, "smallest": [0, 2, 14], "smooth": [6, 7], "so": [2, 3, 6, 11], "soc": 2, "soft": [6, 7], "softwar": [2, 6, 7], "solid": 6, "solut": 2, "some": [2, 6], "sort": [1, 2, 3, 8], "sort_kei": 8, "sort_valu": [6, 7], "sortingredi": [1, 2], "sourc": [1, 2, 3, 4, 5, 6, 7, 8, 9], "space": [2, 3, 5], "spars": 2, "sparse_to_dens": [1, 2], "spec": 2, "special": [2, 6, 7], "specif": [2, 6, 8], "specifi": [2, 3, 6, 7, 8, 9], "specifii": 6, "specular": 6, "speed": 2, "speedup": 2, "spencer": 2, "sph": [6, 7], "sph1": [6, 7], "sphee": 2, "sphere": [0, 2, 3, 4, 6, 7, 14], "sphere_mesh": 6, "sphere_obj": 6, "sphere_radius_100": [0, 14], "spherehalton": [1, 2], "spheres_sst": [2, 5], "spheres_sst_plac": [2, 3], "spheressst": [0, 5, 14], "spheretre": [0, 14], "spheric": [2, 6], "spline": [0, 2, 6, 7, 14], "split_ingredient_data": [2, 5], "spot": [6, 7], "sprin": 6, "spring": [2, 6], "sqrt": 6, "squar": [2, 4], "squaretil": [0, 14], "squash": 11, "srfpt": 2, "stabl": [2, 11], "stackoverflow": 2, "stage": 11, "stamp": 2, "standard": 6, "stare": 3, "start": [3, 6, 7], "starting_po": 3, "starting_rot": 3, "startingpoint": 3, "state": [2, 3, 6, 7], "static": [2, 3, 5, 7, 8, 9], "static_id": [1, 2, 3], "statu": [6, 7], "std": [2, 3], "step": [2, 6, 11], "stepbystep": 3, "stepsiz": 3, "steve": 2, "stif": 6, "still": 11, "stop": [2, 6], "storag": [2, 7], "store": [1, 2], "store_asjson": [1, 2], "store_metadata": [6, 7], "store_packed_object": [1, 2, 3], "store_result_fil": [6, 7], "str": [2, 4, 6, 8, 9], "strict": 2, "string": [0, 2, 3, 6, 7, 9, 14], "string_or_dict": 2, "strng": 6, "structur": [2, 4], "style": [2, 3], "sub": [2, 4], "sub_dir": 5, "sub_folder_nam": 2, "sub_point": 7, "subclass": 8, "subdivis": [6, 7], "submit": 10, "submodul": [1, 13], "subpackag": 13, "substitut": 2, "success": [2, 3], "suitabl": 2, "sum": [2, 6], "sun": [2, 6, 7], "super": [0, 2, 14], "superfin": [0, 2, 14], "superimpos": 2, "support": [2, 6, 7, 8], "sure": [2, 10], "surfac": [0, 2, 3, 4, 14], "surfacepoint": 2, "surfacepointsnorm": 2, "surfanc": 3, "surfptsbbnorm": 2, "surpris": 6, "surround": 2, "swap": [2, 3], "sxyz": 2, "system": [2, 6], "t": [0, 2, 3, 6, 7, 8, 11, 12, 14], "tag": [10, 11], "tail": [6, 7], "tailcoord": 6, "take": [0, 2, 3, 4, 6, 7, 8, 14], "tan": 2, "tarbal": 12, "target": [2, 3, 6], "target_grid_point_posit": 3, "target_point": 3, "targeta": 6, "targeted_master_grid_point": 3, "task": [2, 9], "tatic": 2, "tau": 3, "te": 2, "team": 11, "techniqu": [2, 3], "temporari": [2, 3], "term": [2, 6, 7], "termin": [2, 12], "terminologi": 2, "test": [0, 2, 3, 5, 8, 10, 11, 14], "test_partner_pack": 5, "test_points_in_bb": [1, 2], "testforescap": [2, 6], "testwhen": 3, "tetha": 6, "tetra": 6, "tetrahedron": [2, 6], "text": [2, 6], "textu": [6, 7], "textur": [6, 7], "texturefacecoordintestovertexcoordin": [6, 7], "than": 2, "thegreenplac": [2, 3], "thei": [0, 2, 6, 10, 14], "them": [2, 3], "theori": 2, "therefor": [2, 6], "theses": 2, "thesi": 2, "theta": [2, 6], "thi": [0, 2, 3, 6, 7, 8, 9, 10, 11, 12, 14], "thin": 2, "third": [2, 6], "thoma": 2, "though": [2, 6], "thread": [6, 7], "three": [2, 6], "threecolorramp": [2, 6], "threshold": 3, "thresholdprior": 2, "through": [2, 6, 10, 12], "thu": 2, "ti": [2, 7], "tiff": [8, 10], "time": [0, 2, 3, 7, 14], "time_point": 7, "time_step_index": 9, "timefunct": [1, 2], "titl": [2, 7], "title_str": 2, "to_json": [1, 2], "tobinari": [1, 2], "todo": [2, 3], "toggl": [2, 6, 7], "toggledisplai": [2, 6, 7], "toggleeditmod": [2, 6], "toggleorganelmatr": [1, 2], "toggleorganelmesh": [1, 2], "toggleorganelsurf": [1, 2], "togglexrai": [2, 6], "toint": 6, "tomat": [2, 6], "too": 3, "tool": 2, "top": [1, 2, 3, 6], "toreplac": 2, "torsion": 6, "tort": 2, "total": [2, 3], "total_step": 9, "totals": 6, "touching_radiu": 2, "tovec": [2, 6, 7], "tox": 11, "tr": 6, "trace": [6, 7], "tragetb": 6, "traj_typ": [1, 2], "trajectori": [1, 13], "tran": [2, 3, 6], "transform": [1, 3, 6, 7, 13], "transformatio": 6, "transformmesh": [1, 2], "transformnod": [6, 7], "transformpoint": [2, 3], "transformpoints2d": [1, 2], "transformpoints_mult": [2, 3], "translat": [2, 3, 6, 7], "translateobj": [2, 6, 7], "translation_matrix": 2, "transpos": [2, 3, 6, 8], "transpose_image_for_project": [2, 8], "transposematrix": [2, 6], "tree": [0, 2, 3, 4, 14], "tri": [2, 3, 7], "triangl": [2, 6], "triangletil": [0, 14], "triangul": [2, 6], "triangulatefac": [2, 6], "triangulatefacearrai": [2, 6], "trimesh": [0, 2, 5, 14], "tripl": 2, "true": [0, 2, 3, 5, 6, 7, 8, 14], "try": [2, 8], "tsri": [6, 7], "tube": 6, "tue": 2, "tupe": 6, "tupl": [2, 6, 8], "tuppl": 6, "turn": [2, 3, 6], "tutori": 11, "twice": [2, 3], "two": [0, 2, 3, 6, 14], "two_d": 2, "twocolorramp": [2, 6], "type": [2, 3, 6, 7, 8], "typeerror": 8, "typesel": [6, 7], "u": [2, 6], "u_length": 3, "uci": [2, 6], "ug": 2, "ui": [6, 7], "ulength": 3, "unallow": [0, 14], "under": [2, 6, 7], "undirect": 6, "undspmesh": [1, 2], "undspsph": [1, 2], "uniform": [2, 3, 6], "uniformli": [2, 3], "uniq": [2, 7], "uniqu": [0, 6, 14], "unique_id": 7, "unit": [2, 3], "unit_length": 3, "unit_vector": [2, 6], "univers": 2, "unless": 2, "unlinktraj": [1, 2], "unpack_curv": [1, 9], "unpack_posit": [1, 9], "until": 6, "untitl": 6, "unus": 2, "up": [2, 6, 10, 11], "updat": [0, 2, 3, 6, 7, 14], "update_after_plac": [1, 2], "update_data_tre": [2, 3], "update_display_rt": [2, 3], "update_distance_distribution_dictionari": [1, 2], "update_doc": [1, 2], "update_elements_in_arrai": [1, 2], "update_in_arrai": 2, "update_ingredient_s": [2, 3], "update_instance_positions_and_rot": [6, 7], "update_largest_smallest_s": [1, 2], "update_or_cr": [1, 2], "update_pairwise_dist": [1, 2], "update_partn": 2, "update_refer": [1, 2], "update_reference_on_doc": [1, 2], "update_splin": [2, 6, 7], "update_titl": [1, 2], "update_variable_ingredient_attribut": [1, 2], "updateappli": [6, 7], "updatearmatur": [2, 6], "updatebox": [2, 6, 7], "updatedist": [1, 2], "updatefrombb": [2, 3], "updategrid": [2, 3], "updatemasterinst": [2, 6, 7], "updatemesh": [6, 7], "updateparticl": [2, 6], "updatepath": [1, 2], "updatepathdeform": [2, 6, 7], "updatepathjson": [1, 2], "updatepoli": [6, 7], "updatepositionsradii": [1, 2, 8], "updaterecipavailablexml": [1, 2], "updatereplacepath": [1, 2], "updatespr": [2, 6], "updatetre": 2, "updatetubemesh": [6, 7], "updatetubeobj": [2, 6], "upi": [1, 2], "upload": [1, 2, 13], "upload_collect": [1, 2], "upload_composit": [1, 2], "upload_data": [1, 2], "upload_doc": [1, 2], "upload_fil": [1, 2], "upload_gradi": [1, 2], "upload_object": [1, 2], "upload_recip": [1, 2], "upload_result": 5, "upload_result_metadata": [1, 2], "upload_single_object": [1, 2], "upper": [3, 6, 7], "uppercirclefunct": [1, 2], "upperrectanglefunct": [1, 2], "upward": 6, "url": [2, 7], "url_exist": [1, 2], "us": [0, 2, 3, 6, 7, 8, 9, 11, 14], "usag": 2, "use_mesh": [2, 3], "use_orient_bia": 3, "use_par": [6, 7], "use_pdb": [2, 3], "use_period": 5, "use_quaternion": 2, "use_rbspher": 3, "use_rotation_axi": 3, "usecylind": 3, "usefix": 2, "useful": 2, "usehalton": 3, "uselength": 3, "usemateri": 6, "usemtl": 2, "useobjectcolor": 6, "usepp": 3, "user": [9, 11], "usexref": [2, 8], "usual": [0, 2, 14], "usus": [6, 7], "ut": [0, 2, 14], "utf": 2, "util": [1, 13], "uv": [2, 6], "v": [2, 3, 6, 7], "v0": [2, 6], "v1": [2, 3, 6, 9, 11], "v1_v2_attribute_chang": [1, 2], "v2": [2, 3, 6, 11], "v3": [3, 6], "v4": 6, "val_dict": 2, "vale": 6, "valid": [2, 3, 6], "validate_distribution_opt": [2, 3], "validate_exist": [1, 2], "validate_gradient_data": [2, 4], "validate_ingredient_info": [2, 3], "validate_input_recipe_path": [1, 2], "validate_invert_set": [2, 4], "validate_mode_set": [2, 4], "validate_weight_mode_set": [2, 4], "valu": [0, 2, 3, 4, 5, 6, 7, 8, 14], "valueerror": 8, "van": 2, "variabl": [2, 6], "variou": [2, 11], "vcross": [1, 2, 6], "vdebug": 2, "vdiff": [1, 2, 6], "vdistanc": [2, 6], "vec": [2, 6], "vec1": 6, "vec2": 6, "vec4": 6, "vecor": [2, 6], "vect1": [3, 6], "vect2": [3, 6], "vector": [2, 3, 4, 6, 7], "vector1": 2, "vector2": 2, "vector_a_to_b": 6, "vector_norm": [2, 6], "vector_product": 2, "verbos": [2, 6, 7], "veri": [2, 11], "verifi": 6, "versa": 6, "version": [2, 5, 6, 7, 8, 10], "vert": [2, 3, 6], "vert_list": 2, "vertex": [2, 6, 7], "vertex_indic": 6, "vertex_point": 2, "vertexindex": 6, "vertic": [2, 6, 7], "vertice_coordin": 6, "vertice_indic": 6, "vertices_coordin": 6, "vertices_indic": 6, "vetor": 6, "vi": 7, "vice": 6, "view": [2, 6, 11], "viewer": [2, 6, 7, 11], "viewertyp": 2, "viewport": [2, 6, 7], "vindic": [2, 6], "virtual": 11, "virtualenv": 10, "visibl": [2, 6, 7], "vision": 2, "visit": 11, "viz_typ": 7, "vlen": [1, 2, 6], "vn": 6, "vnorm": [1, 2, 6], "vnormal": [2, 6], "void": 9, "volum": [0, 2, 14], "vote": 2, "voxel": [0, 1, 2, 3, 8, 14], "voxel_data": 2, "voxel_model": 2, "voxel_s": [2, 3, 8], "vrangestart": 2, "vrml": 2, "vsurfacearea": 2, "vtestid": 2, "vthreshstart": 2, "vtk": 2, "w": 2, "w1": 2, "w2": 2, "wa": 2, "wai": [2, 3, 6], "walkignmod": 3, "walkingmod": 3, "walklattic": [2, 3], "walklatticesurfac": [2, 3], "walkspher": [2, 3], "want": [2, 6, 7], "warranti": [2, 6, 7], "waveren": 2, "wb": 2, "we": [2, 3, 6, 7], "weakref": [2, 3], "web": 11, "websit": 10, "wed": 2, "weight": [2, 3, 4], "weight_mod": 4, "weight_mode_nam": 4, "weight_mode_set": 4, "weight_mode_settings_dict": 4, "weighted_choice_sub": [2, 3], "weightmod": [2, 4], "weightmodeopt": [2, 4], "welcom": 10, "well": [2, 11], "what": 3, "when": [0, 2, 3, 10, 11, 14], "where": [2, 6], "whether": [0, 2, 14], "which": [0, 2, 3, 6, 7, 8, 11, 14], "which_db": [1, 2], "while": [0, 14], "white": [2, 3], "whitespac": 8, "who": [6, 7], "whole": 6, "width": 2, "window": 6, "wirefram": 2, "with_colon": [2, 4], "within": 2, "without": [2, 6, 7], "work": [2, 6, 7, 10, 11], "workflow": [2, 9], "world": [3, 6, 7], "worldsiz": 2, "would": 8, "wrap": [0, 2, 14], "write": [1, 2, 6, 7, 8], "write_creds_path": [1, 2], "write_json_fil": [2, 5], "write_username_to_cr": [1, 2], "writearraystofil": [1, 2], "writedx": [2, 6], "writejson": [1, 2], "writemeshtofil": [2, 6], "writer": [1, 2], "writetofil": [2, 6, 7], "written": 2, "wrl": 2, "wu": 2, "www": [2, 6, 7], "x": [0, 2, 3, 4, 6, 7, 14], "x_label": 2, "x_n": 2, "x_width": [2, 3], "xaxi": 2, "xaxis_titl": 7, "xgl": 2, "xml": [2, 8], "xmlnode": 2, "xrai": 6, "xtrace": 7, "xy": 6, "xyz": [2, 6, 7], "xyztoijk": [1, 2], "xyztrajectori": [1, 2], "y": [0, 2, 3, 4, 6, 7, 14], "y_label": 2, "y_n": 2, "y_width": [2, 3], "yaxi": 2, "yaxis_titl": 7, "yet": 2, "yml": 9, "you": [2, 6, 7, 8, 10, 11, 12], "your": [2, 6, 7, 10, 11, 12], "your_development_typ": 10, "your_name_her": 10, "yourself": 11, "ytrace": 7, "z": [0, 2, 3, 4, 6, 7, 8, 14], "z_n": 2, "z_width": [2, 3], "zaxi": 2, "zissermann": 2, "\u00e5": 2}, "titles": ["Cellpack Recipe Schema 1.0", "cellpack package", "cellpack.autopack package", "cellpack.autopack.ingredient package", "cellpack.autopack.interface_objects package", "cellpack.autopack.loaders package", "cellpack.autopack.upy package", "cellpack.autopack.upy.simularium package", "cellpack.autopack.writers package", "cellpack.bin package", "Contributing", "Welcome to cellPack\u2019s documentation!", "Installation", "cellpack", "Cellpack Recipe Schema 1.0"], "titleterms": {"": 11, "0": [0, 14], "00": 2, "1": [0, 2, 14], "20": 2, "2012": 2, "23": 2, "50": 2, "53": 2, "The": [2, 6, 7], "_hackfreept": [0, 14], "_timer": [0, 14], "abstract": [6, 7], "agent": 3, "an": 4, "analysi": 2, "analysis_config_load": 5, "analyz": 9, "autopack": [2, 3, 4, 5, 6, 7, 8], "aw": 11, "awshandl": 2, "basegrid": 2, "bin": 9, "binvox_rw": 2, "boundingbox": [0, 14], "canceldialog": [0, 14], "cellpack": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 13, 14], "cheat": 11, "class": [2, 7], "clean": 9, "cleanup_task": 9, "code": 11, "color": [0, 6, 14], "compart": 2, "compartmentlist": 2, "computegridparam": [0, 14], "config_load": 5, "content": [1, 2, 3, 4, 5, 6, 7, 8, 9], "contribut": [10, 11], "convers": 11, "coordsystem": [0, 14], "count": [0, 14], "creat": 2, "cutoff_boundari": [0, 14], "cutoff_surfac": [0, 14], "data": 4, "databas": 11, "database_id": 4, "dbrecipehandl": 2, "default_valu": 4, "definit": [0, 14], "deploi": 10, "develop": 11, "differ": 4, "document": 11, "encapsulating_radiu": [0, 14], "environ": 2, "enviroonli": [0, 14], "exampl": [0, 14], "excluded_partners_nam": [0, 14], "firebas": 11, "firebasehandl": 2, "firestor": 11, "freeptsupdatethreshold": [0, 14], "fri": 2, "from": 12, "geometrytool": 2, "get": [9, 10], "gradient": [0, 2, 14], "gradient_data": 4, "graphic": 2, "grid": 2, "grow": 3, "helper": [6, 7], "hold": 4, "hosthelp": 6, "imagewrit": 8, "indic": 11, "ingredi": [0, 3, 4, 14], "ingredient_typ": 4, "ingrlookforneighbour": [0, 14], "innergridmethod": [0, 14], "instal": 12, "interface_object": 4, "introduct": 11, "ioutil": 2, "is_attractor": [0, 14], "jitter_attempt": [0, 14], "jul": 2, "largestproteins": [0, 14], "ldsequenc": 2, "loader": 5, "max_jitt": [0, 14], "meshfil": [0, 14], "meshnam": [0, 14], "meshstor": 2, "meta_enum": 4, "migrate_v1_to_v2": 5, "migrate_v2_to_v2_1": 5, "modul": [1, 2, 3, 4, 5, 6, 7, 8, 9], "molar": [0, 14], "multi_cylind": 3, "multi_spher": 3, "name": [0, 14], "object": [4, 6], "octre": 2, "offset": [0, 9, 14], "option": [0, 14], "organ": [0, 14], "orientbiasrotrangemax": [0, 14], "orientbiasrotrangemin": [0, 14], "outputsimularium": 2, "overwriteplacemethod": [0, 14], "pack": [9, 11], "packag": [1, 2, 3, 4, 5, 6, 7, 8, 9], "packed_object": 4, "packing_mod": [0, 14], "partner": 4, "partners_nam": [0, 14], "partners_posit": [0, 14], "partners_weight": [0, 14], "pdb": [0, 9, 14], "perturb_axis_amplitud": [0, 14], "pickrandpt": [0, 14], "pickweightedingr": [0, 14], "place_method": [0, 14], "plot": 7, "plotly_result": 2, "posit": [0, 14], "positions2": [0, 14], "prerequisit": 11, "principal_vector": [0, 14], "prioriti": [0, 14], "proba_bind": [0, 14], "proba_not_bind": [0, 14], "properti": [0, 14], "radii": [0, 14], "rai": 2, "randomrot": 2, "recip": [0, 2, 14], "recipe_load": 5, "rejection_threshold": [0, 14], "releas": 12, "remot": 11, "represent": 4, "requir": 2, "result_fil": [0, 14], "rotation_axi": [0, 14], "rotation_rang": [0, 14], "run": 11, "runtimedisplai": [0, 14], "s3": 11, "saturdai": 2, "saveresult": [0, 14], "schema": [0, 14], "score": [0, 14], "septemb": 2, "serializ": 2, "setup": 11, "sheet": 11, "simularium": 7, "simularium_convert": 9, "simularium_help": 7, "single_cub": 3, "single_cylind": 3, "single_spher": 3, "smallestproteins": [0, 14], "sourc": 12, "spherefil": [0, 14], "stabl": 12, "start": 10, "submodul": [2, 3, 4, 5, 6, 7, 8, 9], "subpackag": [1, 2, 6], "tabl": 11, "thi": 4, "trajectori": 2, "transform": 2, "type": [0, 4, 14], "upi": [6, 7], "upload": 9, "use_gradi": [0, 14], "use_orient_bia": [0, 14], "use_period": [0, 14], "use_rotation_axi": [0, 14], "util": [2, 3, 5], "v1_v2_attribute_chang": 5, "version": [0, 14], "weight": [0, 14], "welcom": 11, "windowss": [0, 14], "writer": 8}})
\ No newline at end of file
+Search.setIndex({"alltitles": {"AWS S3": [[11, "aws-s3"]], "Cellpack Recipe Schema 1.0": [[0, "cellpack-recipe-schema-1-0"], [14, "cellpack-recipe-schema-1-0"]], "Contributing": [[10, "contributing"]], "Contributing cheat sheet": [[11, "contributing-cheat-sheet"]], "Created on Fri Jul 20 23:53:00 2012": [[2, "created-on-fri-jul-20-23-53-00-2012"]], "Created on Saturday September 1 1:50:00 2012": [[2, "created-on-saturday-september-1-1-50-00-2012"]], "Deploying": [[10, "deploying"]], "Development": [[11, "development"]], "Documentation": [[11, "documentation"]], "EnviroOnly": [[0, "enviroonly"], [14, "enviroonly"]], "Firebase Firestore": [[11, "firebase-firestore"]], "From sources": [[12, "from-sources"]], "Get Started!": [[10, "get-started"]], "Indices and tables": [[11, "indices-and-tables"]], "Ingredient Properties": [[0, "ingredient-properties"], [14, "ingredient-properties"]], "Installation": [[12, "installation"]], "Introduction to Remote Databases": [[11, "introduction-to-remote-databases"]], "Module contents": [[1, "module-cellpack"], [2, "module-cellpack.autopack"], [3, "module-cellpack.autopack.ingredient"], [4, "module-cellpack.autopack.interface_objects"], [5, "module-cellpack.autopack.loaders"], [6, "module-cellpack.autopack.upy"], [7, "module-cellpack.autopack.upy.simularium"], [8, "module-cellpack.autopack.writers"], [9, "module-cellpack.bin"]], "Options properties": [[0, "options-properties"], [14, "options-properties"]], "Prerequisite": [[11, "prerequisite"]], "Recipe definition properties": [[0, "recipe-definition-properties"], [14, "recipe-definition-properties"]], "Requirements": [[2, "requirements"]], "Run conversion code": [[11, "run-conversion-code"]], "Run pack code": [[11, "run-pack-code"]], "Setup": [[11, "setup"]], "Stable release": [[12, "stable-release"]], "Submodules": [[2, "submodules"], [3, "submodules"], [4, "submodules"], [5, "submodules"], [6, "submodules"], [7, "submodules"], [8, "submodules"], [9, "submodules"]], "Subpackages": [[1, "subpackages"], [2, "subpackages"], [6, "subpackages"]], "The Compartment class": [[2, "the-compartment-class"]], "The CompartmentList class": [[2, "the-compartmentlist-class"]], "The Environment class": [[2, "the-environment-class"]], "The Gradient class": [[2, "the-gradient-class"]], "The Grid class": [[2, "the-grid-class"], [2, "id1"]], "The Helper abstract Object": [[6, "the-helper-abstract-object"]], "The Simularium helper abstract class": [[7, "the-simularium-helper-abstract-class"]], "This object holds the different representation types for an ingredient": [[4, "this-object-holds-the-different-representation-types-for-an-ingredient"]], "This object holds the partner data": [[4, "this-object-holds-the-partner-data"]], "Welcome to cellPack\u2019s documentation!": [[11, "welcome-to-cellpack-s-documentation"]], "_hackFreepts": [[0, "hackfreepts"], [14, "hackfreepts"]], "_timer": [[0, "timer"], [14, "timer"]], "boundingBox": [[0, "boundingbox"], [14, "boundingbox"]], "cancelDialog": [[0, "canceldialog"], [14, "canceldialog"]], "cellPack": [[11, "cellpack"]], "cellpack": [[13, "cellpack"]], "cellpack package": [[1, "cellpack-package"]], "cellpack.autopack package": [[2, "cellpack-autopack-package"]], "cellpack.autopack.AWSHandler module": [[2, "module-cellpack.autopack.AWSHandler"]], "cellpack.autopack.Analysis module": [[2, "module-cellpack.autopack.Analysis"]], "cellpack.autopack.BaseGrid module": [[2, "module-cellpack.autopack.BaseGrid"]], "cellpack.autopack.Compartment module": [[2, "module-cellpack.autopack.Compartment"]], "cellpack.autopack.DBRecipeHandler module": [[2, "module-cellpack.autopack.DBRecipeHandler"]], "cellpack.autopack.Environment module": [[2, "module-cellpack.autopack.Environment"]], "cellpack.autopack.FirebaseHandler module": [[2, "module-cellpack.autopack.FirebaseHandler"]], "cellpack.autopack.GeometryTools module": [[2, "module-cellpack.autopack.GeometryTools"]], "cellpack.autopack.Gradient module": [[2, "module-cellpack.autopack.Gradient"]], "cellpack.autopack.Graphics module": [[2, "module-cellpack.autopack.Graphics"]], "cellpack.autopack.Grid module": [[2, "module-cellpack.autopack.Grid"]], "cellpack.autopack.IOutils module": [[2, "module-cellpack.autopack.IOutils"]], "cellpack.autopack.MeshStore module": [[2, "module-cellpack.autopack.MeshStore"]], "cellpack.autopack.OutputSimularium module": [[2, "cellpack-autopack-outputsimularium-module"]], "cellpack.autopack.Recipe module": [[2, "module-cellpack.autopack.Recipe"]], "cellpack.autopack.Serializable module": [[2, "module-cellpack.autopack.Serializable"]], "cellpack.autopack.binvox_rw module": [[2, "module-cellpack.autopack.binvox_rw"]], "cellpack.autopack.ingredient package": [[3, "cellpack-autopack-ingredient-package"]], "cellpack.autopack.ingredient.Ingredient module": [[3, "module-cellpack.autopack.ingredient.Ingredient"]], "cellpack.autopack.ingredient.agent module": [[3, "module-cellpack.autopack.ingredient.agent"]], "cellpack.autopack.ingredient.grow module": [[3, "module-cellpack.autopack.ingredient.grow"]], "cellpack.autopack.ingredient.multi_cylinder module": [[3, "module-cellpack.autopack.ingredient.multi_cylinder"]], "cellpack.autopack.ingredient.multi_sphere module": [[3, "module-cellpack.autopack.ingredient.multi_sphere"]], "cellpack.autopack.ingredient.single_cube module": [[3, "module-cellpack.autopack.ingredient.single_cube"]], "cellpack.autopack.ingredient.single_cylinder module": [[3, "module-cellpack.autopack.ingredient.single_cylinder"]], "cellpack.autopack.ingredient.single_sphere module": [[3, "module-cellpack.autopack.ingredient.single_sphere"]], "cellpack.autopack.ingredient.utils module": [[3, "module-cellpack.autopack.ingredient.utils"]], "cellpack.autopack.interface_objects package": [[4, "cellpack-autopack-interface-objects-package"]], "cellpack.autopack.interface_objects.database_ids module": [[4, "module-cellpack.autopack.interface_objects.database_ids"]], "cellpack.autopack.interface_objects.default_values module": [[4, "module-cellpack.autopack.interface_objects.default_values"]], "cellpack.autopack.interface_objects.gradient_data module": [[4, "module-cellpack.autopack.interface_objects.gradient_data"]], "cellpack.autopack.interface_objects.ingredient_types module": [[4, "module-cellpack.autopack.interface_objects.ingredient_types"]], "cellpack.autopack.interface_objects.meta_enum module": [[4, "module-cellpack.autopack.interface_objects.meta_enum"]], "cellpack.autopack.interface_objects.packed_objects module": [[4, "module-cellpack.autopack.interface_objects.packed_objects"]], "cellpack.autopack.interface_objects.partners module": [[4, "module-cellpack.autopack.interface_objects.partners"]], "cellpack.autopack.interface_objects.representations module": [[4, "module-cellpack.autopack.interface_objects.representations"]], "cellpack.autopack.ldSequence module": [[2, "module-cellpack.autopack.ldSequence"]], "cellpack.autopack.loaders package": [[5, "cellpack-autopack-loaders-package"]], "cellpack.autopack.loaders.analysis_config_loader module": [[5, "module-cellpack.autopack.loaders.analysis_config_loader"]], "cellpack.autopack.loaders.config_loader module": [[5, "module-cellpack.autopack.loaders.config_loader"]], "cellpack.autopack.loaders.migrate_v1_to_v2 module": [[5, "module-cellpack.autopack.loaders.migrate_v1_to_v2"]], "cellpack.autopack.loaders.migrate_v2_to_v2_1 module": [[5, "module-cellpack.autopack.loaders.migrate_v2_to_v2_1"]], "cellpack.autopack.loaders.recipe_loader module": [[5, "module-cellpack.autopack.loaders.recipe_loader"]], "cellpack.autopack.loaders.utils module": [[5, "module-cellpack.autopack.loaders.utils"]], "cellpack.autopack.loaders.v1_v2_attribute_changes module": [[5, "module-cellpack.autopack.loaders.v1_v2_attribute_changes"]], "cellpack.autopack.octree module": [[2, "module-cellpack.autopack.octree"]], "cellpack.autopack.plotly_result module": [[2, "module-cellpack.autopack.plotly_result"]], "cellpack.autopack.randomRot module": [[2, "module-cellpack.autopack.randomRot"]], "cellpack.autopack.ray module": [[2, "module-cellpack.autopack.ray"]], "cellpack.autopack.trajectory module": [[2, "module-cellpack.autopack.trajectory"]], "cellpack.autopack.transformation module": [[2, "module-cellpack.autopack.transformation"]], "cellpack.autopack.upy package": [[6, "cellpack-autopack-upy-package"]], "cellpack.autopack.upy.colors module": [[6, "module-cellpack.autopack.upy.colors"]], "cellpack.autopack.upy.hostHelper module": [[6, "module-cellpack.autopack.upy.hostHelper"]], "cellpack.autopack.upy.simularium package": [[7, "cellpack-autopack-upy-simularium-package"]], "cellpack.autopack.upy.simularium.plots module": [[7, "module-cellpack.autopack.upy.simularium.plots"]], "cellpack.autopack.upy.simularium.simularium_helper module": [[7, "module-cellpack.autopack.upy.simularium.simularium_helper"]], "cellpack.autopack.utils module": [[2, "module-cellpack.autopack.utils"]], "cellpack.autopack.writers package": [[8, "cellpack-autopack-writers-package"]], "cellpack.autopack.writers.ImageWriter module": [[8, "module-cellpack.autopack.writers.ImageWriter"]], "cellpack.bin package": [[9, "cellpack-bin-package"]], "cellpack.bin.analyze module": [[9, "module-cellpack.bin.analyze"]], "cellpack.bin.clean module": [[9, "module-cellpack.bin.clean"]], "cellpack.bin.cleanup_tasks module": [[9, "module-cellpack.bin.cleanup_tasks"]], "cellpack.bin.get-pdb-offset module": [[9, "cellpack-bin-get-pdb-offset-module"]], "cellpack.bin.pack module": [[9, "module-cellpack.bin.pack"]], "cellpack.bin.simularium_converter module": [[9, "module-cellpack.bin.simularium_converter"]], "cellpack.bin.upload module": [[9, "module-cellpack.bin.upload"]], "color": [[0, "color"], [14, "color"]], "computeGridParams": [[0, "computegridparams"], [14, "computegridparams"]], "coordsystem": [[0, "coordsystem"], [14, "coordsystem"]], "count": [[0, "count"], [14, "count"]], "cutoff_boundary": [[0, "cutoff-boundary"], [14, "cutoff-boundary"]], "cutoff_surface": [[0, "cutoff-surface"], [14, "cutoff-surface"]], "encapsulating_radius": [[0, "encapsulating-radius"], [14, "encapsulating-radius"]], "example Options:": [[0, "example-options"], [14, "example-options"]], "example ingredient": [[0, "example-ingredient"], [14, "example-ingredient"]], "example:": [[0, "example"], [14, "example"]], "excluded_partners_name": [[0, "excluded-partners-name"], [14, "excluded-partners-name"]], "freePtsUpdateThreshold": [[0, "freeptsupdatethreshold"], [14, "freeptsupdatethreshold"]], "gradient": [[0, "gradient"], [14, "gradient"]], "gradients": [[0, "gradients"], [14, "gradients"]], "ingrLookForNeighbours": [[0, "ingrlookforneighbours"], [14, "ingrlookforneighbours"]], "innerGridMethod": [[0, "innergridmethod"], [14, "innergridmethod"]], "is_attractor": [[0, "is-attractor"], [14, "is-attractor"]], "jitter_attempts": [[0, "jitter-attempts"], [14, "jitter-attempts"]], "largestProteinSize": [[0, "largestproteinsize"], [14, "largestproteinsize"]], "max_jitter": [[0, "max-jitter"], [14, "max-jitter"]], "meshFile": [[0, "meshfile"], [14, "meshfile"]], "meshName": [[0, "meshname"], [14, "meshname"]], "molarity": [[0, "molarity"], [14, "molarity"]], "name": [[0, "name"], [0, "id81"], [14, "name"], [14, "id81"]], "offset": [[0, "offset"], [14, "offset"]], "organism": [[0, "organism"], [14, "organism"]], "orientBiasRotRangeMax": [[0, "orientbiasrotrangemax"], [14, "orientbiasrotrangemax"]], "orientBiasRotRangeMin": [[0, "orientbiasrotrangemin"], [14, "orientbiasrotrangemin"]], "overwritePlaceMethod": [[0, "overwriteplacemethod"], [14, "overwriteplacemethod"]], "packing_mode": [[0, "packing-mode"], [14, "packing-mode"]], "partners_name": [[0, "partners-name"], [14, "partners-name"]], "partners_position": [[0, "partners-position"], [14, "partners-position"]], "partners_weight": [[0, "partners-weight"], [14, "partners-weight"]], "pdb": [[0, "pdb"], [14, "pdb"]], "perturb_axis_amplitude": [[0, "perturb-axis-amplitude"], [14, "perturb-axis-amplitude"]], "pickRandPt": [[0, "pickrandpt"], [14, "pickrandpt"]], "pickWeightedIngr": [[0, "pickweightedingr"], [14, "pickweightedingr"]], "place_method": [[0, "place-method"], [0, "id162"], [14, "place-method"], [14, "id162"]], "positions": [[0, "positions"], [14, "positions"]], "positions2": [[0, "positions2"], [14, "positions2"]], "principal_vector": [[0, "principal-vector"], [14, "principal-vector"]], "priority": [[0, "priority"], [14, "priority"]], "proba_binding": [[0, "proba-binding"], [14, "proba-binding"]], "proba_not_binding": [[0, "proba-not-binding"], [14, "proba-not-binding"]], "properties": [[0, "properties"], [14, "properties"]], "radii": [[0, "radii"], [14, "radii"]], "rejection_threshold": [[0, "rejection-threshold"], [14, "rejection-threshold"]], "result_file": [[0, "result-file"], [14, "result-file"]], "rotation_axis": [[0, "rotation-axis"], [14, "rotation-axis"]], "rotation_range": [[0, "rotation-range"], [14, "rotation-range"]], "runTimeDisplay": [[0, "runtimedisplay"], [14, "runtimedisplay"]], "saveResult": [[0, "saveresult"], [14, "saveresult"]], "score": [[0, "score"], [14, "score"]], "smallestProteinSize": [[0, "smallestproteinsize"], [14, "smallestproteinsize"]], "sphereFile": [[0, "spherefile"], [14, "spherefile"]], "type": [[0, "type"], [14, "type"]], "use_gradient": [[0, "use-gradient"], [14, "use-gradient"]], "use_orient_bias": [[0, "use-orient-bias"], [14, "use-orient-bias"]], "use_periodicity": [[0, "use-periodicity"], [14, "use-periodicity"]], "use_rotation_axis": [[0, "use-rotation-axis"], [14, "use-rotation-axis"]], "version": [[0, "version"], [14, "version"]], "weight": [[0, "weight"], [14, "weight"]], "windowsSize": [[0, "windowssize"], [14, "windowssize"]]}, "docnames": ["RECIPE_SCHEMA", "cellpack", "cellpack.autopack", "cellpack.autopack.ingredient", "cellpack.autopack.interface_objects", "cellpack.autopack.loaders", "cellpack.autopack.upy", "cellpack.autopack.upy.simularium", "cellpack.autopack.writers", "cellpack.bin", "contributing", "index", "installation", "modules", "recipe-schema"], "envversion": {"sphinx": 61, "sphinx.domains.c": 3, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 9, "sphinx.domains.index": 1, "sphinx.domains.javascript": 3, "sphinx.domains.math": 2, "sphinx.domains.python": 4, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinx.ext.viewcode": 1}, "filenames": ["RECIPE_SCHEMA.md", "cellpack.rst", "cellpack.autopack.rst", "cellpack.autopack.ingredient.rst", "cellpack.autopack.interface_objects.rst", "cellpack.autopack.loaders.rst", "cellpack.autopack.upy.rst", "cellpack.autopack.upy.simularium.rst", "cellpack.autopack.writers.rst", "cellpack.bin.rst", "contributing.rst", "index.rst", "installation.rst", "modules.rst", "recipe-schema.rst"], "indexentries": {"actiningredient (class in cellpack.autopack.ingredient.grow)": [[3, "cellpack.autopack.ingredient.grow.ActinIngredient", false]], "add() (cellpack.autopack.interface_objects.packed_objects.packedobjects method)": [[4, "cellpack.autopack.interface_objects.packed_objects.PackedObjects.add", false]], "add_circle() (cellpack.autopack.plotly_result.plotlyanalysis method)": [[2, "cellpack.autopack.plotly_result.PlotlyAnalysis.add_circle", false]], "add_compartment() (cellpack.autopack.compartment.compartmentlist static method)": [[2, "cellpack.autopack.Compartment.CompartmentList.add_compartment", false]], "add_compartment_to_scene() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.add_compartment_to_scene", false]], "add_grid_data_to_scene() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.add_grid_data_to_scene", false]], "add_histogram() (cellpack.autopack.upy.simularium.plots.plotdata method)": [[7, "cellpack.autopack.upy.simularium.plots.PlotData.add_histogram", false]], "add_ingredient_positions() (cellpack.autopack.plotly_result.plotlyanalysis method)": [[2, "cellpack.autopack.plotly_result.PlotlyAnalysis.add_ingredient_positions", false]], "add_ingredient_positions_to_plot() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.add_ingredient_positions_to_plot", false]], "add_instance() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.add_instance", false]], "add_mesh_to_scene() (cellpack.autopack.meshstore.meshstore method)": [[2, "cellpack.autopack.MeshStore.MeshStore.add_mesh_to_scene", false]], "add_new_instance_and_update_time() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.add_new_instance_and_update_time", false]], "add_object_to_scene() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.add_object_to_scene", false]], "add_partner() (cellpack.autopack.interface_objects.partners.partners method)": [[4, "cellpack.autopack.interface_objects.partners.Partners.add_partner", false]], "add_scatter() (cellpack.autopack.upy.simularium.plots.plotdata method)": [[7, "cellpack.autopack.upy.simularium.plots.PlotData.add_scatter", false]], "add_seed_number_to_base_name() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.add_seed_number_to_base_name", false]], "add_square() (cellpack.autopack.plotly_result.plotlyanalysis method)": [[2, "cellpack.autopack.plotly_result.PlotlyAnalysis.add_square", false]], "addbone() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.addBone", false]], "addcameratoscene() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.addCameraToScene", false]], "addcameratoscene() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.addCameraToScene", false]], "addcompartment() (cellpack.autopack.serializable.scompartment method)": [[2, "cellpack.autopack.Serializable.sCompartment.addCompartment", false]], "addcompartmentfromgeom() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.addCompartmentFromGeom", false]], "addcompartments() (in module cellpack.autopack.ioutils)": [[2, "cellpack.autopack.IOutils.addCompartments", false]], "addconstraint() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.addConstraint", false]], "addingredient() (cellpack.autopack.recipe.recipe method)": [[2, "cellpack.autopack.Recipe.Recipe.addIngredient", false]], "addingredient() (cellpack.autopack.serializable.singredientgroup method)": [[2, "cellpack.autopack.Serializable.sIngredientGroup.addIngredient", false]], "addingredientfromgeom() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.addIngredientFromGeom", false]], "addingredientgroup() (cellpack.autopack.serializable.scompartment method)": [[2, "cellpack.autopack.Serializable.sCompartment.addIngredientGroup", false]], "addlamptoscene() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.addLampToScene", false]], "addlamptoscene() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.addLampToScene", false]], "addmasteringr() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.addMasterIngr", false]], "addmaterial() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.addMaterial", false]], "addmaterial() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.addMaterial", false]], "addmaterialfromdic() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.addMaterialFromDic", false]], "addmeshedge() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.addMeshEdge", false]], "addmeshedges() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.addMeshEdges", false]], "addmeshface() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.addMeshFace", false]], "addmeshfaces() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.addMeshFaces", false]], "addmeshrborganelle() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.addMeshRBOrganelle", false]], "addmeshvertice() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.addMeshVertice", false]], "addmeshvertices() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.addMeshVertices", false]], "addnode() (cellpack.autopack.octree.octree method)": [[2, "cellpack.autopack.octree.Octree.addNode", false]], "addobject() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.AddObject", false]], "addobjecttoscene() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.addObjectToScene", false]], "addrb() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.addRB", false]], "advance_randpoint_onsphere() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.advance_randpoint_onsphere", false]], "agent (class in cellpack.autopack.ingredient.agent)": [[3, "cellpack.autopack.ingredient.agent.Agent", false]], "alignrotation() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.alignRotation", false]], "analysis (class in cellpack.autopack.analysis)": [[2, "cellpack.autopack.Analysis.Analysis", false]], "analysisconfigloader (class in cellpack.autopack.loaders.analysis_config_loader)": [[5, "cellpack.autopack.loaders.analysis_config_loader.AnalysisConfigLoader", false]], "analyze() (in module cellpack.bin.analyze)": [[9, "cellpack.bin.analyze.analyze", false]], "angle_between_vectors() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.angle_between_vectors", false]], "animationstart() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.animationStart", false]], "animationstop() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.animationStop", false]], "appendingrinstance() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.appendIngrInstance", false]], "apply_rotation() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.apply_rotation", false]], "applymatrix() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.ApplyMatrix", false]], "applymatrix() (in module cellpack.autopack.ingredient.utils)": [[3, "cellpack.autopack.ingredient.utils.ApplyMatrix", false]], "applystate() (cellpack.autopack.trajectory.trajectory method)": [[2, "cellpack.autopack.trajectory.Trajectory.applyState", false]], "applystate_cb() (cellpack.autopack.trajectory.trajectory method)": [[2, "cellpack.autopack.trajectory.Trajectory.applyState_cb", false]], "applystate_name() (cellpack.autopack.trajectory.molbtrajectory method)": [[2, "cellpack.autopack.trajectory.molbTrajectory.applyState_name", false]], "applystate_name() (cellpack.autopack.trajectory.trajectory method)": [[2, "cellpack.autopack.trajectory.Trajectory.applyState_name", false]], "applystate_primitive_name() (cellpack.autopack.trajectory.molbtrajectory method)": [[2, "cellpack.autopack.trajectory.molbTrajectory.applyState_primitive_name", false]], "applystate_primitive_name() (cellpack.autopack.trajectory.trajectory method)": [[2, "cellpack.autopack.trajectory.Trajectory.applyState_primitive_name", false]], "applystep() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.applyStep", false]], "arguments (cellpack.autopack.ingredient.grow.growingredient attribute)": [[3, "cellpack.autopack.ingredient.grow.GrowIngredient.ARGUMENTS", false]], "arguments (cellpack.autopack.ingredient.ingredient.ingredient attribute)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.ARGUMENTS", false]], "armature() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.armature", false]], "as_dict() (cellpack.autopack.dbrecipehandler.compositiondoc method)": [[2, "cellpack.autopack.DBRecipeHandler.CompositionDoc.as_dict", false]], "as_dict() (cellpack.autopack.dbrecipehandler.datadoc method)": [[2, "cellpack.autopack.DBRecipeHandler.DataDoc.as_dict", false]], "as_dict() (cellpack.autopack.dbrecipehandler.objectdoc method)": [[2, "cellpack.autopack.DBRecipeHandler.ObjectDoc.as_dict", false]], "assignmaterial() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.assignMaterial", false]], "assignmaterial() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.assignMaterial", false]], "assignnewmaterial() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.assignNewMaterial", false]], "attempt_to_pack_at_grid_location() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.attempt_to_pack_at_grid_location", false]], "autopackviewer (class in cellpack.autopack.graphics)": [[2, "cellpack.autopack.Graphics.AutopackViewer", false]], "aws (cellpack.autopack.interface_objects.database_ids.database_ids attribute)": [[4, "cellpack.autopack.interface_objects.database_ids.DATABASE_IDS.AWS", false]], "awshandler (class in cellpack.autopack.awshandler)": [[2, "cellpack.autopack.AWSHandler.AWSHandler", false]], "basegrid (class in cellpack.autopack.basegrid)": [[2, "cellpack.autopack.BaseGrid.BaseGrid", false]], "binary (cellpack.autopack.interface_objects.gradient_data.pickmodes attribute)": [[4, "cellpack.autopack.interface_objects.gradient_data.PickModes.BINARY", false]], "bones (cellpack.autopack.upy.hosthelper.helper attribute)": [[6, "cellpack.autopack.upy.hostHelper.Helper.BONES", false]], "box() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.box", false]], "box() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.Box", false], [7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.box", false]], "build_axis_weight_map() (cellpack.autopack.gradient.gradient method)": [[2, "cellpack.autopack.Gradient.Gradient.build_axis_weight_map", false]], "build_compartment_grids() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.build_compartment_grids", false]], "build_directional_weight_map() (cellpack.autopack.gradient.gradient method)": [[2, "cellpack.autopack.Gradient.Gradient.build_directional_weight_map", false]], "build_grid() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.build_grid", false]], "build_grid_sphere() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.build_grid_sphere", false]], "build_mesh() (cellpack.autopack.meshstore.meshstore method)": [[2, "cellpack.autopack.MeshStore.MeshStore.build_mesh", false]], "build_radial_weight_map() (cellpack.autopack.gradient.gradient method)": [[2, "cellpack.autopack.Gradient.Gradient.build_radial_weight_map", false]], "build_surface_distance_weight_map() (cellpack.autopack.gradient.gradient method)": [[2, "cellpack.autopack.Gradient.Gradient.build_surface_distance_weight_map", false]], "build_weight_map() (cellpack.autopack.gradient.gradient method)": [[2, "cellpack.autopack.Gradient.Gradient.build_weight_map", false]], "buildcompartmentsgrids() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.BuildCompartmentsGrids", false]], "buildgrid() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.BuildGrid", false]], "buildgrid() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.buildGrid", false]], "buildgrid_bhtree() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.BuildGrid_bhtree", false]], "buildgrid_binvox() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.BuildGrid_binvox", false]], "buildgrid_box() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.BuildGrid_box", false]], "buildgrid_kevin() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.BuildGrid_kevin", false]], "buildgrid_multisdf() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.BuildGrid_multisdf", false]], "buildgrid_pyray() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.BuildGrid_pyray", false]], "buildgrid_ray() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.BuildGrid_ray", false]], "buildgrid_scanline() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.BuildGrid_scanline", false]], "buildgrid_trimesh() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.BuildGrid_trimesh", false]], "buildgrid_utsdf() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.BuildGrid_utsdf", false]], "buildgridenviroonly() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.BuildGridEnviroOnly", false]], "buildingrprimitive() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.buildIngrPrimitive", false]], "buildmesh() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.buildMesh", false]], "buildmesh() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.buildMesh", false]], "buildsphere() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.buildSphere", false]], "bullet_checkcollision_mp() (in module cellpack.autopack.ingredient.utils)": [[3, "cellpack.autopack.ingredient.utils.bullet_checkCollision_mp", false]], "calc_pairwise_distances() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.calc_pairwise_distances", false]], "calc_scaled_distances_for_positions() (cellpack.autopack.meshstore.meshstore static method)": [[2, "cellpack.autopack.MeshStore.MeshStore.calc_scaled_distances_for_positions", false]], "calc_volume() (cellpack.autopack.geometrytools.geometrytools method)": [[2, "cellpack.autopack.GeometryTools.GeometryTools.calc_volume", false]], "callfunction() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.callFunction", false]], "callfunction() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.callFunction", false]], "cam_options (cellpack.autopack.upy.hosthelper.helper attribute)": [[6, "cellpack.autopack.upy.hostHelper.Helper.CAM_OPTIONS", false]], "cartesian() (cellpack.autopack.basegrid.basegrid method)": [[2, "cellpack.autopack.BaseGrid.BaseGrid.cartesian", false]], "cartesian() (cellpack.autopack.binvox_rw.voxels method)": [[2, "cellpack.autopack.binvox_rw.Voxels.cartesian", false]], "cartesian_to_sph() (cellpack.autopack.analysis.analysis static method)": [[2, "cellpack.autopack.Analysis.Analysis.cartesian_to_sph", false]], "cellpack": [[1, "module-cellpack", false]], "cellpack.autopack": [[2, "module-cellpack.autopack", false]], "cellpack.autopack.analysis": [[2, "module-cellpack.autopack.Analysis", false]], "cellpack.autopack.awshandler": [[2, "module-cellpack.autopack.AWSHandler", false]], "cellpack.autopack.basegrid": [[2, "module-cellpack.autopack.BaseGrid", false]], "cellpack.autopack.binvox_rw": [[2, "module-cellpack.autopack.binvox_rw", false]], "cellpack.autopack.compartment": [[2, "module-cellpack.autopack.Compartment", false]], "cellpack.autopack.dbrecipehandler": [[2, "module-cellpack.autopack.DBRecipeHandler", false]], "cellpack.autopack.environment": [[2, "module-cellpack.autopack.Environment", false]], "cellpack.autopack.firebasehandler": [[2, "module-cellpack.autopack.FirebaseHandler", false]], "cellpack.autopack.geometrytools": [[2, "module-cellpack.autopack.GeometryTools", false]], "cellpack.autopack.gradient": [[2, "module-cellpack.autopack.Gradient", false]], "cellpack.autopack.graphics": [[2, "module-cellpack.autopack.Graphics", false]], "cellpack.autopack.grid": [[2, "module-cellpack.autopack.Grid", false]], "cellpack.autopack.ingredient": [[3, "module-cellpack.autopack.ingredient", false]], "cellpack.autopack.ingredient.agent": [[3, "module-cellpack.autopack.ingredient.agent", false]], "cellpack.autopack.ingredient.grow": [[3, "module-cellpack.autopack.ingredient.grow", false]], "cellpack.autopack.ingredient.ingredient": [[3, "module-cellpack.autopack.ingredient.Ingredient", false]], "cellpack.autopack.ingredient.multi_cylinder": [[3, "module-cellpack.autopack.ingredient.multi_cylinder", false]], "cellpack.autopack.ingredient.multi_sphere": [[3, "module-cellpack.autopack.ingredient.multi_sphere", false]], "cellpack.autopack.ingredient.single_cube": [[3, "module-cellpack.autopack.ingredient.single_cube", false]], "cellpack.autopack.ingredient.single_cylinder": [[3, "module-cellpack.autopack.ingredient.single_cylinder", false]], "cellpack.autopack.ingredient.single_sphere": [[3, "module-cellpack.autopack.ingredient.single_sphere", false]], "cellpack.autopack.ingredient.utils": [[3, "module-cellpack.autopack.ingredient.utils", false]], "cellpack.autopack.interface_objects": [[4, "module-cellpack.autopack.interface_objects", false]], "cellpack.autopack.interface_objects.database_ids": [[4, "module-cellpack.autopack.interface_objects.database_ids", false]], "cellpack.autopack.interface_objects.default_values": [[4, "module-cellpack.autopack.interface_objects.default_values", false]], "cellpack.autopack.interface_objects.gradient_data": [[4, "module-cellpack.autopack.interface_objects.gradient_data", false]], "cellpack.autopack.interface_objects.ingredient_types": [[4, "module-cellpack.autopack.interface_objects.ingredient_types", false]], "cellpack.autopack.interface_objects.meta_enum": [[4, "module-cellpack.autopack.interface_objects.meta_enum", false]], "cellpack.autopack.interface_objects.packed_objects": [[4, "module-cellpack.autopack.interface_objects.packed_objects", false]], "cellpack.autopack.interface_objects.partners": [[4, "module-cellpack.autopack.interface_objects.partners", false]], "cellpack.autopack.interface_objects.representations": [[4, "module-cellpack.autopack.interface_objects.representations", false]], "cellpack.autopack.ioutils": [[2, "module-cellpack.autopack.IOutils", false]], "cellpack.autopack.ldsequence": [[2, "module-cellpack.autopack.ldSequence", false]], "cellpack.autopack.loaders": [[5, "module-cellpack.autopack.loaders", false]], "cellpack.autopack.loaders.analysis_config_loader": [[5, "module-cellpack.autopack.loaders.analysis_config_loader", false]], "cellpack.autopack.loaders.config_loader": [[5, "module-cellpack.autopack.loaders.config_loader", false]], "cellpack.autopack.loaders.migrate_v1_to_v2": [[5, "module-cellpack.autopack.loaders.migrate_v1_to_v2", false]], "cellpack.autopack.loaders.migrate_v2_to_v2_1": [[5, "module-cellpack.autopack.loaders.migrate_v2_to_v2_1", false]], "cellpack.autopack.loaders.recipe_loader": [[5, "module-cellpack.autopack.loaders.recipe_loader", false]], "cellpack.autopack.loaders.utils": [[5, "module-cellpack.autopack.loaders.utils", false]], "cellpack.autopack.loaders.v1_v2_attribute_changes": [[5, "module-cellpack.autopack.loaders.v1_v2_attribute_changes", false]], "cellpack.autopack.meshstore": [[2, "module-cellpack.autopack.MeshStore", false]], "cellpack.autopack.octree": [[2, "module-cellpack.autopack.octree", false]], "cellpack.autopack.plotly_result": [[2, "module-cellpack.autopack.plotly_result", false]], "cellpack.autopack.randomrot": [[2, "module-cellpack.autopack.randomRot", false]], "cellpack.autopack.ray": [[2, "module-cellpack.autopack.ray", false]], "cellpack.autopack.recipe": [[2, "module-cellpack.autopack.Recipe", false]], "cellpack.autopack.serializable": [[2, "module-cellpack.autopack.Serializable", false]], "cellpack.autopack.trajectory": [[2, "module-cellpack.autopack.trajectory", false]], "cellpack.autopack.transformation": [[2, "module-cellpack.autopack.transformation", false]], "cellpack.autopack.upy": [[6, "module-cellpack.autopack.upy", false]], "cellpack.autopack.upy.colors": [[6, "module-cellpack.autopack.upy.colors", false]], "cellpack.autopack.upy.hosthelper": [[6, "module-cellpack.autopack.upy.hostHelper", false]], "cellpack.autopack.upy.simularium": [[7, "module-cellpack.autopack.upy.simularium", false]], "cellpack.autopack.upy.simularium.plots": [[7, "module-cellpack.autopack.upy.simularium.plots", false]], "cellpack.autopack.upy.simularium.simularium_helper": [[7, "module-cellpack.autopack.upy.simularium.simularium_helper", false]], "cellpack.autopack.utils": [[2, "module-cellpack.autopack.utils", false]], "cellpack.autopack.writers": [[8, "module-cellpack.autopack.writers", false]], "cellpack.autopack.writers.imagewriter": [[8, "module-cellpack.autopack.writers.ImageWriter", false]], "cellpack.bin": [[9, "module-cellpack.bin", false]], "cellpack.bin.analyze": [[9, "module-cellpack.bin.analyze", false]], "cellpack.bin.clean": [[9, "module-cellpack.bin.clean", false]], "cellpack.bin.cleanup_tasks": [[9, "module-cellpack.bin.cleanup_tasks", false]], "cellpack.bin.pack": [[9, "module-cellpack.bin.pack", false]], "cellpack.bin.simularium_converter": [[9, "module-cellpack.bin.simularium_converter", false]], "cellpack.bin.upload": [[9, "module-cellpack.bin.upload", false]], "center (cellpack.autopack.interface_objects.gradient_data.modeoptions attribute)": [[4, "cellpack.autopack.interface_objects.gradient_data.ModeOptions.center", false]], "chaltonsequence3 (class in cellpack.autopack.ldsequence)": [[2, "cellpack.autopack.ldSequence.cHaltonSequence3", false]], "changecolor() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.changeColor", false]], "changecolor() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.changeColor", false]], "changecoloro() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.changeColorO", false]], "changematerialproperty() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.changeMaterialProperty", false]], "changeobjcolormat() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.changeObjColorMat", false]], "changeobjcolormat() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.changeObjColorMat", false]], "check_against_one_packed_ingr() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.check_against_one_packed_ingr", false]], "check_and_replace_references() (cellpack.autopack.dbrecipehandler.compositiondoc method)": [[2, "cellpack.autopack.DBRecipeHandler.CompositionDoc.check_and_replace_references", false]], "check_new_placement() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.check_new_placement", false]], "check_paired_key() (in module cellpack.autopack.utils)": [[2, "cellpack.autopack.utils.check_paired_key", false]], "check_rectangle_oustide() (cellpack.autopack.geometrytools.geometrytools method)": [[2, "cellpack.autopack.GeometryTools.GeometryTools.check_rectangle_oustide", false]], "check_required_attributes() (in module cellpack.autopack.loaders.migrate_v1_to_v2)": [[5, "cellpack.autopack.loaders.migrate_v1_to_v2.check_required_attributes", false]], "check_sphere_inside() (cellpack.autopack.geometrytools.geometrytools method)": [[2, "cellpack.autopack.GeometryTools.GeometryTools.check_sphere_inside", false]], "checkcreateempty() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.checkCreateEmpty", false]], "checkcylcollisions() (cellpack.autopack.ingredient.multi_cylinder.multicylindersingr method)": [[3, "cellpack.autopack.ingredient.multi_cylinder.MultiCylindersIngr.checkCylCollisions", false]], "checkcylcollisions() (cellpack.autopack.ingredient.single_cylinder.singlecylinderingr method)": [[3, "cellpack.autopack.ingredient.single_cylinder.SingleCylinderIngr.checkCylCollisions", false]], "checkdistance() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.checkDistance", false]], "checkerrorinpath() (in module cellpack.autopack)": [[2, "cellpack.autopack.checkErrorInPath", false]], "checkifupdate() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.checkIfUpdate", false]], "checkingrpartnerproperties() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.checkIngrPartnerProperties", false]], "checkingrspheres() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.checkIngrSpheres", false]], "checkismesh() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.checkIsMesh", false]], "checkname() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.checkName", false]], "checkpath() (in module cellpack.autopack)": [[2, "cellpack.autopack.checkPath", false]], "checkpointinsidebb() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.checkPointInsideBB", false]], "checkrecipeavailable() (in module cellpack.autopack)": [[2, "cellpack.autopack.checkRecipeAvailable", false]], "checkrotformat() (in module cellpack.autopack.ioutils)": [[2, "cellpack.autopack.IOutils.checkRotFormat", false]], "circle() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.Circle", false]], "clean() (in module cellpack.bin.clean)": [[9, "cellpack.bin.clean.clean", false]], "clean_arguments() (cellpack.autopack.ioutils.ioingredienttool static method)": [[2, "cellpack.autopack.IOutils.IOingredientTool.clean_arguments", false]], "clean_grid_cache() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.clean_grid_cache", false]], "cleanup_results() (cellpack.autopack.dbrecipehandler.dbmaintenance method)": [[2, "cellpack.autopack.DBRecipeHandler.DBMaintenance.cleanup_results", false]], "clear() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.clear", false]], "clear() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.clear", false]], "clearall() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.clearAll", false]], "clearcaches() (in module cellpack.autopack)": [[2, "cellpack.autopack.clearCaches", false]], "clearfill() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.clearFill", false]], "clearingr() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.clearIngr", false]], "clearrbingredient() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.clearRBingredient", false]], "clearrecipe() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.clearRecipe", false]], "clone() (cellpack.autopack.binvox_rw.voxels method)": [[2, "cellpack.autopack.binvox_rw.Voxels.clone", false]], "close_partner_check() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.close_partner_check", false]], "cmp_to_key() (in module cellpack.autopack.utils)": [[2, "cellpack.autopack.utils.cmp_to_key", false]], "colladaexporter (class in cellpack.autopack.graphics)": [[2, "cellpack.autopack.Graphics.ColladaExporter", false]], "collect_and_sort_data() (cellpack.autopack.dbrecipehandler.dbrecipeloader static method)": [[2, "cellpack.autopack.DBRecipeHandler.DBRecipeLoader.collect_and_sort_data", false]], "collect_docs_by_id() (cellpack.autopack.dbrecipehandler.dbrecipeloader method)": [[2, "cellpack.autopack.DBRecipeHandler.DBRecipeLoader.collect_docs_by_id", false]], "collectresult() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.collectResult", false]], "collectresultperingredient() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.collectResultPerIngredient", false]], "collides_with_compartment() (cellpack.autopack.ingredient.multi_cylinder.multicylindersingr method)": [[3, "cellpack.autopack.ingredient.multi_cylinder.MultiCylindersIngr.collides_with_compartment", false]], "collides_with_compartment() (cellpack.autopack.ingredient.multi_sphere.multisphereingr method)": [[3, "cellpack.autopack.ingredient.multi_sphere.MultiSphereIngr.collides_with_compartment", false]], "collides_with_compartment() (cellpack.autopack.ingredient.single_cube.singlecubeingr method)": [[3, "cellpack.autopack.ingredient.single_cube.SingleCubeIngr.collides_with_compartment", false]], "collides_with_compartment() (cellpack.autopack.ingredient.single_cylinder.singlecylinderingr method)": [[3, "cellpack.autopack.ingredient.single_cylinder.SingleCylinderIngr.collides_with_compartment", false]], "collides_with_compartment() (cellpack.autopack.ingredient.single_sphere.singlesphereingr method)": [[3, "cellpack.autopack.ingredient.single_sphere.SingleSphereIngr.collides_with_compartment", false]], "collision_jitter() (cellpack.autopack.ingredient.multi_cylinder.multicylindersingr method)": [[3, "cellpack.autopack.ingredient.multi_cylinder.MultiCylindersIngr.collision_jitter", false]], "collision_jitter() (cellpack.autopack.ingredient.multi_sphere.multisphereingr method)": [[3, "cellpack.autopack.ingredient.multi_sphere.MultiSphereIngr.collision_jitter", false]], "collision_jitter() (cellpack.autopack.ingredient.single_cube.singlecubeingr method)": [[3, "cellpack.autopack.ingredient.single_cube.SingleCubeIngr.collision_jitter", false]], "collision_jitter() (cellpack.autopack.ingredient.single_cylinder.singlecylinderingr method)": [[3, "cellpack.autopack.ingredient.single_cylinder.SingleCylinderIngr.collision_jitter", false]], "collision_jitter() (cellpack.autopack.ingredient.single_sphere.singlesphereingr method)": [[3, "cellpack.autopack.ingredient.single_sphere.SingleSphereIngr.collision_jitter", false]], "color() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.color", false]], "colorbydistancefrom() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.colorByDistanceFrom", false]], "colorbyorder() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.colorByOrder", false]], "colormaterial() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.colorMaterial", false]], "colorobject() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.colorObject", false]], "colorpt() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.colorPT", false]], "combine_results_from_ingredients() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.combine_results_from_ingredients", false]], "combine_results_from_seeds() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.combine_results_from_seeds", false]], "combinedaemeshdata() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.combineDaeMeshData", false]], "compartment (class in cellpack.autopack.compartment)": [[2, "cellpack.autopack.Compartment.Compartment", false]], "compartment_id_for_nearest_grid_point() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.compartment_id_for_nearest_grid_point", false]], "compartmentlist (class in cellpack.autopack.compartment)": [[2, "cellpack.autopack.Compartment.CompartmentList", false]], "compile_db_recipe_data() (cellpack.autopack.dbrecipehandler.dbrecipeloader static method)": [[2, "cellpack.autopack.DBRecipeHandler.DBRecipeLoader.compile_db_recipe_data", false]], "completemapping() (cellpack.autopack.trajectory.trajectory method)": [[2, "cellpack.autopack.trajectory.Trajectory.completeMapping", false]], "compositiondoc (class in cellpack.autopack.dbrecipehandler)": [[2, "cellpack.autopack.DBRecipeHandler.CompositionDoc", false]], "compute_volume_and_set_count() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.compute_volume_and_set_count", false]], "computeexteriorvolume() (cellpack.autopack.basegrid.basegrid method)": [[2, "cellpack.autopack.BaseGrid.BaseGrid.computeExteriorVolume", false]], "computegridnumberofpoint() (cellpack.autopack.basegrid.basegrid method)": [[2, "cellpack.autopack.BaseGrid.BaseGrid.computeGridNumberOfPoint", false]], "computevolume() (cellpack.autopack.basegrid.basegrid method)": [[2, "cellpack.autopack.BaseGrid.BaseGrid.computeVolume", false]], "concatenate_image_data() (cellpack.autopack.writers.imagewriter.imagewriter method)": [[8, "cellpack.autopack.writers.ImageWriter.ImageWriter.concatenate_image_data", false]], "concatobjectmatrix() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.concatObjectMatrix", false]], "concatobjectmatrix() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.concatObjectMatrix", false]], "configloader (class in cellpack.autopack.loaders.config_loader)": [[5, "cellpack.autopack.loaders.config_loader.ConfigLoader", false]], "constraintlookat() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.constraintLookAt", false]], "contains_point() (cellpack.autopack.meshstore.meshstore method)": [[2, "cellpack.autopack.MeshStore.MeshStore.contains_point", false]], "contains_points_mesh() (cellpack.autopack.meshstore.meshstore method)": [[2, "cellpack.autopack.MeshStore.MeshStore.contains_points_mesh", false]], "convert() (in module cellpack.autopack.loaders.migrate_v1_to_v2)": [[5, "cellpack.autopack.loaders.migrate_v1_to_v2.convert", false]], "convert() (in module cellpack.autopack.loaders.migrate_v2_to_v2_1)": [[5, "cellpack.autopack.loaders.migrate_v2_to_v2_1.convert", false]], "convert_db_shortname_to_url() (in module cellpack.autopack)": [[2, "cellpack.autopack.convert_db_shortname_to_url", false]], "convert_gradients() (in module cellpack.autopack.loaders.migrate_v2_to_v2_1)": [[5, "cellpack.autopack.loaders.migrate_v2_to_v2_1.convert_gradients", false]], "convert_partners() (in module cellpack.autopack.loaders.migrate_v2_to_v2_1)": [[5, "cellpack.autopack.loaders.migrate_v2_to_v2_1.convert_partners", false]], "convert_positions_in_representation() (cellpack.autopack.dbrecipehandler.objectdoc static method)": [[2, "cellpack.autopack.DBRecipeHandler.ObjectDoc.convert_positions_in_representation", false]], "convert_representation() (cellpack.autopack.dbrecipehandler.objectdoc static method)": [[2, "cellpack.autopack.DBRecipeHandler.ObjectDoc.convert_representation", false]], "convert_rotation_range() (in module cellpack.autopack.loaders.migrate_v1_to_v2)": [[5, "cellpack.autopack.loaders.migrate_v1_to_v2.convert_rotation_range", false]], "convertcolor() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.convertColor", false]], "convertpickletotext() (cellpack.autopack.environment.environment class method)": [[2, "cellpack.autopack.Environment.Environment.convertPickleToText", false]], "converttosimularium (class in cellpack.bin.simularium_converter)": [[9, "cellpack.bin.simularium_converter.ConvertToSimularium", false]], "convolve_channel() (cellpack.autopack.writers.imagewriter.imagewriter static method)": [[8, "cellpack.autopack.writers.ImageWriter.ImageWriter.convolve_channel", false]], "convolve_image() (cellpack.autopack.writers.imagewriter.imagewriter method)": [[8, "cellpack.autopack.writers.ImageWriter.ImageWriter.convolve_image", false]], "correctbb() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.correctBB", false]], "create3dpointlookup() (cellpack.autopack.basegrid.haltongrid method)": [[2, "cellpack.autopack.BaseGrid.HaltonGrid.create3DPointLookup", false]], "create3dpointlookup() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.create3DPointLookup", false]], "create3dpointlookup() (cellpack.autopack.grid.grid method)": [[2, "cellpack.autopack.Grid.Grid.create3DPointLookup", false]], "create_box_psf() (cellpack.autopack.writers.imagewriter.imagewriter static method)": [[8, "cellpack.autopack.writers.ImageWriter.ImageWriter.create_box_psf", false]], "create_circular_mask() (cellpack.autopack.ingredient.single_sphere.singlesphereingr static method)": [[3, "cellpack.autopack.ingredient.single_sphere.SingleSphereIngr.create_circular_mask", false]], "create_compartment() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.create_compartment", false]], "create_divergent_color_map_with_scaled_values() (in module cellpack.autopack.upy.colors)": [[6, "cellpack.autopack.upy.colors.create_divergent_color_map_with_scaled_values", false]], "create_file_info_object_from_full_path() (in module cellpack.autopack.loaders.utils)": [[5, "cellpack.autopack.loaders.utils.create_file_info_object_from_full_path", false]], "create_gaussian_psf() (cellpack.autopack.writers.imagewriter.imagewriter static method)": [[8, "cellpack.autopack.writers.ImageWriter.ImageWriter.create_gaussian_psf", false]], "create_grid_point_positions() (cellpack.autopack.basegrid.basegrid method)": [[2, "cellpack.autopack.BaseGrid.BaseGrid.create_grid_point_positions", false]], "create_ingredient() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.create_ingredient", false]], "create_mesh() (cellpack.autopack.meshstore.meshstore method)": [[2, "cellpack.autopack.MeshStore.MeshStore.create_mesh", false]], "create_objects() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.create_objects", false]], "create_output_dir() (in module cellpack.autopack.loaders.utils)": [[5, "cellpack.autopack.loaders.utils.create_output_dir", false]], "create_path() (cellpack.autopack.firebasehandler.firebasehandler static method)": [[2, "cellpack.autopack.FirebaseHandler.FirebaseHandler.create_path", false]], "create_presigned_url() (cellpack.autopack.awshandler.awshandler method)": [[2, "cellpack.autopack.AWSHandler.AWSHandler.create_presigned_url", false]], "create_rbnode() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.create_rbnode", false]], "create_report() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.create_report", false]], "create_sphere() (cellpack.autopack.meshstore.meshstore method)": [[2, "cellpack.autopack.MeshStore.MeshStore.create_sphere", false]], "create_sphere_data() (cellpack.autopack.meshstore.meshstore method)": [[2, "cellpack.autopack.MeshStore.MeshStore.create_sphere_data", false]], "create_timestamp() (cellpack.autopack.firebasehandler.firebasehandler static method)": [[2, "cellpack.autopack.FirebaseHandler.FirebaseHandler.create_timestamp", false]], "create_voxelization() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.create_voxelization", false]], "create_voxelization() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.create_voxelization", false]], "create_voxelization() (cellpack.autopack.gradient.gradient method)": [[2, "cellpack.autopack.Gradient.Gradient.create_voxelization", false]], "create_voxelization() (cellpack.autopack.ingredient.single_sphere.singlesphereingr method)": [[3, "cellpack.autopack.ingredient.single_sphere.SingleSphereIngr.create_voxelization", false]], "create_voxelized_mask() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.create_voxelized_mask", false]], "createcolorsmat() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.createColorsMat", false]], "createingrmesh() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.createIngrMesh", false]], "creatematerial() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.createMaterial", false]], "createorganelmesh() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.createOrganelMesh", false]], "createsnmesh() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.createsNmesh", false]], "createspring() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.createSpring", false]], "createsurfacepoints() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.createSurfacePoints", false]], "createtemplate() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.createTemplate", false]], "createtemplatecompartment() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.createTemplateCompartment", false]], "createtexturedmaterial() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.createTexturedMaterial", false]], "cube (cellpack.autopack.interface_objects.gradient_data.weightmodes attribute)": [[4, "cellpack.autopack.interface_objects.gradient_data.WeightModes.CUBE", false]], "cube() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.Cube", false]], "cube_surface_distance() (cellpack.autopack.ingredient.single_cube.singlecubeingr method)": [[3, "cellpack.autopack.ingredient.single_cube.SingleCubeIngr.cube_surface_distance", false]], "cylinder() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.Cylinder", false]], "cylinder() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.cylinder", false]], "cylinderheadtails() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.CylinderHeadTails", false]], "cylinders() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.Cylinders", false]], "database (cellpack.autopack.interface_objects.representations.representations attribute)": [[4, "cellpack.autopack.interface_objects.representations.Representations.DATABASE", false]], "database (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper attribute)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.DATABASE", false]], "database_ids (class in cellpack.autopack.interface_objects.database_ids)": [[4, "cellpack.autopack.interface_objects.database_ids.DATABASE_IDS", false]], "datadoc (class in cellpack.autopack.dbrecipehandler)": [[2, "cellpack.autopack.DBRecipeHandler.DataDoc", false]], "db_name() (cellpack.autopack.firebasehandler.firebasehandler method)": [[2, "cellpack.autopack.FirebaseHandler.FirebaseHandler.db_name", false]], "dbmaintenance (class in cellpack.autopack.dbrecipehandler)": [[2, "cellpack.autopack.DBRecipeHandler.DBMaintenance", false]], "dbrecipeloader (class in cellpack.autopack.dbrecipehandler)": [[2, "cellpack.autopack.DBRecipeHandler.DBRecipeLoader", false]], "dbuploader (class in cellpack.autopack.dbrecipehandler)": [[2, "cellpack.autopack.DBRecipeHandler.DBUploader", false]], "dcd (cellpack.autopack.trajectory.dcdtrajectory attribute)": [[2, "cellpack.autopack.trajectory.dcdTrajectory.dcd", false]], "dcdtrajectory (class in cellpack.autopack.trajectory)": [[2, "cellpack.autopack.trajectory.dcdTrajectory", false]], "debug (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper attribute)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.DEBUG", false]], "decay_length (cellpack.autopack.interface_objects.gradient_data.weightmodeoptions attribute)": [[4, "cellpack.autopack.interface_objects.gradient_data.WeightModeOptions.decay_length", false]], "decompose4x4() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.Decompose4x4", false]], "decompose_mesh() (cellpack.autopack.meshstore.meshstore method)": [[2, "cellpack.autopack.MeshStore.MeshStore.decompose_mesh", false]], "decomposecolladageom() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.decomposeColladaGeom", false]], "decomposemesh() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.DecomposeMesh", false]], "decomposemesh() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.DecomposeMesh", false]], "deep_merge() (in module cellpack.autopack.utils)": [[2, "cellpack.autopack.utils.deep_merge", false]], "default() (cellpack.autopack.writers.numpyarrayencoder method)": [[8, "cellpack.autopack.writers.NumpyArrayEncoder.default", false]], "default_geo_type (cellpack.bin.simularium_converter.converttosimularium attribute)": [[9, "cellpack.bin.simularium_converter.ConvertToSimularium.DEFAULT_GEO_TYPE", false]], "default_input_recipe (cellpack.bin.simularium_converter.converttosimularium attribute)": [[9, "cellpack.bin.simularium_converter.ConvertToSimularium.DEFAULT_INPUT_RECIPE", false]], "default_output_directory (cellpack.bin.simularium_converter.converttosimularium attribute)": [[9, "cellpack.bin.simularium_converter.ConvertToSimularium.DEFAULT_OUTPUT_DIRECTORY", false]], "default_packing_result (cellpack.bin.simularium_converter.converttosimularium attribute)": [[9, "cellpack.bin.simularium_converter.ConvertToSimularium.DEFAULT_PACKING_RESULT", false]], "default_scale_factor (cellpack.bin.simularium_converter.converttosimularium attribute)": [[9, "cellpack.bin.simularium_converter.ConvertToSimularium.DEFAULT_SCALE_FACTOR", false]], "default_values (cellpack.autopack.dbrecipehandler.compositiondoc attribute)": [[2, "cellpack.autopack.DBRecipeHandler.CompositionDoc.DEFAULT_VALUES", false]], "default_values (cellpack.autopack.interface_objects.gradient_data.gradientdata attribute)": [[4, "cellpack.autopack.interface_objects.gradient_data.GradientData.default_values", false]], "default_values (cellpack.autopack.loaders.analysis_config_loader.analysisconfigloader attribute)": [[5, "cellpack.autopack.loaders.analysis_config_loader.AnalysisConfigLoader.default_values", false]], "default_values (cellpack.autopack.loaders.config_loader.configloader attribute)": [[5, "cellpack.autopack.loaders.config_loader.ConfigLoader.default_values", false]], "default_values (cellpack.autopack.loaders.recipe_loader.recipeloader attribute)": [[5, "cellpack.autopack.loaders.recipe_loader.RecipeLoader.default_values", false]], "defaultfunction() (cellpack.autopack.gradient.gradient method)": [[2, "cellpack.autopack.Gradient.Gradient.defaultFunction", false]], "delete_doc() (cellpack.autopack.firebasehandler.firebasehandler method)": [[2, "cellpack.autopack.FirebaseHandler.FirebaseHandler.delete_doc", false]], "deleteblist() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.deleteblist", false]], "deletechildrens() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.deleteChildrens", false]], "deleteinstance() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.deleteInstance", false]], "deletemeshedges() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.deleteMeshEdges", false]], "deletemeshfaces() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.deleteMeshFaces", false]], "deletemeshvertices() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.deleteMeshVertices", false]], "deleteobject() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.deleteObject", false]], "delingr() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.delIngr", false]], "delingredient() (cellpack.autopack.recipe.recipe method)": [[2, "cellpack.autopack.Recipe.Recipe.delIngredient", false]], "delingredientgrow() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.delIngredientGrow", false]], "delrb() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.delRB", false]], "dense_to_sparse() (in module cellpack.autopack.binvox_rw)": [[2, "cellpack.autopack.binvox_rw.dense_to_sparse", false]], "dihedral() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.dihedral", false]], "direction (cellpack.autopack.interface_objects.gradient_data.modeoptions attribute)": [[4, "cellpack.autopack.interface_objects.gradient_data.ModeOptions.direction", false]], "displaycompartment() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.displayCompartment", false]], "displaycompartmentpoints() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.displayCompartmentPoints", false]], "displaycompartments() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.displayCompartments", false]], "displaycompartmentsingredients() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.displayCompartmentsIngredients", false]], "displaycompartmentspoints() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.displayCompartmentsPoints", false]], "displaycytoplasmingredients() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.displayCytoplasmIngredients", false]], "displaydistance() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.displayDistance", false]], "displayenv() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.displayEnv", false]], "displayfill() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.displayFill", false]], "displayfillbox() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.displayFillBox", false]], "displayfreepoints() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.displayFreePoints", false]], "displayfreepointsasps() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.displayFreePointsAsPS", false]], "displaygradient() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.displayGradient", false]], "displayingrcylinders() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.displayIngrCylinders", false]], "displayingredients() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.displayIngredients", false]], "displayingrgrow() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.displayIngrGrow", false]], "displayingrgrows() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.displayIngrGrows", false]], "displayingrmesh() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.displayIngrMesh", false]], "displayingrresults() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.displayIngrResults", false]], "displayingrspheres() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.displayIngrSpheres", false]], "displayinstancesingredient() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.displayInstancesIngredient", false]], "displayleafoctree() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.displayLeafOctree", false]], "displayoctree() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.displayOctree", false]], "displayoctreeleaf() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.displayOctreeLeaf", false]], "displayonenodeoctree() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.displayOneNodeOctree", false]], "displayparticlevolumedistance() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.displayParticleVolumeDistance", false]], "displaypoints() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.displayPoints", false]], "displayprefill() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.displayPreFill", false]], "displayroot() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.displayRoot", false]], "displaysubnode() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.displaysubnode", false]], "distance (cellpack.autopack.interface_objects.gradient_data.invertoptions attribute)": [[4, "cellpack.autopack.interface_objects.gradient_data.InvertOptions.distance", false]], "distance_check_failed() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.distance_check_failed", false]], "distancefunction() (cellpack.autopack.interface_objects.partners.partner method)": [[4, "cellpack.autopack.interface_objects.partners.Partner.distanceFunction", false]], "distributionoptions (class in cellpack.autopack.ingredient.ingredient)": [[3, "cellpack.autopack.ingredient.Ingredient.DistributionOptions", false]], "distributiontypes (class in cellpack.autopack.ingredient.ingredient)": [[3, "cellpack.autopack.ingredient.Ingredient.DistributionTypes", false]], "doc_id() (cellpack.autopack.firebasehandler.firebasehandler static method)": [[2, "cellpack.autopack.FirebaseHandler.FirebaseHandler.doc_id", false]], "doc_to_dict() (cellpack.autopack.firebasehandler.firebasehandler static method)": [[2, "cellpack.autopack.FirebaseHandler.FirebaseHandler.doc_to_dict", false]], "dodecahedron() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.Dodecahedron", false], [6, "cellpack.autopack.upy.hostHelper.Helper.dodecahedron", false]], "doloop() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.doloop", false]], "dot() (in module cellpack.autopack.ray)": [[2, "cellpack.autopack.ray.dot", false]], "dot() (in module cellpack.autopack.upy.hosthelper)": [[6, "cellpack.autopack.upy.hostHelper.dot", false]], "download_file() (cellpack.autopack.awshandler.awshandler method)": [[2, "cellpack.autopack.AWSHandler.AWSHandler.download_file", false]], "download_file() (in module cellpack.autopack)": [[2, "cellpack.autopack.download_file", false]], "drawgradientline() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.drawGradientLine", false]], "drawptcol() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.drawPtCol", false]], "droponeingr() (cellpack.autopack.environment.environment class method)": [[2, "cellpack.autopack.Environment.Environment.dropOneIngr", false]], "droponeingrjson() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.dropOneIngrJson", false]], "dspmesh() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.dspMesh", false]], "dspsph() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.dspSph", false]], "duplivert (cellpack.autopack.upy.hosthelper.helper attribute)": [[6, "cellpack.autopack.upy.hostHelper.Helper.dupliVert", false]], "empty (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper attribute)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.EMPTY", false]], "environment (class in cellpack.autopack.environment)": [[2, "cellpack.autopack.Environment.Environment", false]], "eulertomatrix() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.eulerToMatrix", false]], "expand_object_using_key() (in module cellpack.autopack.utils)": [[2, "cellpack.autopack.utils.expand_object_using_key", false]], "exponential (cellpack.autopack.interface_objects.gradient_data.weightmodes attribute)": [[4, "cellpack.autopack.interface_objects.gradient_data.WeightModes.EXPONENTIAL", false]], "export_image() (cellpack.autopack.writers.imagewriter.imagewriter method)": [[8, "cellpack.autopack.writers.ImageWriter.ImageWriter.export_image", false]], "exportasindexedmeshs() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.exportAsIndexedMeshs", false]], "exportcollada (class in cellpack.autopack.ioutils)": [[2, "cellpack.autopack.IOutils.ExportCollada", false]], "exportingredient() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.exportIngredient", false]], "exportrecipeingredients() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.exportRecipeIngredients", false]], "exporttobd_box() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.exportToBD_BOX", false]], "exporttoreaddy() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.exportToReaDDy", false]], "exporttotem() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.exportToTEM", false]], "exporttotem_sim() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.exportToTEM_SIM", false]], "extend_bounding_box_for_compartments() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.extend_bounding_box_for_compartments", false]], "extendgridarrays() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.extendGridArrays", false]], "extractmeshcomponent() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.extractMeshComponent", false]], "f_dot_product() (in module cellpack.autopack.ray)": [[2, "cellpack.autopack.ray.f_dot_product", false]], "f_ray_intersect_polyhedron() (in module cellpack.autopack.ray)": [[2, "cellpack.autopack.ray.f_ray_intersect_polyhedron", false]], "far_enough_from_surfaces() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.far_enough_from_surfaces", false]], "fill_in_empty_fiber_data() (cellpack.bin.simularium_converter.converttosimularium method)": [[9, "cellpack.bin.simularium_converter.ConvertToSimularium.fill_in_empty_fiber_data", false]], "filltrianglecolor() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.fillTriangleColor", false]], "filter_surface_pts_to_fill_box() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.filter_surface_pts_to_fill_box", false]], "find_nearest() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.find_nearest", false]], "findbranch() (cellpack.autopack.octree.octree method)": [[2, "cellpack.autopack.octree.Octree.findBranch", false]], "findclosestpoint() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.findClosestPoint", false]], "findpointscenter() (in module cellpack.autopack.ray)": [[2, "cellpack.autopack.ray.findPointsCenter", false]], "findposition() (cellpack.autopack.octree.octree method)": [[2, "cellpack.autopack.octree.Octree.findPosition", false]], "finishwithwater() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.finishWithWater", false]], "firebase (cellpack.autopack.interface_objects.database_ids.database_ids attribute)": [[4, "cellpack.autopack.interface_objects.database_ids.DATABASE_IDS.FIREBASE", false]], "firebasehandler (class in cellpack.autopack.firebasehandler)": [[2, "cellpack.autopack.FirebaseHandler.FirebaseHandler", false]], "fit_view3d() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.fit_view3D", false]], "fixnormals() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.FixNormals", false]], "fixonepath() (in module cellpack.autopack)": [[2, "cellpack.autopack.fixOnePath", false]], "fixpath() (in module cellpack.autopack)": [[2, "cellpack.autopack.fixPath", false]], "format_color() (cellpack.autopack.plotly_result.plotlyanalysis static method)": [[2, "cellpack.autopack.plotly_result.PlotlyAnalysis.format_color", false]], "format_rgb_color() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper static method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.format_rgb_color", false]], "frameadvanced() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.frameAdvanced", false]], "fromvec() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.FromVec", false]], "gatherresult() (in module cellpack.autopack.ioutils)": [[2, "cellpack.autopack.IOutils.gatherResult", false]], "gblob (cellpack.autopack.interface_objects.gradient_data.modeoptions attribute)": [[4, "cellpack.autopack.interface_objects.gradient_data.ModeOptions.gblob", false]], "generalapply() (cellpack.autopack.trajectory.trajectory method)": [[2, "cellpack.autopack.trajectory.Trajectory.generalApply", false]], "geom() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.Geom", false]], "geometrytools (class in cellpack.autopack.geometrytools)": [[2, "cellpack.autopack.GeometryTools.GeometryTools", false]], "get() (cellpack.autopack.randomrot.randomrot method)": [[2, "cellpack.autopack.randomRot.RandomRot.get", false]], "get_active() (cellpack.autopack.interface_objects.representations.representations method)": [[4, "cellpack.autopack.interface_objects.representations.Representations.get_active", false]], "get_active_data() (cellpack.autopack.interface_objects.representations.representations method)": [[4, "cellpack.autopack.interface_objects.representations.Representations.get_active_data", false]], "get_adjusted_position() (cellpack.autopack.interface_objects.representations.representations method)": [[4, "cellpack.autopack.interface_objects.representations.Representations.get_adjusted_position", false]], "get_all() (cellpack.autopack.interface_objects.packed_objects.packedobjects method)": [[4, "cellpack.autopack.interface_objects.packed_objects.PackedObjects.get_all", false]], "get_all_distances() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.get_all_distances", false]], "get_all_docs() (cellpack.autopack.firebasehandler.firebasehandler method)": [[2, "cellpack.autopack.FirebaseHandler.FirebaseHandler.get_all_docs", false]], "get_all_ingredients() (cellpack.autopack.loaders.recipe_loader.recipeloader method)": [[5, "cellpack.autopack.loaders.recipe_loader.RecipeLoader.get_all_ingredients", false]], "get_all_positions_to_check() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.get_all_positions_to_check", false]], "get_alternate_position() (cellpack.autopack.ingredient.grow.growingredient method)": [[3, "cellpack.autopack.ingredient.grow.GrowIngredient.get_alternate_position", false]], "get_alternate_position_p() (cellpack.autopack.ingredient.grow.growingredient method)": [[3, "cellpack.autopack.ingredient.grow.GrowIngredient.get_alternate_position_p", false]], "get_and_store_v2_object() (in module cellpack.autopack.loaders.migrate_v1_to_v2)": [[5, "cellpack.autopack.loaders.migrate_v1_to_v2.get_and_store_v2_object", false]], "get_attributes_to_update() (cellpack.autopack.environment.environment static method)": [[2, "cellpack.autopack.Environment.Environment.get_attributes_to_update", false]], "get_aws_object_key() (cellpack.autopack.awshandler.awshandler method)": [[2, "cellpack.autopack.AWSHandler.AWSHandler.get_aws_object_key", false]], "get_bbox() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.get_bbox", false]], "get_bounding_box() (cellpack.bin.simularium_converter.converttosimularium method)": [[9, "cellpack.bin.simularium_converter.ConvertToSimularium.get_bounding_box", false]], "get_bounding_box_limits() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.get_bounding_box_limits", false]], "get_cache_location() (in module cellpack.autopack)": [[2, "cellpack.autopack.get_cache_location", false]], "get_center() (cellpack.autopack.gradient.gradient method)": [[2, "cellpack.autopack.Gradient.Gradient.get_center", false]], "get_centroid() (cellpack.autopack.meshstore.meshstore method)": [[2, "cellpack.autopack.MeshStore.MeshStore.get_centroid", false]], "get_closest_ingredients() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.get_closest_ingredients", false]], "get_collada_material() (cellpack.autopack.meshstore.meshstore static method)": [[2, "cellpack.autopack.MeshStore.MeshStore.get_collada_material", false]], "get_collection_id_from_path() (cellpack.autopack.firebasehandler.firebasehandler static method)": [[2, "cellpack.autopack.FirebaseHandler.FirebaseHandler.get_collection_id_from_path", false]], "get_combined_gradient_weight() (cellpack.autopack.gradient.gradient static method)": [[2, "cellpack.autopack.Gradient.Gradient.get_combined_gradient_weight", false]], "get_compartment() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.get_compartment", false]], "get_compartment() (cellpack.autopack.interface_objects.packed_objects.packedobjects method)": [[4, "cellpack.autopack.interface_objects.packed_objects.PackedObjects.get_compartment", false]], "get_compartment_object_by_name() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.get_compartment_object_by_name", false]], "get_creds() (cellpack.autopack.firebasehandler.firebasehandler static method)": [[2, "cellpack.autopack.FirebaseHandler.FirebaseHandler.get_creds", false]], "get_cuttoff_value() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.get_cuttoff_value", false]], "get_cuttoff_value() (cellpack.autopack.ingredient.multi_cylinder.multicylindersingr method)": [[3, "cellpack.autopack.ingredient.multi_cylinder.MultiCylindersIngr.get_cuttoff_value", false]], "get_cuttoff_value() (cellpack.autopack.ingredient.single_cylinder.singlecylinderingr method)": [[3, "cellpack.autopack.ingredient.single_cylinder.SingleCylinderIngr.get_cuttoff_value", false]], "get_deepest_level() (cellpack.autopack.interface_objects.representations.representations method)": [[4, "cellpack.autopack.interface_objects.representations.Representations.get_deepest_level", false]], "get_dev_creds() (cellpack.autopack.firebasehandler.firebasehandler static method)": [[2, "cellpack.autopack.FirebaseHandler.FirebaseHandler.get_dev_creds", false]], "get_display_data() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.get_display_data", false]], "get_distance() (in module cellpack.autopack.utils)": [[2, "cellpack.autopack.utils.get_distance", false]], "get_distances() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.get_distances", false]], "get_distances_and_angles() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.get_distances_and_angles", false]], "get_distances_from_point() (in module cellpack.autopack.utils)": [[2, "cellpack.autopack.utils.get_distances_from_point", false]], "get_doc_by_id() (cellpack.autopack.firebasehandler.firebasehandler method)": [[2, "cellpack.autopack.FirebaseHandler.FirebaseHandler.get_doc_by_id", false]], "get_doc_by_name() (cellpack.autopack.firebasehandler.firebasehandler method)": [[2, "cellpack.autopack.FirebaseHandler.FirebaseHandler.get_doc_by_name", false]], "get_doc_by_ref() (cellpack.autopack.firebasehandler.firebasehandler method)": [[2, "cellpack.autopack.FirebaseHandler.FirebaseHandler.get_doc_by_ref", false]], "get_dpad() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.get_dpad", false]], "get_encapsulating_radii() (cellpack.autopack.interface_objects.packed_objects.packedobjects method)": [[4, "cellpack.autopack.interface_objects.packed_objects.PackedObjects.get_encapsulating_radii", false]], "get_euler() (cellpack.bin.simularium_converter.converttosimularium method)": [[9, "cellpack.bin.simularium_converter.ConvertToSimularium.get_euler", false]], "get_euler_from_matrix() (cellpack.bin.simularium_converter.converttosimularium method)": [[9, "cellpack.bin.simularium_converter.ConvertToSimularium.get_euler_from_matrix", false]], "get_euler_from_quat() (cellpack.bin.simularium_converter.converttosimularium method)": [[9, "cellpack.bin.simularium_converter.ConvertToSimularium.get_euler_from_quat", false]], "get_gauss_weights() (cellpack.autopack.gradient.gradient method)": [[2, "cellpack.autopack.Gradient.Gradient.get_gauss_weights", false]], "get_ingredient_angles() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.get_ingredient_angles", false]], "get_ingredient_by_name() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.get_ingredient_by_name", false]], "get_ingredient_data() (cellpack.bin.simularium_converter.converttosimularium method)": [[9, "cellpack.bin.simularium_converter.ConvertToSimularium.get_ingredient_data", false]], "get_ingredient_display_data() (cellpack.bin.simularium_converter.converttosimularium method)": [[9, "cellpack.bin.simularium_converter.ConvertToSimularium.get_ingredient_display_data", false]], "get_ingredient_key_from_object_or_comp_name() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.get_ingredient_key_from_object_or_comp_name", false]], "get_ingredient_radii() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.get_ingredient_radii", false]], "get_ingredients() (cellpack.autopack.interface_objects.packed_objects.packedobjects method)": [[4, "cellpack.autopack.interface_objects.packed_objects.PackedObjects.get_ingredients", false]], "get_ingredients_in_tree() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.get_ingredients_in_tree", false]], "get_list_of_dims() (cellpack.autopack.analysis.analysis static method)": [[2, "cellpack.autopack.Analysis.Analysis.get_list_of_dims", false]], "get_list_of_free_indices() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.get_list_of_free_indices", false]], "get_local_file_location() (in module cellpack.autopack)": [[2, "cellpack.autopack.get_local_file_location", false]], "get_max_value_from_distribution() (in module cellpack.autopack.utils)": [[2, "cellpack.autopack.utils.get_max_value_from_distribution", false]], "get_mesh() (cellpack.autopack.meshstore.meshstore method)": [[2, "cellpack.autopack.MeshStore.MeshStore.get_mesh", false]], "get_mesh_data() (cellpack.bin.simularium_converter.converttosimularium static method)": [[9, "cellpack.bin.simularium_converter.ConvertToSimularium.get_mesh_data", false]], "get_mesh_filepath_and_extension() (cellpack.autopack.meshstore.meshstore static method)": [[2, "cellpack.autopack.MeshStore.MeshStore.get_mesh_filepath_and_extension", false]], "get_mesh_format() (cellpack.autopack.interface_objects.representations.representations method)": [[4, "cellpack.autopack.interface_objects.representations.Representations.get_mesh_format", false]], "get_mesh_name() (cellpack.autopack.interface_objects.representations.representations method)": [[4, "cellpack.autopack.interface_objects.representations.Representations.get_mesh_name", false]], "get_mesh_path() (cellpack.autopack.interface_objects.representations.representations method)": [[4, "cellpack.autopack.interface_objects.representations.Representations.get_mesh_path", false]], "get_midpoint() (cellpack.autopack.meshstore.meshstore static method)": [[2, "cellpack.autopack.MeshStore.MeshStore.get_midpoint", false]], "get_min_max_radius() (cellpack.autopack.interface_objects.representations.representations method)": [[4, "cellpack.autopack.interface_objects.representations.Representations.get_min_max_radius", false]], "get_min_value_from_distribution() (in module cellpack.autopack.utils)": [[2, "cellpack.autopack.utils.get_min_value_from_distribution", false]], "get_minimum_expected_distance_from_recipe() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.get_minimum_expected_distance_from_recipe", false]], "get_module_version() (in module cellpack)": [[1, "cellpack.get_module_version", false]], "get_new_distance_values() (cellpack.autopack.ingredient.grow.growingredient method)": [[3, "cellpack.autopack.ingredient.grow.GrowIngredient.get_new_distance_values", false]], "get_new_distance_values() (cellpack.autopack.ingredient.multi_sphere.multisphereingr method)": [[3, "cellpack.autopack.ingredient.multi_sphere.MultiSphereIngr.get_new_distance_values", false]], "get_new_distance_values() (cellpack.autopack.ingredient.single_cube.singlecubeingr method)": [[3, "cellpack.autopack.ingredient.single_cube.SingleCubeIngr.get_new_distance_values", false]], "get_new_distance_values() (cellpack.autopack.ingredient.single_sphere.singlesphereingr method)": [[3, "cellpack.autopack.ingredient.single_sphere.SingleSphereIngr.get_new_distance_values", false]], "get_new_distances_and_inside_points() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.get_new_distances_and_inside_points", false]], "get_new_jitter_location_and_rotation() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.get_new_jitter_location_and_rotation", false]], "get_new_pos() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.get_new_pos", false]], "get_noise() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.get_noise", false]], "get_normal() (cellpack.autopack.meshstore.meshstore method)": [[2, "cellpack.autopack.MeshStore.MeshStore.get_normal", false]], "get_normal_for_point() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.get_normal_for_point", false]], "get_nsphere() (cellpack.autopack.meshstore.meshstore method)": [[2, "cellpack.autopack.MeshStore.MeshStore.get_nsphere", false]], "get_number_of_ingredients_packed() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.get_number_of_ingredients_packed", false]], "get_obj_dict() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.get_obj_dict", false]], "get_object() (cellpack.autopack.meshstore.meshstore method)": [[2, "cellpack.autopack.MeshStore.MeshStore.get_object", false]], "get_packed_minimum_distance() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.get_packed_minimum_distance", false]], "get_paired_key() (in module cellpack.autopack.utils)": [[2, "cellpack.autopack.utils.get_paired_key", false]], "get_partner_by_ingr_name() (cellpack.autopack.interface_objects.partners.partners method)": [[4, "cellpack.autopack.interface_objects.partners.Partners.get_partner_by_ingr_name", false]], "get_partner_pair_dict() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.get_partner_pair_dict", false]], "get_partners() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.get_partners", false]], "get_path_from_ref() (cellpack.autopack.firebasehandler.firebasehandler static method)": [[2, "cellpack.autopack.FirebaseHandler.FirebaseHandler.get_path_from_ref", false]], "get_pdb_path() (cellpack.autopack.interface_objects.representations.representations method)": [[4, "cellpack.autopack.interface_objects.representations.Representations.get_pdb_path", false]], "get_point() (cellpack.autopack.interface_objects.partners.partner method)": [[4, "cellpack.autopack.interface_objects.partners.Partner.get_point", false]], "get_positions() (cellpack.autopack.interface_objects.packed_objects.packedobjects method)": [[4, "cellpack.autopack.interface_objects.packed_objects.PackedObjects.get_positions", false]], "get_positions() (cellpack.autopack.interface_objects.representations.representations method)": [[4, "cellpack.autopack.interface_objects.representations.Representations.get_positions", false]], "get_positions_for_ingredient() (cellpack.autopack.interface_objects.packed_objects.packedobjects method)": [[4, "cellpack.autopack.interface_objects.packed_objects.PackedObjects.get_positions_for_ingredient", false]], "get_positions_per_ingredient() (cellpack.bin.simularium_converter.converttosimularium method)": [[9, "cellpack.bin.simularium_converter.ConvertToSimularium.get_positions_per_ingredient", false]], "get_radii() (cellpack.autopack.interface_objects.packed_objects.packedobjects method)": [[4, "cellpack.autopack.interface_objects.packed_objects.PackedObjects.get_radii", false]], "get_radii() (cellpack.autopack.interface_objects.representations.representations method)": [[4, "cellpack.autopack.interface_objects.representations.Representations.get_radii", false]], "get_radius() (cellpack.autopack.ingredient.multi_sphere.multisphereingr method)": [[3, "cellpack.autopack.ingredient.multi_sphere.MultiSphereIngr.get_radius", false]], "get_radius() (cellpack.autopack.ingredient.single_sphere.singlesphereingr method)": [[3, "cellpack.autopack.ingredient.single_sphere.SingleSphereIngr.get_radius", false]], "get_rb_model() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.get_rb_model", false]], "get_rb_model() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.get_rb_model", false]], "get_rbnodes() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.get_rbNodes", false]], "get_recipe_metadata() (in module cellpack.bin.upload)": [[9, "cellpack.bin.upload.get_recipe_metadata", false]], "get_rectangle_cercle_area() (cellpack.autopack.geometrytools.geometrytools method)": [[2, "cellpack.autopack.GeometryTools.GeometryTools.get_rectangle_cercle_area", false]], "get_reference_data() (cellpack.autopack.dbrecipehandler.compositiondoc static method)": [[2, "cellpack.autopack.DBRecipeHandler.CompositionDoc.get_reference_data", false]], "get_reference_in_obj() (cellpack.autopack.dbrecipehandler.compositiondoc static method)": [[2, "cellpack.autopack.DBRecipeHandler.CompositionDoc.get_reference_in_obj", false]], "get_reflected_point() (in module cellpack.autopack.ingredient.utils)": [[3, "cellpack.autopack.ingredient.utils.get_reflected_point", false]], "get_representations() (in module cellpack.autopack.loaders.migrate_v1_to_v2)": [[5, "cellpack.autopack.loaders.migrate_v1_to_v2.get_representations", false]], "get_rotation() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.get_rotation", false]], "get_rotations_for_ingredient() (cellpack.autopack.interface_objects.packed_objects.packedobjects method)": [[4, "cellpack.autopack.interface_objects.packed_objects.PackedObjects.get_rotations_for_ingredient", false]], "get_scaled_distances_between_surfaces() (cellpack.autopack.meshstore.meshstore method)": [[2, "cellpack.autopack.MeshStore.MeshStore.get_scaled_distances_between_surfaces", false]], "get_seed_list() (in module cellpack.autopack.utils)": [[2, "cellpack.autopack.utils.get_seed_list", false]], "get_signed_distance() (cellpack.autopack.ingredient.grow.growingredient method)": [[3, "cellpack.autopack.ingredient.grow.GrowIngredient.get_signed_distance", false]], "get_signed_distance() (cellpack.autopack.ingredient.multi_sphere.multisphereingr method)": [[3, "cellpack.autopack.ingredient.multi_sphere.MultiSphereIngr.get_signed_distance", false]], "get_signed_distance() (cellpack.autopack.ingredient.single_cube.singlecubeingr method)": [[3, "cellpack.autopack.ingredient.single_cube.SingleCubeIngr.get_signed_distance", false]], "get_signed_distance() (cellpack.autopack.ingredient.single_cylinder.singlecylinderingr method)": [[3, "cellpack.autopack.ingredient.single_cylinder.SingleCylinderIngr.get_signed_distance", false]], "get_signed_distance() (cellpack.autopack.ingredient.single_sphere.singlesphereingr method)": [[3, "cellpack.autopack.ingredient.single_sphere.SingleSphereIngr.get_signed_distance", false]], "get_size_of_bounding_box() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.get_size_of_bounding_box", false]], "get_smallest_radius() (cellpack.autopack.meshstore.meshstore method)": [[2, "cellpack.autopack.MeshStore.MeshStore.get_smallest_radius", false]], "get_staging_creds() (cellpack.autopack.firebasehandler.firebasehandler static method)": [[2, "cellpack.autopack.FirebaseHandler.FirebaseHandler.get_staging_creds", false]], "get_username() (cellpack.autopack.firebasehandler.firebasehandler static method)": [[2, "cellpack.autopack.FirebaseHandler.FirebaseHandler.get_username", false]], "get_value() (cellpack.autopack.firebasehandler.firebasehandler method)": [[2, "cellpack.autopack.FirebaseHandler.FirebaseHandler.get_value", false]], "get_value_from_distribution() (in module cellpack.autopack.utils)": [[2, "cellpack.autopack.utils.get_value_from_distribution", false]], "get_weights_by_distance() (cellpack.autopack.ingredient.agent.agent method)": [[3, "cellpack.autopack.ingredient.agent.Agent.get_weights_by_distance", false]], "geta() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.getA", false]], "getabsposuntilroot() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.GetAbsPosUntilRoot", false]], "getactiveing() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.getActiveIng", false]], "getallmaterials() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.getAllMaterials", false]], "getallmaterials() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.getAllMaterials", false]], "getallposrot() (in module cellpack.autopack.ioutils)": [[2, "cellpack.autopack.IOutils.getAllPosRot", false]], "getangleaxis() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.getAngleAxis", false]], "getaxisrotation() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.getAxisRotation", false]], "getbiasedrotation() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.getBiasedRotation", false]], "getbigbb() (cellpack.autopack.ingredient.multi_cylinder.multicylindersingr method)": [[3, "cellpack.autopack.ingredient.multi_cylinder.MultiCylindersIngr.getBigBB", false]], "getbigbb() (cellpack.autopack.ingredient.single_cylinder.singlecylinderingr method)": [[3, "cellpack.autopack.ingredient.single_cylinder.SingleCylinderIngr.getBigBB", false]], "getbinaryweighted() (cellpack.autopack.gradient.gradient method)": [[2, "cellpack.autopack.Gradient.Gradient.getBinaryWeighted", false]], "getboundary() (cellpack.autopack.geometrytools.geometrytools method)": [[2, "cellpack.autopack.GeometryTools.GeometryTools.getBoundary", false]], "getboundingbox() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.getBoundingBox", false]], "getboxsize() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.getBoxSize", false]], "getcenter() (cellpack.autopack.basegrid.basegrid method)": [[2, "cellpack.autopack.BaseGrid.BaseGrid.getCenter", false]], "getcenter() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.getCenter", false]], "getcenter() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.getCenter", false]], "getchilds() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.getChilds", false]], "getclosestfreegridpoint() (cellpack.autopack.basegrid.basegrid method)": [[2, "cellpack.autopack.BaseGrid.BaseGrid.getClosestFreeGridPoint", false]], "getclosestgridpoint() (cellpack.autopack.basegrid.basegrid method)": [[2, "cellpack.autopack.BaseGrid.BaseGrid.getClosestGridPoint", false]], "getcolladamaterial() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.getColladaMaterial", false]], "getcornerpointcube() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.getCornerPointCube", false]], "getcornerpointcube() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.getCornerPointCube", false]], "getcurrentscene() (cellpack.autopack.upy.hosthelper.helper class method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.getCurrentScene", false]], "getcurrentscene() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.getCurrentScene", false]], "getcurrentscenename() (cellpack.autopack.upy.hosthelper.helper class method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.getCurrentSceneName", false]], "getcurrentselection() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.getCurrentSelection", false]], "getcurrentselection() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.getCurrentSelection", false]], "getdata() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.getData", false]], "getdiagonal() (cellpack.autopack.basegrid.basegrid method)": [[2, "cellpack.autopack.BaseGrid.BaseGrid.getDiagonal", false]], "getdihedral() (in module cellpack.autopack.ingredient.utils)": [[3, "cellpack.autopack.ingredient.utils.getDihedral", false]], "getdistance() (cellpack.autopack.geometrytools.geometrytools method)": [[2, "cellpack.autopack.GeometryTools.GeometryTools.GetDistance", false]], "getencapsulatingradius() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.getEncapsulatingRadius", false]], "getface() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.getFace", false]], "getface() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.getFace", false]], "getfaceedges() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.getFaceEdges", false]], "getfacenormals() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.getFaceNormals", false]], "getfacenormalsarea() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.getFaceNormalsArea", false]], "getfaces() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.getFaces", false]], "getfacesfromv() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.getFacesfromV", false]], "getfacesnfromv() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.getFacesNfromV", false]], "getfirstpoint() (cellpack.autopack.ingredient.grow.growingredient method)": [[3, "cellpack.autopack.ingredient.grow.GrowIngredient.getFirstPoint", false]], "getforwweight() (cellpack.autopack.gradient.gradient method)": [[2, "cellpack.autopack.Gradient.Gradient.getForwWeight", false]], "gethaltonunique() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.getHaltonUnique", false]], "gethclass() (in module cellpack.autopack.upy)": [[6, "cellpack.autopack.upy.getHClass", false]], "gethelperclass() (in module cellpack.autopack.upy)": [[6, "cellpack.autopack.upy.getHelperClass", false]], "getijk() (cellpack.autopack.basegrid.basegrid method)": [[2, "cellpack.autopack.BaseGrid.BaseGrid.getIJK", false]], "getijk() (cellpack.autopack.grid.grid method)": [[2, "cellpack.autopack.Grid.Grid.getIJK", false]], "getimage() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.getImage", false]], "getindex() (cellpack.autopack.binvox_rw.voxels method)": [[2, "cellpack.autopack.binvox_rw.Voxels.getIndex", false]], "getindexdata() (cellpack.autopack.binvox_rw.voxels method)": [[2, "cellpack.autopack.binvox_rw.Voxels.getIndexData", false]], "getingredientinstancepos() (cellpack.autopack.trajectory.trajectory method)": [[2, "cellpack.autopack.trajectory.Trajectory.getIngredientInstancePos", false]], "getingredientsinbox() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.getIngredientsInBox", false]], "getingrfromnameinrecipe() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.getIngrFromNameInRecipe", false]], "getinterpolatednormal() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.getInterpolatedNormal", false]], "getinterpolatedsphere() (cellpack.autopack.ingredient.grow.growingredient method)": [[3, "cellpack.autopack.ingredient.grow.GrowIngredient.getInterpolatedSphere", false]], "getjtransrot() (cellpack.autopack.ingredient.grow.growingredient method)": [[3, "cellpack.autopack.ingredient.grow.GrowIngredient.getJtransRot", false]], "getjtransrot_r() (cellpack.autopack.ingredient.grow.growingredient method)": [[3, "cellpack.autopack.ingredient.grow.GrowIngredient.getJtransRot_r", false]], "getlayers() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.getLayers", false]], "getlinearweighted() (cellpack.autopack.gradient.gradient method)": [[2, "cellpack.autopack.Gradient.Gradient.getLinearWeighted", false]], "getlistcompfrommask() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.getListCompFromMask", false]], "getmasterinstance() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.getMasterInstance", false]], "getmaterial() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.getMaterial", false]], "getmaterial() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.getMaterial", false]], "getmaterialname() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.getMaterialName", false]], "getmaterialobject() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.getMaterialObject", false]], "getmaterialproperty() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.getMaterialProperty", false]], "getmaxjitter() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.getMaxJitter", false]], "getmaxweight() (cellpack.autopack.gradient.gradient method)": [[2, "cellpack.autopack.Gradient.Gradient.getMaxWeight", false]], "getmesh() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.getMesh", false]], "getmesh() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.getMesh", false]], "getmesh() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.getMesh", false]], "getmesh() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.getMesh", false]], "getmeshedge() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.getMeshEdge", false]], "getmeshedges() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.getMeshEdges", false]], "getmeshedges() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.getMeshEdges", false]], "getmeshfaces() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.getMeshFaces", false]], "getmeshfaces() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.getMeshFaces", false]], "getmeshnormales() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.getMeshNormales", false]], "getmeshnormales() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.getMeshNormales", false]], "getmeshvertice() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.getMeshVertice", false]], "getmeshvertices() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.getMeshVertices", false]], "getmeshvertices() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.getMeshVertices", false]], "getminmaxproteinsize() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.getMinMaxProteinSize", false]], "getminmaxproteinsize() (cellpack.autopack.recipe.recipe method)": [[2, "cellpack.autopack.Recipe.Recipe.getMinMaxProteinSize", false]], "getminweight() (cellpack.autopack.gradient.gradient method)": [[2, "cellpack.autopack.Gradient.Gradient.getMinWeight", false]], "getname() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.getName", false]], "getname() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.getName", false]], "getnbgridpoints() (cellpack.autopack.basegrid.haltongrid method)": [[2, "cellpack.autopack.BaseGrid.HaltonGrid.getNBgridPoints", false]], "getnextpoint() (cellpack.autopack.ingredient.grow.growingredient method)": [[3, "cellpack.autopack.ingredient.grow.GrowIngredient.getNextPoint", false]], "getnextptindcyl() (cellpack.autopack.ingredient.grow.growingredient method)": [[3, "cellpack.autopack.ingredient.grow.GrowIngredient.getNextPtIndCyl", false]], "getnormals() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.getNormals", false]], "getnormedvector() (in module cellpack.autopack.ingredient.utils)": [[3, "cellpack.autopack.ingredient.utils.getNormedVector", false]], "getnormedvectorones() (in module cellpack.autopack.ingredient.utils)": [[3, "cellpack.autopack.ingredient.utils.getNormedVectorOnes", false]], "getnormedvectoru() (in module cellpack.autopack.ingredient.utils)": [[3, "cellpack.autopack.ingredient.utils.getNormedVectorU", false]], "getobject() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.getObject", false]], "getobject() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.getObject", false]], "getobjectname() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.getObjectName", false]], "getold() (cellpack.autopack.randomrot.randomrot method)": [[2, "cellpack.autopack.randomRot.RandomRot.getOld", false]], "getoneingr() (cellpack.autopack.environment.environment class method)": [[2, "cellpack.autopack.Environment.Environment.getOneIngr", false]], "getoneingrjson() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.getOneIngrJson", false]], "getorder() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.getOrder", false]], "getparticles() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.getParticles", false]], "getparticulesposition() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.getParticulesPosition", false]], "getpointfrom3d() (cellpack.autopack.basegrid.basegrid method)": [[2, "cellpack.autopack.BaseGrid.BaseGrid.getPointFrom3D", false]], "getpointfrom3d() (cellpack.autopack.basegrid.haltongrid method)": [[2, "cellpack.autopack.BaseGrid.HaltonGrid.getPointFrom3D", false]], "getpointsincube() (cellpack.autopack.basegrid.basegrid method)": [[2, "cellpack.autopack.BaseGrid.BaseGrid.getPointsInCube", false]], "getpointsincubefillbb() (cellpack.autopack.basegrid.basegrid method)": [[2, "cellpack.autopack.BaseGrid.BaseGrid.getPointsInCubeFillBB", false]], "getpointsinsphere() (cellpack.autopack.basegrid.basegrid method)": [[2, "cellpack.autopack.BaseGrid.BaseGrid.getPointsInSphere", false]], "getpointtodrop() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.getPointToDrop", false]], "getposat() (cellpack.autopack.trajectory.dcdtrajectory method)": [[2, "cellpack.autopack.trajectory.dcdTrajectory.getPosAt", false]], "getposat() (cellpack.autopack.trajectory.molbtrajectory method)": [[2, "cellpack.autopack.trajectory.molbTrajectory.getPosAt", false]], "getposat() (cellpack.autopack.trajectory.xyztrajectory method)": [[2, "cellpack.autopack.trajectory.xyzTrajectory.getPosAt", false]], "getpositionperidocity() (cellpack.autopack.basegrid.basegrid method)": [[2, "cellpack.autopack.BaseGrid.BaseGrid.getPositionPeridocity", false]], "getposline() (cellpack.autopack.trajectory.xyztrajectory method)": [[2, "cellpack.autopack.trajectory.xyzTrajectory.getPosLine", false]], "getposuntilroot() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.getPosUntilRoot", false]], "getproperty() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.getProperty", false]], "getpropertyobject() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.getPropertyObject", false]], "getradius() (cellpack.autopack.basegrid.basegrid method)": [[2, "cellpack.autopack.BaseGrid.BaseGrid.getRadius", false]], "getradius() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.getRadius", false]], "getramp() (in module cellpack.autopack.upy.colors)": [[6, "cellpack.autopack.upy.colors.getRamp", false]], "getrndweighted() (cellpack.autopack.gradient.gradient method)": [[2, "cellpack.autopack.Gradient.Gradient.getRndWeighted", false]], "getrottransrb() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.getRotTransRB", false]], "getscale() (cellpack.autopack.basegrid.haltongrid method)": [[2, "cellpack.autopack.BaseGrid.HaltonGrid.getScale", false]], "getscale() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.getScale", false]], "getsize() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.getSize", false]], "getsizexyz() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.getSizeXYZ", false]], "getsortedactiveingredients() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.getSortedActiveIngredients", false]], "getstringvalueoptions() (in module cellpack.autopack.ioutils)": [[2, "cellpack.autopack.IOutils.getStringValueOptions", false]], "getsubweighted() (cellpack.autopack.gradient.gradient method)": [[2, "cellpack.autopack.Gradient.Gradient.getSubWeighted", false]], "getsubweighted() (cellpack.autopack.ingredient.agent.agent method)": [[3, "cellpack.autopack.ingredient.agent.Agent.getSubWeighted", false]], "getsurfaceinnerpoints() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.getSurfaceInnerPoints", false]], "getsurfaceinnerpoints_kevin() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.getSurfaceInnerPoints_kevin", false]], "getsurfaceinnerpoints_sdf() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.getSurfaceInnerPoints_sdf", false]], "getsurfaceinnerpoints_sdf_interpolate() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.getSurfaceInnerPoints_sdf_interpolate", false]], "getsurfacepoint() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.getSurfacePoint", false]], "gettotalnbobject() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.getTotalNbObject", false]], "gettransformation() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.getTransformation", false]], "gettranslation() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.getTranslation", false]], "gettranslation() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.getTranslation", false]], "gettubeproperties() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.getTubeProperties", false]], "gettubepropertiesmatrix() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.getTubePropertiesMatrix", false]], "gettype() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.getType", false]], "getuv() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.getUV", false]], "getuvs() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.getUVs", false]], "getv3() (cellpack.autopack.ingredient.grow.growingredient method)": [[3, "cellpack.autopack.ingredient.grow.GrowIngredient.getV3", false]], "getvertexnormals() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.getVertexNormals", false]], "getvisibility() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.getVisibility", false]], "getvisibility() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.getVisibility", false]], "getvnfromf() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.getVNfromF", false]], "github (cellpack.autopack.interface_objects.database_ids.database_ids attribute)": [[4, "cellpack.autopack.interface_objects.database_ids.DATABASE_IDS.GITHUB", false]], "grab() (cellpack.autopack.ioutils.grabresult method)": [[2, "cellpack.autopack.IOutils.GrabResult.grab", false]], "grabresult (class in cellpack.autopack.ioutils)": [[2, "cellpack.autopack.IOutils.GrabResult", false]], "gradient (class in cellpack.autopack.gradient)": [[2, "cellpack.autopack.Gradient.Gradient", false]], "gradient_list_to_dict() (cellpack.autopack.dbrecipehandler.compositiondoc static method)": [[2, "cellpack.autopack.DBRecipeHandler.CompositionDoc.gradient_list_to_dict", false]], "gradientdata (class in cellpack.autopack.interface_objects.gradient_data)": [[4, "cellpack.autopack.interface_objects.gradient_data.GradientData", false]], "gradientdoc (class in cellpack.autopack.dbrecipehandler)": [[2, "cellpack.autopack.DBRecipeHandler.GradientDoc", false]], "gradientmodes (class in cellpack.autopack.interface_objects.gradient_data)": [[4, "cellpack.autopack.interface_objects.gradient_data.GradientModes", false]], "grid (class in cellpack.autopack.grid)": [[2, "cellpack.autopack.Grid.Grid", false]], "gridpoint (class in cellpack.autopack.basegrid)": [[2, "cellpack.autopack.BaseGrid.gridPoint", false]], "grow (cellpack.autopack.interface_objects.ingredient_types.ingredient_type attribute)": [[4, "cellpack.autopack.interface_objects.ingredient_types.INGREDIENT_TYPE.GROW", false]], "grow() (cellpack.autopack.ingredient.grow.growingredient method)": [[3, "cellpack.autopack.ingredient.grow.GrowIngredient.grow", false]], "grow_place() (cellpack.autopack.ingredient.grow.growingredient method)": [[3, "cellpack.autopack.ingredient.grow.GrowIngredient.grow_place", false]], "growingredient (class in cellpack.autopack.ingredient.grow)": [[3, "cellpack.autopack.ingredient.grow.GrowIngredient", false]], "halton() (in module cellpack.autopack.ldsequence)": [[2, "cellpack.autopack.ldSequence.halton", false]], "halton2() (in module cellpack.autopack.ldsequence)": [[2, "cellpack.autopack.ldSequence.halton2", false]], "halton3() (in module cellpack.autopack.ldsequence)": [[2, "cellpack.autopack.ldSequence.halton3", false]], "halton_sequence() (in module cellpack.autopack.ldsequence)": [[2, "cellpack.autopack.ldSequence.halton_sequence", false]], "haltongrid (class in cellpack.autopack.basegrid)": [[2, "cellpack.autopack.BaseGrid.HaltonGrid", false]], "haltonsequence (class in cellpack.autopack.ldsequence)": [[2, "cellpack.autopack.ldSequence.HaltonSequence", false]], "haltonterm() (in module cellpack.autopack.ldsequence)": [[2, "cellpack.autopack.ldSequence.haltonterm", false]], "handle_expired_results() (cellpack.autopack.dbrecipehandler.resultdoc method)": [[2, "cellpack.autopack.DBRecipeHandler.ResultDoc.handle_expired_results", false]], "handle_real_time_visualization() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.handle_real_time_visualization", false]], "handlers() (cellpack.autopack.interface_objects.database_ids.database_ids class method)": [[4, "cellpack.autopack.interface_objects.database_ids.DATABASE_IDS.handlers", false]], "has_mesh() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.has_mesh", false]], "has_mesh() (cellpack.autopack.interface_objects.representations.representations method)": [[4, "cellpack.autopack.interface_objects.representations.Representations.has_mesh", false]], "has_pdb() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.has_pdb", false]], "has_pdb() (cellpack.autopack.interface_objects.representations.representations method)": [[4, "cellpack.autopack.interface_objects.representations.Representations.has_pdb", false]], "helper (class in cellpack.autopack.upy.hosthelper)": [[6, "cellpack.autopack.upy.hostHelper.Helper", false]], "hexahedron() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.Hexahedron", false], [6, "cellpack.autopack.upy.hostHelper.Helper.hexahedron", false]], "hextorgb() (in module cellpack.autopack.upy.colors)": [[6, "cellpack.autopack.upy.colors.hexToRgb", false]], "hideingrprimitive() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.hideIngrPrimitive", false]], "histogram() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.histogram", false]], "host (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper attribute)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.host", false]], "icosahedron() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.Icosahedron", false], [6, "cellpack.autopack.upy.hostHelper.Helper.icosahedron", false]], "ijktoindex() (cellpack.autopack.binvox_rw.voxels method)": [[2, "cellpack.autopack.binvox_rw.Voxels.ijkToIndex", false]], "ijktoxyz() (cellpack.autopack.binvox_rw.voxels method)": [[2, "cellpack.autopack.binvox_rw.Voxels.ijkToxyz", false]], "ik (cellpack.autopack.upy.hosthelper.helper attribute)": [[6, "cellpack.autopack.upy.hostHelper.Helper.IK", false]], "imagewriter (class in cellpack.autopack.writers.imagewriter)": [[8, "cellpack.autopack.writers.ImageWriter.ImageWriter", false]], "inbox() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.inBox", false]], "inc() (cellpack.autopack.ldsequence.chaltonsequence3 method)": [[2, "cellpack.autopack.ldSequence.cHaltonSequence3.inc", false]], "includeingredientrecipe() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.includeIngredientRecipe", false]], "includeingrrecipe() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.includeIngrRecipe", false]], "includeingrrecipes() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.includeIngrRecipes", false]], "increment_static() (cellpack.autopack.upy.simularium.simularium_helper.instance method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.Instance.increment_static", false]], "increment_static_objects() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.increment_static_objects", false]], "increment_time() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.increment_time", false]], "indexedpolgonstotripoints() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.IndexedPolgonsToTriPoints", false]], "indexedpolygons() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.IndexedPolygons", false]], "ingredient (class in cellpack.autopack.ingredient.ingredient)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient", false]], "ingredient_compare0() (in module cellpack.autopack.utils)": [[2, "cellpack.autopack.utils.ingredient_compare0", false]], "ingredient_compare1() (in module cellpack.autopack.utils)": [[2, "cellpack.autopack.utils.ingredient_compare1", false]], "ingredient_compare2() (in module cellpack.autopack.utils)": [[2, "cellpack.autopack.utils.ingredient_compare2", false]], "ingredient_type (class in cellpack.autopack.interface_objects.ingredient_types)": [[4, "cellpack.autopack.interface_objects.ingredient_types.INGREDIENT_TYPE", false]], "ingredientinstancedrop (class in cellpack.autopack.ingredient.ingredient)": [[3, "cellpack.autopack.ingredient.Ingredient.IngredientInstanceDrop", false]], "ingrid() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.inGrid", false]], "ingrjsonnode() (cellpack.autopack.ioutils.ioingredienttool method)": [[2, "cellpack.autopack.IOutils.IOingredientTool.ingrJsonNode", false]], "ingrjsonnode() (cellpack.autopack.writers.ioingredienttool method)": [[8, "cellpack.autopack.writers.IOingredientTool.ingrJsonNode", false]], "ingrpythonnode() (cellpack.autopack.ioutils.ioingredienttool method)": [[2, "cellpack.autopack.IOutils.IOingredientTool.ingrPythonNode", false]], "init_scene_with_objects() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.init_scene_with_objects", false]], "initialize_mesh() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.initialize_mesh", false]], "initialize_mesh() (cellpack.autopack.ingredient.multi_cylinder.multicylindersingr method)": [[3, "cellpack.autopack.ingredient.multi_cylinder.MultiCylindersIngr.initialize_mesh", false]], "initialize_mesh() (cellpack.autopack.ingredient.single_cylinder.singlecylinderingr method)": [[3, "cellpack.autopack.ingredient.single_cylinder.SingleCylinderIngr.initialize_mesh", false]], "initialize_mesh() (cellpack.autopack.ingredient.single_sphere.singlesphereingr method)": [[3, "cellpack.autopack.ingredient.single_sphere.SingleSphereIngr.initialize_mesh", false]], "initialize_shape() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.initialize_shape", false]], "inner_grid_methods (class in cellpack.autopack.loaders.config_loader)": [[5, "cellpack.autopack.loaders.config_loader.Inner_Grid_Methods", false]], "insertnode() (cellpack.autopack.octree.octree method)": [[2, "cellpack.autopack.octree.Octree.insertNode", false]], "instance (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper attribute)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.INSTANCE", false]], "instance (class in cellpack.autopack.upy.simularium.simularium_helper)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.Instance", false]], "instancepolygon() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.instancePolygon", false]], "instancescylinder() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.instancesCylinder", false]], "instancessphere() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.instancesSphere", false]], "instancestocollada() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.instancesToCollada", false]], "invertoptions (class in cellpack.autopack.interface_objects.gradient_data)": [[4, "cellpack.autopack.interface_objects.gradient_data.InvertOptions", false]], "ioingredienttool (class in cellpack.autopack.ioutils)": [[2, "cellpack.autopack.IOutils.IOingredientTool", false]], "ioingredienttool (class in cellpack.autopack.writers)": [[8, "cellpack.autopack.writers.IOingredientTool", false]], "is_db_dict() (cellpack.autopack.dbrecipehandler.datadoc static method)": [[2, "cellpack.autopack.DBRecipeHandler.DataDoc.is_db_dict", false]], "is_fiber() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper static method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.is_fiber", false]], "is_firebase_obj() (cellpack.autopack.firebasehandler.firebasehandler static method)": [[2, "cellpack.autopack.FirebaseHandler.FirebaseHandler.is_firebase_obj", false]], "is_full_url() (in module cellpack.autopack)": [[2, "cellpack.autopack.is_full_url", false]], "is_key() (cellpack.autopack.dbrecipehandler.datadoc static method)": [[2, "cellpack.autopack.DBRecipeHandler.DataDoc.is_key", false]], "is_key() (cellpack.autopack.recipe.recipe static method)": [[2, "cellpack.autopack.Recipe.Recipe.is_key", false]], "is_matrix() (cellpack.bin.simularium_converter.converttosimularium method)": [[9, "cellpack.bin.simularium_converter.ConvertToSimularium.is_matrix", false]], "is_member() (cellpack.autopack.interface_objects.meta_enum.metaenum class method)": [[4, "cellpack.autopack.interface_objects.meta_enum.MetaEnum.is_member", false]], "is_nested_list() (cellpack.autopack.dbrecipehandler.datadoc static method)": [[2, "cellpack.autopack.DBRecipeHandler.DataDoc.is_nested_list", false]], "is_obj() (cellpack.autopack.dbrecipehandler.datadoc static method)": [[2, "cellpack.autopack.DBRecipeHandler.DataDoc.is_obj", false]], "is_partner() (cellpack.autopack.interface_objects.partners.partners method)": [[4, "cellpack.autopack.interface_objects.partners.Partners.is_partner", false]], "is_point_in_correct_region() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.is_point_in_correct_region", false]], "is_point_inside_bb() (cellpack.autopack.basegrid.basegrid method)": [[2, "cellpack.autopack.BaseGrid.BaseGrid.is_point_inside_bb", false]], "is_point_inside_mesh() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.is_point_inside_mesh", false]], "is_reference() (cellpack.autopack.firebasehandler.firebasehandler static method)": [[2, "cellpack.autopack.FirebaseHandler.FirebaseHandler.is_reference", false]], "is_remote_path() (in module cellpack.autopack)": [[2, "cellpack.autopack.is_remote_path", false]], "is_s3_url() (in module cellpack.autopack)": [[2, "cellpack.autopack.is_s3_url", false]], "is_two_d() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.is_two_d", false]], "is_url_valid() (cellpack.autopack.awshandler.awshandler method)": [[2, "cellpack.autopack.AWSHandler.AWSHandler.is_url_valid", false]], "isindexedpolyon() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.isIndexedPolyon", false]], "issphere() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.isSphere", false]], "jitter (cellpack.autopack.loaders.config_loader.place_methods attribute)": [[5, "cellpack.autopack.loaders.config_loader.Place_Methods.JITTER", false]], "jitter_place() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.jitter_place", false]], "jitterposition() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.jitterPosition", false]], "joinsobjects() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.JoinsObjects", false]], "key_to_dict_mapping (cellpack.autopack.dbrecipehandler.compositiondoc attribute)": [[2, "cellpack.autopack.DBRecipeHandler.CompositionDoc.KEY_TO_DICT_MAPPING", false]], "labels() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.Labels", false]], "light_options (cellpack.autopack.upy.hosthelper.helper attribute)": [[6, "cellpack.autopack.upy.hostHelper.Helper.LIGHT_OPTIONS", false]], "linear (cellpack.autopack.interface_objects.gradient_data.pickmodes attribute)": [[4, "cellpack.autopack.interface_objects.gradient_data.PickModes.LINEAR", false]], "linear (cellpack.autopack.interface_objects.gradient_data.weightmodes attribute)": [[4, "cellpack.autopack.interface_objects.gradient_data.WeightModes.LINEAR", false]], "linktraj() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.linkTraj", false]], "list (cellpack.autopack.ingredient.ingredient.distributiontypes attribute)": [[3, "cellpack.autopack.ingredient.Ingredient.DistributionTypes.LIST", false]], "list_values (cellpack.autopack.ingredient.ingredient.distributionoptions attribute)": [[3, "cellpack.autopack.ingredient.Ingredient.DistributionOptions.LIST_VALUES", false]], "load_asjson() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.load_asJson", false]], "load_astxt() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.load_asTxt", false]], "load_file() (in module cellpack.autopack)": [[2, "cellpack.autopack.load_file", false]], "load_json() (in module cellpack.autopack.ioutils)": [[2, "cellpack.autopack.IOutils.load_Json", false]], "load_jsonstring() (in module cellpack.autopack.ioutils)": [[2, "cellpack.autopack.IOutils.load_JsonString", false]], "load_mixedasjson() (in module cellpack.autopack.ioutils)": [[2, "cellpack.autopack.IOutils.load_MixedasJson", false]], "load_object_from_pickle() (in module cellpack.autopack.utils)": [[2, "cellpack.autopack.utils.load_object_from_pickle", false]], "loadfreepoint() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.loadFreePoint", false]], "loadjson() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.loadJSON", false]], "loadresult() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.loadResult", false]], "lookforneighbours() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.lookForNeighbours", false]], "loopthroughingr() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.loopThroughIngr", false]], "lowercirclefunction() (cellpack.autopack.geometrytools.geometrytools method)": [[2, "cellpack.autopack.GeometryTools.GeometryTools.LowerCircleFunction", false]], "lowerrectanglefunction() (cellpack.autopack.geometrytools.geometrytools method)": [[2, "cellpack.autopack.GeometryTools.GeometryTools.LowerRectangleFunction", false]], "main() (in module cellpack.bin.analyze)": [[9, "cellpack.bin.analyze.main", false]], "main() (in module cellpack.bin.clean)": [[9, "cellpack.bin.clean.main", false]], "main() (in module cellpack.bin.pack)": [[9, "cellpack.bin.pack.main", false]], "main() (in module cellpack.bin.simularium_converter)": [[9, "cellpack.bin.simularium_converter.main", false]], "main() (in module cellpack.bin.upload)": [[9, "cellpack.bin.upload.main", false]], "make_and_show_heatmap() (cellpack.autopack.plotly_result.plotlyanalysis method)": [[2, "cellpack.autopack.plotly_result.PlotlyAnalysis.make_and_show_heatmap", false]], "make_directory_if_needed() (in module cellpack.autopack)": [[2, "cellpack.autopack.make_directory_if_needed", false]], "make_grid_heatmap() (cellpack.autopack.plotly_result.plotlyanalysis method)": [[2, "cellpack.autopack.plotly_result.PlotlyAnalysis.make_grid_heatmap", false]], "makeingredient() (cellpack.autopack.ioutils.ioingredienttool method)": [[2, "cellpack.autopack.IOutils.IOingredientTool.makeIngredient", false]], "makeingredientfromjson() (cellpack.autopack.ioutils.ioingredienttool method)": [[2, "cellpack.autopack.IOutils.IOingredientTool.makeIngredientFromJson", false]], "makeingrmapping() (cellpack.autopack.trajectory.trajectory method)": [[2, "cellpack.autopack.trajectory.Trajectory.makeIngrMapping", false]], "makemarchingcube() (in module cellpack.autopack.ray)": [[2, "cellpack.autopack.ray.makeMarchingCube", false]], "maketexture() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.makeTexture", false]], "map_colors() (in module cellpack.autopack.upy.colors)": [[6, "cellpack.autopack.upy.colors.map_colors", false]], "mask_sphere_points() (cellpack.autopack.ingredient.grow.growingredient method)": [[3, "cellpack.autopack.ingredient.grow.GrowIngredient.mask_sphere_points", false]], "mask_sphere_points_angle() (cellpack.autopack.ingredient.grow.growingredient method)": [[3, "cellpack.autopack.ingredient.grow.GrowIngredient.mask_sphere_points_angle", false]], "mask_sphere_points_boundary() (cellpack.autopack.ingredient.grow.growingredient method)": [[3, "cellpack.autopack.ingredient.grow.GrowIngredient.mask_sphere_points_boundary", false]], "mask_sphere_points_dihedral() (cellpack.autopack.ingredient.grow.growingredient method)": [[3, "cellpack.autopack.ingredient.grow.GrowIngredient.mask_sphere_points_dihedral", false]], "mask_sphere_points_ingredients() (cellpack.autopack.ingredient.grow.growingredient method)": [[3, "cellpack.autopack.ingredient.grow.GrowIngredient.mask_sphere_points_ingredients", false]], "mask_sphere_points_vector() (cellpack.autopack.ingredient.grow.growingredient method)": [[3, "cellpack.autopack.ingredient.grow.GrowIngredient.mask_sphere_points_vector", false]], "matrixtofacesmesh() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.matrixToFacesMesh", false]], "matrixtovnmesh() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.matrixToVNMesh", false]], "max (cellpack.autopack.ingredient.ingredient.distributionoptions attribute)": [[3, "cellpack.autopack.ingredient.Ingredient.DistributionOptions.MAX", false]], "max (cellpack.autopack.interface_objects.gradient_data.pickmodes attribute)": [[4, "cellpack.autopack.interface_objects.gradient_data.PickModes.MAX", false]], "mean (cellpack.autopack.ingredient.ingredient.distributionoptions attribute)": [[3, "cellpack.autopack.ingredient.Ingredient.DistributionOptions.MEAN", false]], "measure_distance() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.measure_distance", false]], "merge_place_results() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.merge_place_results", false]], "mesh (cellpack.autopack.interface_objects.ingredient_types.ingredient_type attribute)": [[4, "cellpack.autopack.interface_objects.ingredient_types.INGREDIENT_TYPE.MESH", false]], "meshstore (class in cellpack.autopack.meshstore)": [[2, "cellpack.autopack.MeshStore.MeshStore", false]], "metaballs() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.metaballs", false]], "metaenum (class in cellpack.autopack.interface_objects.meta_enum)": [[4, "cellpack.autopack.interface_objects.meta_enum.MetaEnum", false]], "midpoint() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.MidPoint", false]], "migrate_ingredient() (in module cellpack.autopack.loaders.migrate_v1_to_v2)": [[5, "cellpack.autopack.loaders.migrate_v1_to_v2.migrate_ingredient", false]], "min (cellpack.autopack.ingredient.ingredient.distributionoptions attribute)": [[3, "cellpack.autopack.ingredient.Ingredient.DistributionOptions.MIN", false]], "min (cellpack.autopack.interface_objects.gradient_data.pickmodes attribute)": [[4, "cellpack.autopack.interface_objects.gradient_data.PickModes.MIN", false]], "modeoptions (class in cellpack.autopack.interface_objects.gradient_data)": [[4, "cellpack.autopack.interface_objects.gradient_data.ModeOptions", false]], "module": [[1, "module-cellpack", false], [2, "module-cellpack.autopack", false], [2, "module-cellpack.autopack.AWSHandler", false], [2, "module-cellpack.autopack.Analysis", false], [2, "module-cellpack.autopack.BaseGrid", false], [2, "module-cellpack.autopack.Compartment", false], [2, "module-cellpack.autopack.DBRecipeHandler", false], [2, "module-cellpack.autopack.Environment", false], [2, "module-cellpack.autopack.FirebaseHandler", false], [2, "module-cellpack.autopack.GeometryTools", false], [2, "module-cellpack.autopack.Gradient", false], [2, "module-cellpack.autopack.Graphics", false], [2, "module-cellpack.autopack.Grid", false], [2, "module-cellpack.autopack.IOutils", false], [2, "module-cellpack.autopack.MeshStore", false], [2, "module-cellpack.autopack.Recipe", false], [2, "module-cellpack.autopack.Serializable", false], [2, "module-cellpack.autopack.binvox_rw", false], [2, "module-cellpack.autopack.ldSequence", false], [2, "module-cellpack.autopack.octree", false], [2, "module-cellpack.autopack.plotly_result", false], [2, "module-cellpack.autopack.randomRot", false], [2, "module-cellpack.autopack.ray", false], [2, "module-cellpack.autopack.trajectory", false], [2, "module-cellpack.autopack.transformation", false], [2, "module-cellpack.autopack.utils", false], [3, "module-cellpack.autopack.ingredient", false], [3, "module-cellpack.autopack.ingredient.Ingredient", false], [3, "module-cellpack.autopack.ingredient.agent", false], [3, "module-cellpack.autopack.ingredient.grow", false], [3, "module-cellpack.autopack.ingredient.multi_cylinder", false], [3, "module-cellpack.autopack.ingredient.multi_sphere", false], [3, "module-cellpack.autopack.ingredient.single_cube", false], [3, "module-cellpack.autopack.ingredient.single_cylinder", false], [3, "module-cellpack.autopack.ingredient.single_sphere", false], [3, "module-cellpack.autopack.ingredient.utils", false], [4, "module-cellpack.autopack.interface_objects", false], [4, "module-cellpack.autopack.interface_objects.database_ids", false], [4, "module-cellpack.autopack.interface_objects.default_values", false], [4, "module-cellpack.autopack.interface_objects.gradient_data", false], [4, "module-cellpack.autopack.interface_objects.ingredient_types", false], [4, "module-cellpack.autopack.interface_objects.meta_enum", false], [4, "module-cellpack.autopack.interface_objects.packed_objects", false], [4, "module-cellpack.autopack.interface_objects.partners", false], [4, "module-cellpack.autopack.interface_objects.representations", false], [5, "module-cellpack.autopack.loaders", false], [5, "module-cellpack.autopack.loaders.analysis_config_loader", false], [5, "module-cellpack.autopack.loaders.config_loader", false], [5, "module-cellpack.autopack.loaders.migrate_v1_to_v2", false], [5, "module-cellpack.autopack.loaders.migrate_v2_to_v2_1", false], [5, "module-cellpack.autopack.loaders.recipe_loader", false], [5, "module-cellpack.autopack.loaders.utils", false], [5, "module-cellpack.autopack.loaders.v1_v2_attribute_changes", false], [6, "module-cellpack.autopack.upy", false], [6, "module-cellpack.autopack.upy.colors", false], [6, "module-cellpack.autopack.upy.hostHelper", false], [7, "module-cellpack.autopack.upy.simularium", false], [7, "module-cellpack.autopack.upy.simularium.plots", false], [7, "module-cellpack.autopack.upy.simularium.simularium_helper", false], [8, "module-cellpack.autopack.writers", false], [8, "module-cellpack.autopack.writers.ImageWriter", false], [9, "module-cellpack.bin", false], [9, "module-cellpack.bin.analyze", false], [9, "module-cellpack.bin.clean", false], [9, "module-cellpack.bin.cleanup_tasks", false], [9, "module-cellpack.bin.pack", false], [9, "module-cellpack.bin.simularium_converter", false], [9, "module-cellpack.bin.upload", false]], "molbtrajectory (class in cellpack.autopack.trajectory)": [[2, "cellpack.autopack.trajectory.molbTrajectory", false]], "move() (cellpack.autopack.upy.simularium.simularium_helper.instance method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.Instance.move", false]], "move_object() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.move_object", false]], "moverbnode() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.moveRBnode", false]], "multi_cylinder (cellpack.autopack.interface_objects.ingredient_types.ingredient_type attribute)": [[4, "cellpack.autopack.interface_objects.ingredient_types.INGREDIENT_TYPE.MULTI_CYLINDER", false]], "multi_sphere (cellpack.autopack.interface_objects.ingredient_types.ingredient_type attribute)": [[4, "cellpack.autopack.interface_objects.ingredient_types.INGREDIENT_TYPE.MULTI_SPHERE", false]], "multicylindersingr (class in cellpack.autopack.ingredient.multi_cylinder)": [[3, "cellpack.autopack.ingredient.multi_cylinder.MultiCylindersIngr", false]], "multisphereingr (class in cellpack.autopack.ingredient.multi_sphere)": [[3, "cellpack.autopack.ingredient.multi_sphere.MultiSphereIngr", false]], "newempty() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.newEmpty", false]], "newempty() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.newEmpty", false]], "newinstance() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.newInstance", false]], "nodetogeom() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.nodeToGeom", false]], "norm() (cellpack.autopack.meshstore.meshstore static method)": [[2, "cellpack.autopack.MeshStore.MeshStore.norm", false]], "norm() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.norm", false]], "normal (cellpack.autopack.ingredient.ingredient.distributiontypes attribute)": [[3, "cellpack.autopack.ingredient.Ingredient.DistributionTypes.NORMAL", false]], "normal_array() (cellpack.autopack.meshstore.meshstore static method)": [[2, "cellpack.autopack.MeshStore.MeshStore.normal_array", false]], "normal_array() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.normal_array", false]], "normalize() (cellpack.autopack.meshstore.meshstore static method)": [[2, "cellpack.autopack.MeshStore.MeshStore.normalize", false]], "normalize() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.normalize", false]], "normalize_v3() (cellpack.autopack.meshstore.meshstore static method)": [[2, "cellpack.autopack.MeshStore.MeshStore.normalize_v3", false]], "normalize_v3() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.normalize_v3", false]], "normalize_vector() (cellpack.autopack.gradient.gradient method)": [[2, "cellpack.autopack.Gradient.Gradient.normalize_vector", false]], "np_check_collision() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.np_check_collision", false]], "numpyarrayencoder (class in cellpack.autopack.writers)": [[8, "cellpack.autopack.writers.NumpyArrayEncoder", false]], "object (cellpack.autopack.interface_objects.gradient_data.modeoptions attribute)": [[4, "cellpack.autopack.interface_objects.gradient_data.ModeOptions.object", false]], "objectdoc (class in cellpack.autopack.dbrecipehandler)": [[2, "cellpack.autopack.DBRecipeHandler.ObjectDoc", false]], "objectsselection() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.ObjectsSelection", false]], "objectsselection() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.ObjectsSelection", false]], "octahedron() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.Octahedron", false], [6, "cellpack.autopack.upy.hostHelper.Helper.octahedron", false]], "octnode (class in cellpack.autopack.octree)": [[2, "cellpack.autopack.octree.OctNode", false]], "octree (class in cellpack.autopack.octree)": [[2, "cellpack.autopack.octree.Octree", false]], "onecolladageom() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.oneColladaGeom", false]], "onecylinder() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.oneCylinder", false]], "onejitter() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.oneJitter", false]], "onemetaball() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.oneMetaBall", false]], "oneprevingredient() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.onePrevIngredient", false]], "open_in_simularium() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper static method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.open_in_simularium", false]], "pack() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.pack", false]], "pack() (in module cellpack.bin.pack)": [[9, "cellpack.bin.pack.pack", false]], "pack_at_grid_pt_location() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.pack_at_grid_pt_location", false]], "pack_at_grid_pt_location() (cellpack.autopack.ingredient.multi_sphere.multisphereingr method)": [[3, "cellpack.autopack.ingredient.multi_sphere.MultiSphereIngr.pack_at_grid_pt_location", false]], "pack_grid() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.pack_grid", false]], "pack_one_seed() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.pack_one_seed", false]], "packedobject (class in cellpack.autopack.interface_objects.packed_objects)": [[4, "cellpack.autopack.interface_objects.packed_objects.PackedObject", false]], "packedobjects (class in cellpack.autopack.interface_objects.packed_objects)": [[4, "cellpack.autopack.interface_objects.packed_objects.PackedObjects", false]], "parse() (cellpack.autopack.trajectory.dcdtrajectory method)": [[2, "cellpack.autopack.trajectory.dcdTrajectory.parse", false]], "parse() (cellpack.autopack.trajectory.molbtrajectory method)": [[2, "cellpack.autopack.trajectory.molbTrajectory.parse", false]], "parse() (cellpack.autopack.trajectory.xyztrajectory method)": [[2, "cellpack.autopack.trajectory.xyzTrajectory.parse", false]], "parse_one_mol() (cellpack.autopack.trajectory.molbtrajectory method)": [[2, "cellpack.autopack.trajectory.molbTrajectory.parse_one_mol", false]], "parse_s3_uri() (in module cellpack.autopack)": [[2, "cellpack.autopack.parse_s3_uri", false]], "particle() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.particle", false]], "partner (class in cellpack.autopack.interface_objects.partners)": [[4, "cellpack.autopack.interface_objects.partners.Partner", false]], "partners (class in cellpack.autopack.interface_objects.partners)": [[4, "cellpack.autopack.interface_objects.partners.Partners", false]], "pathdeform() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.pathDeform", false]], "pathdeform() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.pathDeform", false]], "pb (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper attribute)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.pb", false]], "perturbaxis() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.perturbAxis", false]], "pick_alternate() (cellpack.autopack.ingredient.grow.growingredient method)": [[3, "cellpack.autopack.ingredient.grow.GrowIngredient.pick_alternate", false]], "pick_partner_grid_index() (cellpack.autopack.ingredient.agent.agent method)": [[3, "cellpack.autopack.ingredient.agent.Agent.pick_partner_grid_index", false]], "pick_point_for_ingredient() (cellpack.autopack.gradient.gradient static method)": [[2, "cellpack.autopack.Gradient.Gradient.pick_point_for_ingredient", false]], "pick_point_from_weight() (cellpack.autopack.gradient.gradient static method)": [[2, "cellpack.autopack.Gradient.Gradient.pick_point_from_weight", false]], "pick_random_alternate() (cellpack.autopack.ingredient.grow.growingredient method)": [[3, "cellpack.autopack.ingredient.grow.GrowIngredient.pick_random_alternate", false]], "pickalternatehalton() (cellpack.autopack.ingredient.grow.growingredient method)": [[3, "cellpack.autopack.ingredient.grow.GrowIngredient.pickAlternateHalton", false]], "pickhalton() (cellpack.autopack.ingredient.grow.growingredient method)": [[3, "cellpack.autopack.ingredient.grow.GrowIngredient.pickHalton", false]], "pickingredient() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.pickIngredient", false]], "pickmodes (class in cellpack.autopack.interface_objects.gradient_data)": [[4, "cellpack.autopack.interface_objects.gradient_data.PickModes", false]], "pickpoint() (cellpack.autopack.gradient.gradient method)": [[2, "cellpack.autopack.Gradient.Gradient.pickPoint", false]], "pickrandomsphere() (cellpack.autopack.ingredient.grow.growingredient method)": [[3, "cellpack.autopack.ingredient.grow.GrowIngredient.pickRandomSphere", false]], "place() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.place", false]], "place_alternate() (cellpack.autopack.ingredient.grow.growingredient method)": [[3, "cellpack.autopack.ingredient.grow.GrowIngredient.place_alternate", false]], "place_alternate_p() (cellpack.autopack.ingredient.grow.growingredient method)": [[3, "cellpack.autopack.ingredient.grow.GrowIngredient.place_alternate_p", false]], "place_methods (class in cellpack.autopack.loaders.config_loader)": [[5, "cellpack.autopack.loaders.config_loader.Place_Methods", false]], "place_object() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.place_object", false]], "plane() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.plane", false]], "plane() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.plane", false]], "platonic() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.Platonic", false]], "plot() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.plot", false]], "plot_distance_distribution() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.plot_distance_distribution", false]], "plot_occurence_distribution() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.plot_occurence_distribution", false]], "plot_position_distribution() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.plot_position_distribution", false]], "plot_position_distribution_total() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.plot_position_distribution_total", false]], "plotdata (class in cellpack.autopack.upy.simularium.plots)": [[7, "cellpack.autopack.upy.simularium.plots.PlotData", false]], "plotlyanalysis (class in cellpack.autopack.plotly_result)": [[2, "cellpack.autopack.plotly_result.PlotlyAnalysis", false]], "point_is_available() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.point_is_available", false]], "pointcloudobject() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.PointCloudObject", false]], "points() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.Points", false]], "polygon (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper attribute)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.POLYGON", false]], "polylines() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.Polylines", false]], "post_and_open_file() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.post_and_open_file", false]], "power (cellpack.autopack.interface_objects.gradient_data.weightmodeoptions attribute)": [[4, "cellpack.autopack.interface_objects.gradient_data.WeightModeOptions.power", false]], "power (cellpack.autopack.interface_objects.gradient_data.weightmodes attribute)": [[4, "cellpack.autopack.interface_objects.gradient_data.WeightModes.POWER", false]], "prep_data_for_db() (cellpack.autopack.dbrecipehandler.dbuploader static method)": [[2, "cellpack.autopack.DBRecipeHandler.DBUploader.prep_data_for_db", false]], "prep_db_doc_for_download() (cellpack.autopack.dbrecipehandler.dbrecipeloader method)": [[2, "cellpack.autopack.DBRecipeHandler.DBRecipeLoader.prep_db_doc_for_download", false]], "prep_molecules_for_save() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.prep_molecules_for_save", false]], "prepare_alternates() (cellpack.autopack.ingredient.grow.growingredient method)": [[3, "cellpack.autopack.ingredient.grow.GrowIngredient.prepare_alternates", false]], "prepare_alternates_proba() (cellpack.autopack.ingredient.grow.growingredient method)": [[3, "cellpack.autopack.ingredient.grow.GrowIngredient.prepare_alternates_proba", false]], "prepare_buildgrid_box() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.prepare_buildgrid_box", false]], "preparedynamic() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.prepareDynamic", false]], "prepareingredient() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.prepareIngredient", false]], "preparemaster() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.prepareMaster", false]], "printfillinfo() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.printFillInfo", false]], "printfillinfo() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.printFillInfo", false]], "printfillinfo() (cellpack.autopack.recipe.recipe method)": [[2, "cellpack.autopack.Recipe.Recipe.printFillInfo", false]], "printingredients() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.printIngredients", false]], "printoneingr() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.printOneIngr", false]], "process_ingredients_in_recipe() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.process_ingredients_in_recipe", false]], "process_one_ingredient() (cellpack.bin.simularium_converter.converttosimularium method)": [[9, "cellpack.bin.simularium_converter.ConvertToSimularium.process_one_ingredient", false]], "progressbar() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.progressBar", false]], "progressbar() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.progressBar", false]], "quaternion_matrix() (cellpack.autopack.randomrot.randomrot method)": [[2, "cellpack.autopack.randomRot.RandomRot.quaternion_matrix", false]], "radial (cellpack.autopack.interface_objects.gradient_data.gradientmodes attribute)": [[4, "cellpack.autopack.interface_objects.gradient_data.GradientModes.RADIAL", false]], "radius (cellpack.autopack.interface_objects.gradient_data.modeoptions attribute)": [[4, "cellpack.autopack.interface_objects.gradient_data.ModeOptions.radius", false]], "random() (in module cellpack.autopack.environment)": [[2, "cellpack.autopack.Environment.random", false]], "random() (in module cellpack.autopack.gradient)": [[2, "cellpack.autopack.Gradient.random", false]], "random() (in module cellpack.autopack.ingredient.agent)": [[3, "cellpack.autopack.ingredient.agent.random", false]], "random() (in module cellpack.autopack.ingredient.grow)": [[3, "cellpack.autopack.ingredient.grow.random", false]], "random() (in module cellpack.autopack.ingredient.ingredient)": [[3, "cellpack.autopack.ingredient.Ingredient.random", false]], "random() (in module cellpack.autopack.recipe)": [[2, "cellpack.autopack.Recipe.random", false]], "random_quaternion() (cellpack.autopack.randomrot.randomrot method)": [[2, "cellpack.autopack.randomRot.RandomRot.random_quaternion", false]], "random_rotation_matrix() (cellpack.autopack.randomrot.randomrot method)": [[2, "cellpack.autopack.randomRot.RandomRot.random_rotation_matrix", false]], "randomize_rotation() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.randomize_rotation", false]], "randomize_translation() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.randomize_translation", false]], "randomrot (class in cellpack.autopack.randomrot)": [[2, "cellpack.autopack.randomRot.RandomRot", false]], "randpoint_onsphere() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.randpoint_onsphere", false]], "ray_intersect_polygon() (in module cellpack.autopack.ray)": [[2, "cellpack.autopack.ray.ray_intersect_polygon", false]], "ray_intersect_polyhedron() (in module cellpack.autopack.ray)": [[2, "cellpack.autopack.ray.ray_intersect_polyhedron", false]], "raycast() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.raycast", false]], "raycast() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.raycast", false]], "raycast_test() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.raycast_test", false]], "raytrace (cellpack.autopack.loaders.config_loader.inner_grid_methods attribute)": [[5, "cellpack.autopack.loaders.config_loader.Inner_Grid_Methods.RAYTRACE", false]], "read() (cellpack.autopack.ioutils.ioingredienttool method)": [[2, "cellpack.autopack.IOutils.IOingredientTool.read", false]], "read() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.read", false]], "read() (in module cellpack.autopack.binvox_rw)": [[2, "cellpack.autopack.binvox_rw.read", false]], "read_as_3d_array() (in module cellpack.autopack.binvox_rw)": [[2, "cellpack.autopack.binvox_rw.read_as_3d_array", false]], "read_as_coord_array() (in module cellpack.autopack.binvox_rw)": [[2, "cellpack.autopack.binvox_rw.read_as_coord_array", false]], "read_dict_from_glob_file() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.read_dict_from_glob_file", false]], "read_header() (in module cellpack.autopack.binvox_rw)": [[2, "cellpack.autopack.binvox_rw.read_header", false]], "read_json_file() (in module cellpack.autopack.loaders.utils)": [[5, "cellpack.autopack.loaders.utils.read_json_file", false]], "read_mesh_file() (cellpack.autopack.meshstore.meshstore method)": [[2, "cellpack.autopack.MeshStore.MeshStore.read_mesh_file", false]], "read_text_file() (in module cellpack.autopack)": [[2, "cellpack.autopack.read_text_file", false]], "readarraysfromfile() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.readArraysFromFile", false]], "readgridfromfile() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.readGridFromFile", false]], "readme_url() (cellpack.autopack.dbrecipehandler.dbmaintenance method)": [[2, "cellpack.autopack.DBRecipeHandler.DBMaintenance.readme_url", false]], "readmeshfromfile() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.readMeshFromFile", false]], "recalc_normals() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.recalc_normals", false]], "recipe (class in cellpack.autopack.recipe)": [[2, "cellpack.autopack.Recipe.Recipe", false]], "recipeloader (class in cellpack.autopack.loaders.recipe_loader)": [[5, "cellpack.autopack.loaders.recipe_loader.RecipeLoader", false]], "rectangle (class in cellpack.autopack.geometrytools)": [[2, "cellpack.autopack.GeometryTools.Rectangle", false]], "redwhiteblueramp() (in module cellpack.autopack.upy.colors)": [[6, "cellpack.autopack.upy.colors.RedWhiteBlueRamp", false]], "reg (cellpack.autopack.interface_objects.gradient_data.pickmodes attribute)": [[4, "cellpack.autopack.interface_objects.gradient_data.PickModes.REG", false]], "reg (cellpack.autopack.trajectory.trajectory attribute)": [[2, "cellpack.autopack.trajectory.Trajectory.reg", false]], "region_1() (cellpack.autopack.geometrytools.geometrytools method)": [[2, "cellpack.autopack.GeometryTools.GeometryTools.region_1", false]], "region_1_2_theta() (cellpack.autopack.geometrytools.geometrytools method)": [[2, "cellpack.autopack.GeometryTools.GeometryTools.region_1_2_theta", false]], "region_2() (cellpack.autopack.geometrytools.geometrytools method)": [[2, "cellpack.autopack.GeometryTools.GeometryTools.region_2", false]], "region_2_integrand() (cellpack.autopack.geometrytools.geometrytools method)": [[2, "cellpack.autopack.GeometryTools.GeometryTools.region_2_integrand", false]], "region_3() (cellpack.autopack.geometrytools.geometrytools method)": [[2, "cellpack.autopack.GeometryTools.GeometryTools.region_3", false]], "region_3_integrand() (cellpack.autopack.geometrytools.geometrytools method)": [[2, "cellpack.autopack.GeometryTools.GeometryTools.region_3_integrand", false]], "reject() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.reject", false]], "remove_from_realtime_display() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.remove_from_realtime_display", false]], "remove_nans() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper static method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.remove_nans", false]], "removefreepoint() (cellpack.autopack.basegrid.basegrid method)": [[2, "cellpack.autopack.BaseGrid.BaseGrid.removeFreePoint", false]], "removeonepoint() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.removeOnePoint", false]], "reorder_free_points() (cellpack.autopack.basegrid.basegrid static method)": [[2, "cellpack.autopack.BaseGrid.BaseGrid.reorder_free_points", false]], "reparent() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.reParent", false]], "reparent() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.reParent", false]], "replaceingrmesh() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.replaceIngrMesh", false]], "reporthook() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.reporthook", false]], "reportprogress() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.reportprogress", false]], "representations (class in cellpack.autopack.interface_objects.representations)": [[4, "cellpack.autopack.interface_objects.representations.Representations", false]], "rerieveaxis() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.rerieveAxis", false]], "reset() (cellpack.autopack.basegrid.basegrid method)": [[2, "cellpack.autopack.BaseGrid.BaseGrid.reset", false]], "reset() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.reset", false]], "reset() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.reset", false]], "reset() (cellpack.autopack.grid.grid method)": [[2, "cellpack.autopack.Grid.Grid.reset", false]], "reset() (cellpack.autopack.ingredient.grow.growingredient method)": [[3, "cellpack.autopack.ingredient.grow.GrowIngredient.reset", false]], "reset() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.reset", false]], "reset() (cellpack.autopack.ioutils.grabresult method)": [[2, "cellpack.autopack.IOutils.GrabResult.reset", false]], "reset() (cellpack.autopack.ldsequence.chaltonsequence3 method)": [[2, "cellpack.autopack.ldSequence.cHaltonSequence3.reset", false]], "resetdefault() (in module cellpack.autopack)": [[2, "cellpack.autopack.resetDefault", false]], "resetingrrecip() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.resetIngrRecip", false]], "resetingrs() (cellpack.autopack.recipe.recipe method)": [[2, "cellpack.autopack.Recipe.Recipe.resetIngrs", false]], "resetlastpoint() (cellpack.autopack.ingredient.grow.growingredient method)": [[3, "cellpack.autopack.ingredient.grow.GrowIngredient.resetLastPoint", false]], "resetprogressbar() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.resetProgressBar", false]], "resetprogressbar() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.resetProgressBar", false]], "resetspheredistribution() (cellpack.autopack.ingredient.grow.growingredient method)": [[3, "cellpack.autopack.ingredient.grow.GrowIngredient.resetSphereDistribution", false]], "resettransformation() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.resetTransformation", false]], "resolution (cellpack.autopack.geometrytools.geometrytools attribute)": [[2, "cellpack.autopack.GeometryTools.GeometryTools.Resolution", false]], "resolve_composition() (cellpack.autopack.recipe.recipe static method)": [[2, "cellpack.autopack.Recipe.Recipe.resolve_composition", false]], "resolve_db_regions() (cellpack.autopack.dbrecipehandler.compositiondoc method)": [[2, "cellpack.autopack.DBRecipeHandler.CompositionDoc.resolve_db_regions", false]], "resolve_gradient_data_objects() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.resolve_gradient_data_objects", false]], "resolve_inheritance() (cellpack.autopack.loaders.recipe_loader.recipeloader static method)": [[5, "cellpack.autopack.loaders.recipe_loader.RecipeLoader.resolve_inheritance", false]], "resolve_local_regions() (cellpack.autopack.dbrecipehandler.compositiondoc method)": [[2, "cellpack.autopack.DBRecipeHandler.CompositionDoc.resolve_local_regions", false]], "resolve_object_data() (cellpack.autopack.dbrecipehandler.compositiondoc method)": [[2, "cellpack.autopack.DBRecipeHandler.CompositionDoc.resolve_object_data", false]], "restore() (cellpack.autopack.basegrid.basegrid method)": [[2, "cellpack.autopack.BaseGrid.BaseGrid.restore", false]], "restore() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.restore", false]], "restore() (cellpack.autopack.grid.grid method)": [[2, "cellpack.autopack.Grid.Grid.restore", false]], "restore_grids_from_pickle() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.restore_grids_from_pickle", false]], "restore_molecules_array() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.restore_molecules_array", false]], "restoreeditmode() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.restoreEditMode", false]], "restorefreepoints() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.restoreFreePoints", false]], "restoregridfromfile() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.restoreGridFromFile", false]], "resultdoc (class in cellpack.autopack.dbrecipehandler)": [[2, "cellpack.autopack.DBRecipeHandler.ResultDoc", false]], "retrievecolormat() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.retrieveColorMat", false]], "retrievehost() (in module cellpack.autopack.upy)": [[6, "cellpack.autopack.upy.retrieveHost", false]], "return_object_value() (cellpack.autopack.writers.writer static method)": [[8, "cellpack.autopack.writers.Writer.return_object_value", false]], "rigid_place() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.rigid_place", false]], "rnd (cellpack.autopack.interface_objects.gradient_data.pickmodes attribute)": [[4, "cellpack.autopack.interface_objects.gradient_data.PickModes.RND", false]], "rotate_about_axis() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.rotate_about_axis", false]], "rotateobj() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.rotateObj", false]], "rotateobj() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.rotateObj", false]], "rotatepoint() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.rotatePoint", false]], "rotation_matrix() (cellpack.autopack.upy.hosthelper.helper class method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.rotation_matrix", false]], "rotax() (in module cellpack.autopack.ingredient.utils)": [[3, "cellpack.autopack.ingredient.utils.rotax", false]], "rotvecttovect() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.rotVectToVect", false]], "rotvecttovect() (in module cellpack.autopack.ingredient.utils)": [[3, "cellpack.autopack.ingredient.utils.rotVectToVect", false]], "run_analysis_workflow() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.run_analysis_workflow", false]], "run_cleanup() (in module cellpack.bin.cleanup_tasks)": [[9, "cellpack.bin.cleanup_tasks.run_cleanup", false]], "run_distance_analysis() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.run_distance_analysis", false]], "run_partner_analysis() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.run_partner_analysis", false]], "runbullet() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.runBullet", false]], "save() (cellpack.autopack.basegrid.basegrid method)": [[2, "cellpack.autopack.BaseGrid.BaseGrid.save", false]], "save() (cellpack.autopack.grid.grid method)": [[2, "cellpack.autopack.Grid.Grid.save", false]], "save() (cellpack.autopack.writers.writer method)": [[8, "cellpack.autopack.writers.Writer.save", false]], "save_as_simularium() (cellpack.autopack.writers.writer method)": [[8, "cellpack.autopack.writers.Writer.save_as_simularium", false]], "save_aspython() (in module cellpack.autopack.ioutils)": [[2, "cellpack.autopack.IOutils.save_asPython", false]], "save_file_and_get_url() (cellpack.autopack.awshandler.awshandler method)": [[2, "cellpack.autopack.AWSHandler.AWSHandler.save_file_and_get_url", false]], "save_grids_to_pickle() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.save_grids_to_pickle", false]], "save_mixed_asjson() (cellpack.autopack.writers.writer method)": [[8, "cellpack.autopack.writers.Writer.save_Mixed_asJson", false]], "save_result() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.save_result", false]], "savedejavumesh() (cellpack.autopack.upy.hosthelper.helper class method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.saveDejaVuMesh", false]], "savegridlogsasjson() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.saveGridLogsAsJson", false]], "savegridtofile() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.saveGridToFile", false]], "savegridtofile() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.saveGridToFile", false]], "saveobjmesh() (cellpack.autopack.upy.hosthelper.helper class method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.saveObjMesh", false]], "saverecipeavailable() (in module cellpack.autopack)": [[2, "cellpack.autopack.saveRecipeAvailable", false]], "saverecipeavailablejson() (in module cellpack.autopack)": [[2, "cellpack.autopack.saveRecipeAvailableJSON", false]], "saveresultbinary() (in module cellpack.autopack.ioutils)": [[2, "cellpack.autopack.IOutils.saveResultBinary", false]], "saveresultbinarydic() (in module cellpack.autopack.ioutils)": [[2, "cellpack.autopack.IOutils.saveResultBinaryDic", false]], "scalar() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.scalar", false]], "scale_between_0_and_1() (cellpack.autopack.gradient.gradient static method)": [[2, "cellpack.autopack.Gradient.Gradient.scale_between_0_and_1", false]], "scale_distance_between (cellpack.autopack.interface_objects.gradient_data.modeoptions attribute)": [[4, "cellpack.autopack.interface_objects.gradient_data.ModeOptions.scale_distance_between", false]], "scaleobj() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.scaleObj", false]], "scaleobj() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.scaleObj", false]], "scanline (cellpack.autopack.loaders.config_loader.inner_grid_methods attribute)": [[5, "cellpack.autopack.loaders.config_loader.Inner_Grid_Methods.SCANLINE", false]], "scompartment (class in cellpack.autopack.serializable)": [[2, "cellpack.autopack.Serializable.sCompartment", false]], "selectedge() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.selectEdge", false]], "selectedges() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.selectEdges", false]], "selectface() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.selectFace", false]], "selectfaces() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.selectFaces", false]], "selectvertice() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.selectVertice", false]], "selectvertices() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.selectVertices", false]], "serializedfromresult() (in module cellpack.autopack.ioutils)": [[2, "cellpack.autopack.IOutils.serializedFromResult", false]], "serializedrecipe() (in module cellpack.autopack.ioutils)": [[2, "cellpack.autopack.IOutils.serializedRecipe", false]], "serializedrecipe_group() (in module cellpack.autopack.ioutils)": [[2, "cellpack.autopack.IOutils.serializedRecipe_group", false]], "serializedrecipe_group_dic() (in module cellpack.autopack.ioutils)": [[2, "cellpack.autopack.IOutils.serializedRecipe_group_dic", false]], "set_active() (cellpack.autopack.interface_objects.representations.representations method)": [[4, "cellpack.autopack.interface_objects.representations.Representations.set_active", false]], "set_doc() (cellpack.autopack.firebasehandler.firebasehandler method)": [[2, "cellpack.autopack.FirebaseHandler.FirebaseHandler.set_doc", false]], "set_gradient() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.set_gradient", false]], "set_ingredient() (cellpack.autopack.interface_objects.partners.partner method)": [[4, "cellpack.autopack.interface_objects.partners.Partner.set_ingredient", false]], "set_ingredient_color() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.set_ingredient_color", false]], "set_mode_properties() (cellpack.autopack.interface_objects.gradient_data.gradientdata method)": [[4, "cellpack.autopack.interface_objects.gradient_data.GradientData.set_mode_properties", false]], "set_object_static() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.set_object_static", false]], "set_partners_ingredient() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.set_partners_ingredient", false]], "set_recipe_ingredient() (cellpack.autopack.ioutils.ioingredienttool method)": [[2, "cellpack.autopack.IOutils.IOingredientTool.set_recipe_ingredient", false]], "set_result_file_name() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.set_result_file_name", false]], "set_sphere_positions() (cellpack.autopack.interface_objects.representations.representations method)": [[4, "cellpack.autopack.interface_objects.representations.Representations.set_sphere_positions", false]], "set_static() (cellpack.autopack.upy.simularium.simularium_helper.instance method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.Instance.set_static", false]], "set_surface_distances() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.set_surface_distances", false]], "set_surfptsbht() (cellpack.autopack.basegrid.basegrid method)": [[2, "cellpack.autopack.BaseGrid.BaseGrid.set_surfPtsBht", false]], "set_surfptscht() (cellpack.autopack.basegrid.basegrid method)": [[2, "cellpack.autopack.BaseGrid.BaseGrid.set_surfPtscht", false]], "set_weights_by_mode() (cellpack.autopack.gradient.gradient method)": [[2, "cellpack.autopack.Gradient.Gradient.set_weights_by_mode", false]], "setcount() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.setCount", false]], "setcount() (cellpack.autopack.recipe.recipe method)": [[2, "cellpack.autopack.Recipe.Recipe.setCount", false]], "setcurrentselection() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.setCurrentSelection", false]], "setexteriorrecipe() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.setExteriorRecipe", false]], "setframe() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.setFrame", false]], "setgeomfaces() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.setGeomFaces", false]], "setgeomfaces() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.setGeomFaces", false]], "sethistovol() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.SetHistoVol", false]], "setinnerrecipe() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.setInnerRecipe", false]], "setinstance() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.setInstance", false]], "setkeyframe() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.setKeyFrame", false]], "setlayers() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.setLayers", false]], "setmesh() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.setMesh", false]], "setmeshedge() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.setMeshEdge", false]], "setmeshedges() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.setMeshEdges", false]], "setmeshface() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.setMeshFace", false]], "setmeshfaces() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.setMeshFaces", false]], "setmeshvertice() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.setMeshVertice", false]], "setmeshvertices() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.setMeshVertices", false]], "setname() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.setName", false]], "setnumber() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.setNumber", false]], "setobjectmatrix() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.setObjectMatrix", false]], "setobjectmatrix() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.setObjectMatrix", false]], "setparticulesposition() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.setParticulesPosition", false]], "setproperty() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.setProperty", false]], "setpropertyobject() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.setPropertyObject", false]], "setrboptions() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.SetRBOptions", false]], "setrigidbody() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.setRigidBody", false]], "setrigidbody() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.setRigidBody", false]], "setseed() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.setSeed", false]], "setseed() (cellpack.autopack.randomrot.randomrot method)": [[2, "cellpack.autopack.randomRot.RandomRot.setSeed", false]], "setsoftbody() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.setSoftBody", false]], "setspringoptions() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.SetSpringOptions", false]], "setsurfacerecipe() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.setSurfaceRecipe", false]], "settilling() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.setTilling", false]], "settransformation() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.setTransformation", false]], "settranslation() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.setTranslation", false]], "settranslation() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.setTranslation", false]], "setup() (cellpack.autopack.basegrid.basegrid method)": [[2, "cellpack.autopack.BaseGrid.BaseGrid.setup", false]], "setupboundaryperiodicity() (cellpack.autopack.basegrid.basegrid method)": [[2, "cellpack.autopack.BaseGrid.BaseGrid.setupBoundaryPeriodicity", false]], "setupfromjsondic() (in module cellpack.autopack.ioutils)": [[2, "cellpack.autopack.IOutils.setupFromJsonDic", false]], "setupoctree() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.setupOctree", false]], "setuprboptions() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.setupRBOptions", false]], "setuv() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.setUV", false]], "setuvs() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.setUVs", false]], "setvaluetojsonnode() (cellpack.autopack.writers.writer static method)": [[8, "cellpack.autopack.writers.Writer.setValueToJsonNode", false]], "setvaluetopythonstr() (in module cellpack.autopack.ioutils)": [[2, "cellpack.autopack.IOutils.setValueToPythonStr", false]], "setviewer() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.setViewer", false]], "setviewport() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.setViewport", false]], "shallow_match (cellpack.autopack.dbrecipehandler.compositiondoc attribute)": [[2, "cellpack.autopack.DBRecipeHandler.CompositionDoc.SHALLOW_MATCH", false]], "should_write() (cellpack.autopack.dbrecipehandler.compositiondoc method)": [[2, "cellpack.autopack.DBRecipeHandler.CompositionDoc.should_write", false]], "should_write() (cellpack.autopack.dbrecipehandler.datadoc method)": [[2, "cellpack.autopack.DBRecipeHandler.DataDoc.should_write", false]], "should_write() (cellpack.autopack.dbrecipehandler.gradientdoc method)": [[2, "cellpack.autopack.DBRecipeHandler.GradientDoc.should_write", false]], "should_write() (cellpack.autopack.dbrecipehandler.objectdoc method)": [[2, "cellpack.autopack.DBRecipeHandler.ObjectDoc.should_write", false]], "show() (cellpack.autopack.plotly_result.plotlyanalysis method)": [[2, "cellpack.autopack.plotly_result.PlotlyAnalysis.show", false]], "showhide() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.showHide", false]], "showingrprimitive() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.showIngrPrimitive", false]], "simpleplot() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.simpleplot", false]], "simulariumhelper (class in cellpack.autopack.upy.simularium.simularium_helper)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper", false]], "single_cube (cellpack.autopack.interface_objects.ingredient_types.ingredient_type attribute)": [[4, "cellpack.autopack.interface_objects.ingredient_types.INGREDIENT_TYPE.SINGLE_CUBE", false]], "single_cylinder (cellpack.autopack.interface_objects.ingredient_types.ingredient_type attribute)": [[4, "cellpack.autopack.interface_objects.ingredient_types.INGREDIENT_TYPE.SINGLE_CYLINDER", false]], "single_sphere (cellpack.autopack.interface_objects.ingredient_types.ingredient_type attribute)": [[4, "cellpack.autopack.interface_objects.ingredient_types.INGREDIENT_TYPE.SINGLE_SPHERE", false]], "singlecubeingr (class in cellpack.autopack.ingredient.single_cube)": [[3, "cellpack.autopack.ingredient.single_cube.SingleCubeIngr", false]], "singlecylinderingr (class in cellpack.autopack.ingredient.single_cylinder)": [[3, "cellpack.autopack.ingredient.single_cylinder.SingleCylinderIngr", false]], "singlesphereingr (class in cellpack.autopack.ingredient.single_sphere)": [[3, "cellpack.autopack.ingredient.single_sphere.SingleSphereIngr", false]], "singredient (class in cellpack.autopack.serializable)": [[2, "cellpack.autopack.Serializable.sIngredient", false]], "singredientfiber (class in cellpack.autopack.serializable)": [[2, "cellpack.autopack.Serializable.sIngredientFiber", false]], "singredientgroup (class in cellpack.autopack.serializable)": [[2, "cellpack.autopack.Serializable.sIngredientGroup", false]], "slow_box_fill() (cellpack.autopack.basegrid.basegrid method)": [[2, "cellpack.autopack.BaseGrid.BaseGrid.slow_box_fill", false]], "sort() (cellpack.autopack.recipe.recipe method)": [[2, "cellpack.autopack.Recipe.Recipe.sort", false]], "sort_values() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper static method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.sort_values", false]], "sortingredient() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.sortIngredient", false]], "sparse_to_dense() (in module cellpack.autopack.binvox_rw)": [[2, "cellpack.autopack.binvox_rw.sparse_to_dense", false]], "sphere (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper attribute)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.SPHERE", false]], "sphere() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.Sphere", false]], "sphere() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.sphere", false]], "spherehalton() (in module cellpack.autopack.ldsequence)": [[2, "cellpack.autopack.ldSequence.SphereHalton", false]], "spheres() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.Spheres", false]], "spheres_sst (cellpack.autopack.loaders.config_loader.place_methods attribute)": [[5, "cellpack.autopack.loaders.config_loader.Place_Methods.SPHERES_SST", false]], "spheres_sst_place() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.spheres_SST_place", false]], "spline (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper attribute)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.SPLINE", false]], "spline() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.spline", false]], "spline() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.spline", false]], "split_ingredient_data() (in module cellpack.autopack.loaders.migrate_v1_to_v2)": [[5, "cellpack.autopack.loaders.migrate_v1_to_v2.split_ingredient_data", false]], "square (cellpack.autopack.interface_objects.gradient_data.weightmodes attribute)": [[4, "cellpack.autopack.interface_objects.gradient_data.WeightModes.SQUARE", false]], "static_id (cellpack.autopack.ingredient.ingredient.ingredient attribute)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.static_id", false]], "static_id (cellpack.autopack.serializable.scompartment attribute)": [[2, "cellpack.autopack.Serializable.sCompartment.static_id", false]], "static_id (cellpack.autopack.serializable.singredient attribute)": [[2, "cellpack.autopack.Serializable.sIngredient.static_id", false]], "static_id (cellpack.autopack.serializable.singredientfiber attribute)": [[2, "cellpack.autopack.Serializable.sIngredientFiber.static_id", false]], "static_id (cellpack.autopack.serializable.singredientgroup attribute)": [[2, "cellpack.autopack.Serializable.sIngredientGroup.static_id", false]], "std (cellpack.autopack.ingredient.ingredient.distributionoptions attribute)": [[3, "cellpack.autopack.ingredient.Ingredient.DistributionOptions.STD", false]], "store() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.store", false]], "store_asjson() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.store_asJson", false]], "store_metadata() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper static method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.store_metadata", false]], "store_packed_object() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.store_packed_object", false]], "store_packed_object() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.store_packed_object", false]], "store_result_file() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper static method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.store_result_file", false]], "sub (cellpack.autopack.interface_objects.gradient_data.pickmodes attribute)": [[4, "cellpack.autopack.interface_objects.gradient_data.PickModes.SUB", false]], "surface (cellpack.autopack.interface_objects.gradient_data.gradientmodes attribute)": [[4, "cellpack.autopack.interface_objects.gradient_data.GradientModes.SURFACE", false]], "swap() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.swap", false]], "test_points_in_bb() (cellpack.autopack.basegrid.basegrid method)": [[2, "cellpack.autopack.BaseGrid.BaseGrid.test_points_in_bb", false]], "testforescape() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.testForEscape", false]], "tetrahedron() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.Tetrahedron", false], [6, "cellpack.autopack.upy.hostHelper.Helper.tetrahedron", false]], "text() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.Text", false]], "texturefacecoordintestovertexcoordinates() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.TextureFaceCoordintesToVertexCoordinates", false]], "threecolorramp() (in module cellpack.autopack.upy.colors)": [[6, "cellpack.autopack.upy.colors.ThreeColorRamp", false]], "timefunction() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.timeFunction", false]], "timefunction() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.timeFunction", false]], "to_json() (cellpack.autopack.serializable.scompartment method)": [[2, "cellpack.autopack.Serializable.sCompartment.to_JSON", false]], "to_json() (cellpack.autopack.serializable.singredient method)": [[2, "cellpack.autopack.Serializable.sIngredient.to_JSON", false]], "to_json() (cellpack.autopack.serializable.singredientfiber method)": [[2, "cellpack.autopack.Serializable.sIngredientFiber.to_JSON", false]], "to_json() (cellpack.autopack.serializable.singredientgroup method)": [[2, "cellpack.autopack.Serializable.sIngredientGroup.to_JSON", false]], "tobinary() (in module cellpack.autopack.ioutils)": [[2, "cellpack.autopack.IOutils.toBinary", false]], "toggle() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.toggle", false]], "toggledisplay() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.toggleDisplay", false]], "toggledisplay() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.toggleDisplay", false]], "toggleeditmode() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.toggleEditMode", false]], "toggleorganelmatr() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.toggleOrganelMatr", false]], "toggleorganelmesh() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.toggleOrganelMesh", false]], "toggleorganelsurf() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.toggleOrganelSurf", false]], "togglexray() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.toggleXray", false]], "tomat() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.ToMat", false]], "tovec() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.ToVec", false]], "tovec() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.ToVec", false]], "traj_type (cellpack.autopack.trajectory.dcdtrajectory attribute)": [[2, "cellpack.autopack.trajectory.dcdTrajectory.traj_type", false]], "traj_type (cellpack.autopack.trajectory.molbtrajectory attribute)": [[2, "cellpack.autopack.trajectory.molbTrajectory.traj_type", false]], "traj_type (cellpack.autopack.trajectory.trajectory attribute)": [[2, "cellpack.autopack.trajectory.Trajectory.traj_type", false]], "traj_type (cellpack.autopack.trajectory.xyztrajectory attribute)": [[2, "cellpack.autopack.trajectory.xyzTrajectory.traj_type", false]], "trajectory (class in cellpack.autopack.trajectory)": [[2, "cellpack.autopack.trajectory.Trajectory", false]], "transformmesh() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.transformMesh", false]], "transformnode() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.transformNode", false]], "transformpoints() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.transformPoints", false]], "transformpoints2d() (cellpack.autopack.plotly_result.plotlyanalysis method)": [[2, "cellpack.autopack.plotly_result.PlotlyAnalysis.transformPoints2D", false]], "transformpoints_mult() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.transformPoints_mult", false]], "translateobj() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.translateObj", false]], "translateobj() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.translateObj", false]], "transpose_image_for_projection() (cellpack.autopack.writers.imagewriter.imagewriter static method)": [[8, "cellpack.autopack.writers.ImageWriter.ImageWriter.transpose_image_for_projection", false]], "transposematrix() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.transposeMatrix", false]], "triangulate() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.triangulate", false]], "triangulateface() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.triangulateFace", false]], "triangulatefacearray() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.triangulateFaceArray", false]], "trimesh (cellpack.autopack.loaders.config_loader.inner_grid_methods attribute)": [[5, "cellpack.autopack.loaders.config_loader.Inner_Grid_Methods.TRIMESH", false]], "twocolorramp() (in module cellpack.autopack.upy.colors)": [[6, "cellpack.autopack.upy.colors.TwoColorRamp", false]], "undspmesh() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.undspMesh", false]], "undspsph() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.undspSph", false]], "uniform (cellpack.autopack.ingredient.ingredient.distributiontypes attribute)": [[3, "cellpack.autopack.ingredient.Ingredient.DistributionTypes.UNIFORM", false]], "unit_vector() (cellpack.autopack.upy.hosthelper.helper class method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.unit_vector", false]], "unlinktraj() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.unlinkTraj", false]], "unpack_curve() (cellpack.bin.simularium_converter.converttosimularium method)": [[9, "cellpack.bin.simularium_converter.ConvertToSimularium.unpack_curve", false]], "unpack_positions() (cellpack.bin.simularium_converter.converttosimularium method)": [[9, "cellpack.bin.simularium_converter.ConvertToSimularium.unpack_positions", false]], "update() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.update", false]], "update() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.update", false]], "update_after_place() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.update_after_place", false]], "update_data_tree() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.update_data_tree", false]], "update_display_rt() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.update_display_rt", false]], "update_distance_distribution_dictionaries() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.update_distance_distribution_dictionaries", false]], "update_doc() (cellpack.autopack.firebasehandler.firebasehandler method)": [[2, "cellpack.autopack.FirebaseHandler.FirebaseHandler.update_doc", false]], "update_elements_in_array() (cellpack.autopack.firebasehandler.firebasehandler static method)": [[2, "cellpack.autopack.FirebaseHandler.FirebaseHandler.update_elements_in_array", false]], "update_ingredient_size() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.update_ingredient_size", false]], "update_instance_positions_and_rotations() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.update_instance_positions_and_rotations", false]], "update_largest_smallest_size() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.update_largest_smallest_size", false]], "update_or_create() (cellpack.autopack.firebasehandler.firebasehandler method)": [[2, "cellpack.autopack.FirebaseHandler.FirebaseHandler.update_or_create", false]], "update_pairwise_distances() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.update_pairwise_distances", false]], "update_reference() (cellpack.autopack.dbrecipehandler.compositiondoc static method)": [[2, "cellpack.autopack.DBRecipeHandler.CompositionDoc.update_reference", false]], "update_reference_on_doc() (cellpack.autopack.firebasehandler.firebasehandler static method)": [[2, "cellpack.autopack.FirebaseHandler.FirebaseHandler.update_reference_on_doc", false]], "update_spline() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.update_spline", false]], "update_spline() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.update_spline", false]], "update_title() (cellpack.autopack.plotly_result.plotlyanalysis method)": [[2, "cellpack.autopack.plotly_result.PlotlyAnalysis.update_title", false]], "update_variable_ingredient_attributes() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.update_variable_ingredient_attributes", false]], "updateappli() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.updateAppli", false]], "updatearmature() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.updateArmature", false]], "updatebox() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.updateBox", false]], "updatebox() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.updateBox", false]], "updatedistances() (cellpack.autopack.basegrid.basegrid static method)": [[2, "cellpack.autopack.BaseGrid.BaseGrid.updateDistances", false]], "updatefrombb() (cellpack.autopack.ingredient.grow.actiningredient method)": [[3, "cellpack.autopack.ingredient.grow.ActinIngredient.updateFromBB", false]], "updategrid() (cellpack.autopack.ingredient.grow.growingredient method)": [[3, "cellpack.autopack.ingredient.grow.GrowIngredient.updateGrid", false]], "updatemasterinstance() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.updateMasterInstance", false]], "updatemasterinstance() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.updateMasterInstance", false]], "updatemesh() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.updateMesh", false]], "updateparticles() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.updateParticles", false]], "updatepath() (in module cellpack.autopack)": [[2, "cellpack.autopack.updatePath", false]], "updatepathdeform() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.updatePathDeform", false]], "updatepathdeform() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.updatePathDeform", false]], "updatepathjson() (in module cellpack.autopack)": [[2, "cellpack.autopack.updatePathJSON", false]], "updatepoly() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.updatePoly", false]], "updatepositionsradii() (in module cellpack.autopack.ioutils)": [[2, "cellpack.autopack.IOutils.updatePositionsRadii", false]], "updatepositionsradii() (in module cellpack.autopack.writers)": [[8, "cellpack.autopack.writers.updatePositionsRadii", false]], "updaterecipavailablexml() (in module cellpack.autopack)": [[2, "cellpack.autopack.updateRecipAvailableXML", false]], "updatereplacepath() (in module cellpack.autopack)": [[2, "cellpack.autopack.updateReplacePath", false]], "updatespring() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.updateSpring", false]], "updatetubemesh() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.updateTubeMesh", false]], "updatetubeobjs() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.updateTubeObjs", false]], "upload() (in module cellpack.bin.upload)": [[9, "cellpack.bin.upload.upload", false]], "upload_collections() (cellpack.autopack.dbrecipehandler.dbuploader method)": [[2, "cellpack.autopack.DBRecipeHandler.DBUploader.upload_collections", false]], "upload_compositions() (cellpack.autopack.dbrecipehandler.dbuploader method)": [[2, "cellpack.autopack.DBRecipeHandler.DBUploader.upload_compositions", false]], "upload_data() (cellpack.autopack.dbrecipehandler.dbuploader method)": [[2, "cellpack.autopack.DBRecipeHandler.DBUploader.upload_data", false]], "upload_doc() (cellpack.autopack.firebasehandler.firebasehandler method)": [[2, "cellpack.autopack.FirebaseHandler.FirebaseHandler.upload_doc", false]], "upload_file() (cellpack.autopack.awshandler.awshandler method)": [[2, "cellpack.autopack.AWSHandler.AWSHandler.upload_file", false]], "upload_gradients() (cellpack.autopack.dbrecipehandler.dbuploader method)": [[2, "cellpack.autopack.DBRecipeHandler.DBUploader.upload_gradients", false]], "upload_objects() (cellpack.autopack.dbrecipehandler.dbuploader method)": [[2, "cellpack.autopack.DBRecipeHandler.DBUploader.upload_objects", false]], "upload_recipe() (cellpack.autopack.dbrecipehandler.dbuploader method)": [[2, "cellpack.autopack.DBRecipeHandler.DBUploader.upload_recipe", false]], "upload_result_metadata() (cellpack.autopack.dbrecipehandler.dbuploader method)": [[2, "cellpack.autopack.DBRecipeHandler.DBUploader.upload_result_metadata", false]], "upload_single_object() (cellpack.autopack.dbrecipehandler.dbuploader method)": [[2, "cellpack.autopack.DBRecipeHandler.DBUploader.upload_single_object", false]], "uppercirclefunction() (cellpack.autopack.geometrytools.geometrytools method)": [[2, "cellpack.autopack.GeometryTools.GeometryTools.UpperCircleFunction", false]], "upperrectanglefunction() (cellpack.autopack.geometrytools.geometrytools method)": [[2, "cellpack.autopack.GeometryTools.GeometryTools.UpperRectangleFunction", false]], "url_exists() (in module cellpack.autopack)": [[2, "cellpack.autopack.url_exists", false]], "use_mesh() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.use_mesh", false]], "use_pdb() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.use_pdb", false]], "validate_distribution_options() (cellpack.autopack.ingredient.ingredient.ingredient static method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.validate_distribution_options", false]], "validate_existence() (cellpack.autopack.dbrecipehandler.resultdoc method)": [[2, "cellpack.autopack.DBRecipeHandler.ResultDoc.validate_existence", false]], "validate_gradient_data() (cellpack.autopack.interface_objects.gradient_data.gradientdata method)": [[4, "cellpack.autopack.interface_objects.gradient_data.GradientData.validate_gradient_data", false]], "validate_ingredient_info() (cellpack.autopack.ingredient.ingredient.ingredient static method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.validate_ingredient_info", false]], "validate_input_recipe_path() (cellpack.autopack.dbrecipehandler.dbrecipeloader method)": [[2, "cellpack.autopack.DBRecipeHandler.DBRecipeLoader.validate_input_recipe_path", false]], "validate_invert_settings() (cellpack.autopack.interface_objects.gradient_data.gradientdata method)": [[4, "cellpack.autopack.interface_objects.gradient_data.GradientData.validate_invert_settings", false]], "validate_mode_settings() (cellpack.autopack.interface_objects.gradient_data.gradientdata method)": [[4, "cellpack.autopack.interface_objects.gradient_data.GradientData.validate_mode_settings", false]], "validate_weight_mode_settings() (cellpack.autopack.interface_objects.gradient_data.gradientdata method)": [[4, "cellpack.autopack.interface_objects.gradient_data.GradientData.validate_weight_mode_settings", false]], "values() (cellpack.autopack.interface_objects.meta_enum.metaenum class method)": [[4, "cellpack.autopack.interface_objects.meta_enum.MetaEnum.values", false]], "vcross() (in module cellpack.autopack.ray)": [[2, "cellpack.autopack.ray.vcross", false]], "vcross() (in module cellpack.autopack.upy.hosthelper)": [[6, "cellpack.autopack.upy.hostHelper.vcross", false]], "vdiff() (in module cellpack.autopack.ray)": [[2, "cellpack.autopack.ray.vdiff", false]], "vdiff() (in module cellpack.autopack.upy.hosthelper)": [[6, "cellpack.autopack.upy.hostHelper.vdiff", false]], "vdistance() (in module cellpack.autopack.upy.hosthelper)": [[6, "cellpack.autopack.upy.hostHelper.vdistance", false]], "vector (cellpack.autopack.interface_objects.gradient_data.gradientmodes attribute)": [[4, "cellpack.autopack.interface_objects.gradient_data.GradientModes.VECTOR", false]], "vector_norm() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.vector_norm", false]], "verbose (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper attribute)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.VERBOSE", false]], "viewer (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper attribute)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.viewer", false]], "vlen() (in module cellpack.autopack.ray)": [[2, "cellpack.autopack.ray.vlen", false]], "vlen() (in module cellpack.autopack.upy.hosthelper)": [[6, "cellpack.autopack.upy.hostHelper.vlen", false]], "vnorm() (in module cellpack.autopack.ray)": [[2, "cellpack.autopack.ray.vnorm", false]], "vnorm() (in module cellpack.autopack.upy.hosthelper)": [[6, "cellpack.autopack.upy.hostHelper.vnorm", false]], "voxels (class in cellpack.autopack.binvox_rw)": [[2, "cellpack.autopack.binvox_rw.Voxels", false]], "walklattice() (cellpack.autopack.ingredient.grow.growingredient method)": [[3, "cellpack.autopack.ingredient.grow.GrowIngredient.walkLattice", false]], "walklatticesurface() (cellpack.autopack.ingredient.grow.growingredient method)": [[3, "cellpack.autopack.ingredient.grow.GrowIngredient.walkLatticeSurface", false]], "walksphere() (cellpack.autopack.ingredient.grow.growingredient method)": [[3, "cellpack.autopack.ingredient.grow.GrowIngredient.walkSphere", false]], "weight (cellpack.autopack.interface_objects.gradient_data.invertoptions attribute)": [[4, "cellpack.autopack.interface_objects.gradient_data.InvertOptions.weight", false]], "weightmodeoptions (class in cellpack.autopack.interface_objects.gradient_data)": [[4, "cellpack.autopack.interface_objects.gradient_data.WeightModeOptions", false]], "weightmodes (class in cellpack.autopack.interface_objects.gradient_data)": [[4, "cellpack.autopack.interface_objects.gradient_data.WeightModes", false]], "which_db() (cellpack.autopack.firebasehandler.firebasehandler static method)": [[2, "cellpack.autopack.FirebaseHandler.FirebaseHandler.which_db", false]], "with_colon() (cellpack.autopack.interface_objects.database_ids.database_ids class method)": [[4, "cellpack.autopack.interface_objects.database_ids.DATABASE_IDS.with_colon", false]], "write() (cellpack.autopack.binvox_rw.voxels method)": [[2, "cellpack.autopack.binvox_rw.Voxels.write", false]], "write() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.write", false]], "write() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.write", false]], "write() (cellpack.autopack.writers.ioingredienttool method)": [[8, "cellpack.autopack.writers.IOingredientTool.write", false]], "write() (in module cellpack.autopack.binvox_rw)": [[2, "cellpack.autopack.binvox_rw.write", false]], "write_creds_path() (cellpack.autopack.firebasehandler.firebasehandler static method)": [[2, "cellpack.autopack.FirebaseHandler.FirebaseHandler.write_creds_path", false]], "write_json_file() (in module cellpack.autopack.loaders.utils)": [[5, "cellpack.autopack.loaders.utils.write_json_file", false]], "write_username_to_creds() (in module cellpack.autopack)": [[2, "cellpack.autopack.write_username_to_creds", false]], "writearraystofile() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.writeArraysToFile", false]], "writedx() (cellpack.autopack.upy.hosthelper.helper class method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.writeDX", false]], "writejson() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.writeJSON", false]], "writemeshtofile() (cellpack.autopack.upy.hosthelper.helper class method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.writeMeshToFile", false]], "writer (class in cellpack.autopack.writers)": [[8, "cellpack.autopack.writers.Writer", false]], "writetofile() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.writeToFile", false]], "writetofile() (cellpack.autopack.upy.simularium.simularium_helper.simulariumhelper method)": [[7, "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.writeToFile", false]], "x (cellpack.autopack.interface_objects.gradient_data.gradientmodes attribute)": [[4, "cellpack.autopack.interface_objects.gradient_data.GradientModes.X", false]], "xyztoijk() (cellpack.autopack.binvox_rw.voxels method)": [[2, "cellpack.autopack.binvox_rw.Voxels.xyzToijk", false]], "xyztrajectory (class in cellpack.autopack.trajectory)": [[2, "cellpack.autopack.trajectory.xyzTrajectory", false]], "y (cellpack.autopack.interface_objects.gradient_data.gradientmodes attribute)": [[4, "cellpack.autopack.interface_objects.gradient_data.GradientModes.Y", false]], "z (cellpack.autopack.interface_objects.gradient_data.gradientmodes attribute)": [[4, "cellpack.autopack.interface_objects.gradient_data.GradientModes.Z", false]]}, "objects": {"": [[1, 0, 0, "-", "cellpack"]], "cellpack": [[2, 0, 0, "-", "autopack"], [9, 0, 0, "-", "bin"], [1, 4, 1, "", "get_module_version"]], "cellpack.autopack": [[2, 0, 0, "-", "AWSHandler"], [2, 0, 0, "-", "Analysis"], [2, 0, 0, "-", "BaseGrid"], [2, 0, 0, "-", "Compartment"], [2, 0, 0, "-", "DBRecipeHandler"], [2, 0, 0, "-", "Environment"], [2, 0, 0, "-", "FirebaseHandler"], [2, 0, 0, "-", "GeometryTools"], [2, 0, 0, "-", "Gradient"], [2, 0, 0, "-", "Graphics"], [2, 0, 0, "-", "Grid"], [2, 0, 0, "-", "IOutils"], [2, 0, 0, "-", "MeshStore"], [2, 0, 0, "-", "Recipe"], [2, 0, 0, "-", "Serializable"], [2, 0, 0, "-", "binvox_rw"], [2, 4, 1, "", "checkErrorInPath"], [2, 4, 1, "", "checkPath"], [2, 4, 1, "", "checkRecipeAvailable"], [2, 4, 1, "", "clearCaches"], [2, 4, 1, "", "convert_db_shortname_to_url"], [2, 4, 1, "", "download_file"], [2, 4, 1, "", "fixOnePath"], [2, 4, 1, "", "fixPath"], [2, 4, 1, "", "get_cache_location"], [2, 4, 1, "", "get_local_file_location"], [3, 0, 0, "-", "ingredient"], [4, 0, 0, "-", "interface_objects"], [2, 4, 1, "", "is_full_url"], [2, 4, 1, "", "is_remote_path"], [2, 4, 1, "", "is_s3_url"], [2, 0, 0, "-", "ldSequence"], [2, 4, 1, "", "load_file"], [5, 0, 0, "-", "loaders"], [2, 4, 1, "", "make_directory_if_needed"], [2, 0, 0, "-", "octree"], [2, 4, 1, "", "parse_s3_uri"], [2, 0, 0, "-", "plotly_result"], [2, 0, 0, "-", "randomRot"], [2, 0, 0, "-", "ray"], [2, 4, 1, "", "read_text_file"], [2, 4, 1, "", "resetDefault"], [2, 4, 1, "", "saveRecipeAvailable"], [2, 4, 1, "", "saveRecipeAvailableJSON"], [2, 0, 0, "-", "trajectory"], [2, 0, 0, "-", "transformation"], [2, 4, 1, "", "updatePath"], [2, 4, 1, "", "updatePathJSON"], [2, 4, 1, "", "updateRecipAvailableXML"], [2, 4, 1, "", "updateReplacePath"], [6, 0, 0, "-", "upy"], [2, 4, 1, "", "url_exists"], [2, 0, 0, "-", "utils"], [2, 4, 1, "", "write_username_to_creds"], [8, 0, 0, "-", "writers"]], "cellpack.autopack.AWSHandler": [[2, 1, 1, "", "AWSHandler"]], "cellpack.autopack.AWSHandler.AWSHandler": [[2, 2, 1, "", "create_presigned_url"], [2, 2, 1, "", "download_file"], [2, 2, 1, "", "get_aws_object_key"], [2, 2, 1, "", "is_url_valid"], [2, 2, 1, "", "save_file_and_get_url"], [2, 2, 1, "", "upload_file"]], "cellpack.autopack.Analysis": [[2, 1, 1, "", "Analysis"]], "cellpack.autopack.Analysis.Analysis": [[2, 2, 1, "", "add_ingredient_positions_to_plot"], [2, 2, 1, "", "build_grid"], [2, 2, 1, "", "cartesian_to_sph"], [2, 2, 1, "", "combine_results_from_ingredients"], [2, 2, 1, "", "combine_results_from_seeds"], [2, 2, 1, "", "create_report"], [2, 2, 1, "", "doloop"], [2, 2, 1, "", "getHaltonUnique"], [2, 2, 1, "", "get_ingredient_key_from_object_or_comp_name"], [2, 2, 1, "", "get_ingredient_radii"], [2, 2, 1, "", "get_list_of_dims"], [2, 2, 1, "", "get_minimum_expected_distance_from_recipe"], [2, 2, 1, "", "get_number_of_ingredients_packed"], [2, 2, 1, "", "get_obj_dict"], [2, 2, 1, "", "get_packed_minimum_distance"], [2, 2, 1, "", "get_partner_pair_dict"], [2, 2, 1, "", "histogram"], [2, 2, 1, "", "loadJSON"], [2, 2, 1, "", "pack"], [2, 2, 1, "", "pack_one_seed"], [2, 2, 1, "", "plot"], [2, 2, 1, "", "plot_distance_distribution"], [2, 2, 1, "", "plot_occurence_distribution"], [2, 2, 1, "", "plot_position_distribution"], [2, 2, 1, "", "plot_position_distribution_total"], [2, 2, 1, "", "process_ingredients_in_recipe"], [2, 2, 1, "", "read_dict_from_glob_file"], [2, 2, 1, "", "run_analysis_workflow"], [2, 2, 1, "", "run_distance_analysis"], [2, 2, 1, "", "run_partner_analysis"], [2, 2, 1, "", "set_ingredient_color"], [2, 2, 1, "", "simpleplot"], [2, 2, 1, "", "update_distance_distribution_dictionaries"], [2, 2, 1, "", "update_pairwise_distances"], [2, 2, 1, "", "writeJSON"]], "cellpack.autopack.BaseGrid": [[2, 1, 1, "", "BaseGrid"], [2, 1, 1, "", "HaltonGrid"], [2, 1, 1, "", "gridPoint"]], "cellpack.autopack.BaseGrid.BaseGrid": [[2, 2, 1, "", "cartesian"], [2, 2, 1, "", "computeExteriorVolume"], [2, 2, 1, "", "computeGridNumberOfPoint"], [2, 2, 1, "", "computeVolume"], [2, 2, 1, "", "create_grid_point_positions"], [2, 2, 1, "", "getCenter"], [2, 2, 1, "", "getClosestFreeGridPoint"], [2, 2, 1, "", "getClosestGridPoint"], [2, 2, 1, "", "getDiagonal"], [2, 2, 1, "", "getIJK"], [2, 2, 1, "", "getPointFrom3D"], [2, 2, 1, "", "getPointsInCube"], [2, 2, 1, "", "getPointsInCubeFillBB"], [2, 2, 1, "", "getPointsInSphere"], [2, 2, 1, "", "getPositionPeridocity"], [2, 2, 1, "", "getRadius"], [2, 2, 1, "", "is_point_inside_bb"], [2, 2, 1, "", "removeFreePoint"], [2, 2, 1, "", "reorder_free_points"], [2, 2, 1, "", "reset"], [2, 2, 1, "", "restore"], [2, 2, 1, "", "save"], [2, 2, 1, "", "set_surfPtsBht"], [2, 2, 1, "", "set_surfPtscht"], [2, 2, 1, "", "setup"], [2, 2, 1, "", "setupBoundaryPeriodicity"], [2, 2, 1, "", "slow_box_fill"], [2, 2, 1, "", "test_points_in_bb"], [2, 2, 1, "", "updateDistances"]], "cellpack.autopack.BaseGrid.HaltonGrid": [[2, 2, 1, "", "create3DPointLookup"], [2, 2, 1, "", "getNBgridPoints"], [2, 2, 1, "", "getPointFrom3D"], [2, 2, 1, "", "getScale"]], "cellpack.autopack.Compartment": [[2, 1, 1, "", "Compartment"], [2, 1, 1, "", "CompartmentList"]], "cellpack.autopack.Compartment.Compartment": [[2, 2, 1, "", "BuildGrid"], [2, 2, 1, "", "BuildGridEnviroOnly"], [2, 2, 1, "", "BuildGrid_bhtree"], [2, 2, 1, "", "BuildGrid_binvox"], [2, 2, 1, "", "BuildGrid_box"], [2, 2, 1, "", "BuildGrid_kevin"], [2, 2, 1, "", "BuildGrid_multisdf"], [2, 2, 1, "", "BuildGrid_pyray"], [2, 2, 1, "", "BuildGrid_ray"], [2, 2, 1, "", "BuildGrid_scanline"], [2, 2, 1, "", "BuildGrid_trimesh"], [2, 2, 1, "", "BuildGrid_utsdf"], [2, 2, 1, "", "buildMesh"], [2, 2, 1, "", "buildSphere"], [2, 2, 1, "", "build_grid_sphere"], [2, 2, 1, "", "checkPointInsideBB"], [2, 2, 1, "", "compute_volume_and_set_count"], [2, 2, 1, "", "create3DPointLookup"], [2, 2, 1, "", "createSurfacePoints"], [2, 2, 1, "", "create_rbnode"], [2, 2, 1, "", "create_voxelization"], [2, 2, 1, "", "create_voxelized_mask"], [2, 2, 1, "", "extendGridArrays"], [2, 2, 1, "", "filter_surface_pts_to_fill_box"], [2, 2, 1, "", "find_nearest"], [2, 2, 1, "", "getBoundingBox"], [2, 2, 1, "", "getCenter"], [2, 2, 1, "", "getFaceNormals"], [2, 2, 1, "", "getFacesNfromV"], [2, 2, 1, "", "getInterpolatedNormal"], [2, 2, 1, "", "getMesh"], [2, 2, 1, "", "getMinMaxProteinSize"], [2, 2, 1, "", "getRadius"], [2, 2, 1, "", "getSizeXYZ"], [2, 2, 1, "", "getSurfaceInnerPoints"], [2, 2, 1, "", "getSurfaceInnerPoints_kevin"], [2, 2, 1, "", "getSurfaceInnerPoints_sdf"], [2, 2, 1, "", "getSurfaceInnerPoints_sdf_interpolate"], [2, 2, 1, "", "getSurfacePoint"], [2, 2, 1, "", "getVNfromF"], [2, 2, 1, "", "getVertexNormals"], [2, 2, 1, "", "get_bbox"], [2, 2, 1, "", "get_normal_for_point"], [2, 2, 1, "", "get_rb_model"], [2, 2, 1, "", "inBox"], [2, 2, 1, "", "inGrid"], [2, 2, 1, "", "initialize_shape"], [2, 2, 1, "", "is_point_inside_mesh"], [2, 2, 1, "", "prepare_buildgrid_box"], [2, 2, 1, "", "printFillInfo"], [2, 2, 1, "", "readGridFromFile"], [2, 2, 1, "", "reset"], [2, 2, 1, "", "saveGridToFile"], [2, 2, 1, "", "setCount"], [2, 2, 1, "", "setGeomFaces"], [2, 2, 1, "", "setInnerRecipe"], [2, 2, 1, "", "setMesh"], [2, 2, 1, "", "setNumber"], [2, 2, 1, "", "setSurfaceRecipe"], [2, 2, 1, "", "set_surface_distances"], [2, 2, 1, "", "store_packed_object"], [2, 2, 1, "", "transformMesh"]], "cellpack.autopack.Compartment.CompartmentList": [[2, 2, 1, "", "add_compartment"]], "cellpack.autopack.DBRecipeHandler": [[2, 1, 1, "", "CompositionDoc"], [2, 1, 1, "", "DBMaintenance"], [2, 1, 1, "", "DBRecipeLoader"], [2, 1, 1, "", "DBUploader"], [2, 1, 1, "", "DataDoc"], [2, 1, 1, "", "GradientDoc"], [2, 1, 1, "", "ObjectDoc"], [2, 1, 1, "", "ResultDoc"]], "cellpack.autopack.DBRecipeHandler.CompositionDoc": [[2, 3, 1, "", "DEFAULT_VALUES"], [2, 3, 1, "", "KEY_TO_DICT_MAPPING"], [2, 3, 1, "", "SHALLOW_MATCH"], [2, 2, 1, "", "as_dict"], [2, 2, 1, "", "check_and_replace_references"], [2, 2, 1, "", "get_reference_data"], [2, 2, 1, "", "get_reference_in_obj"], [2, 2, 1, "", "gradient_list_to_dict"], [2, 2, 1, "", "resolve_db_regions"], [2, 2, 1, "", "resolve_local_regions"], [2, 2, 1, "", "resolve_object_data"], [2, 2, 1, "", "should_write"], [2, 2, 1, "", "update_reference"]], "cellpack.autopack.DBRecipeHandler.DBMaintenance": [[2, 2, 1, "", "cleanup_results"], [2, 2, 1, "", "readme_url"]], "cellpack.autopack.DBRecipeHandler.DBRecipeLoader": [[2, 2, 1, "", "collect_and_sort_data"], [2, 2, 1, "", "collect_docs_by_id"], [2, 2, 1, "", "compile_db_recipe_data"], [2, 2, 1, "", "prep_db_doc_for_download"], [2, 2, 1, "", "validate_input_recipe_path"]], "cellpack.autopack.DBRecipeHandler.DBUploader": [[2, 2, 1, "", "prep_data_for_db"], [2, 2, 1, "", "upload_collections"], [2, 2, 1, "", "upload_compositions"], [2, 2, 1, "", "upload_data"], [2, 2, 1, "", "upload_gradients"], [2, 2, 1, "", "upload_objects"], [2, 2, 1, "", "upload_recipe"], [2, 2, 1, "", "upload_result_metadata"], [2, 2, 1, "", "upload_single_object"]], "cellpack.autopack.DBRecipeHandler.DataDoc": [[2, 2, 1, "", "as_dict"], [2, 2, 1, "", "is_db_dict"], [2, 2, 1, "", "is_key"], [2, 2, 1, "", "is_nested_list"], [2, 2, 1, "", "is_obj"], [2, 2, 1, "", "should_write"]], "cellpack.autopack.DBRecipeHandler.GradientDoc": [[2, 2, 1, "", "should_write"]], "cellpack.autopack.DBRecipeHandler.ObjectDoc": [[2, 2, 1, "", "as_dict"], [2, 2, 1, "", "convert_positions_in_representation"], [2, 2, 1, "", "convert_representation"], [2, 2, 1, "", "should_write"]], "cellpack.autopack.DBRecipeHandler.ResultDoc": [[2, 2, 1, "", "handle_expired_results"], [2, 2, 1, "", "validate_existence"]], "cellpack.autopack.Environment": [[2, 1, 1, "", "Environment"], [2, 4, 1, "", "random"]], "cellpack.autopack.Environment.Environment": [[2, 2, 1, "", "BuildCompartmentsGrids"], [2, 2, 1, "", "SetRBOptions"], [2, 2, 1, "", "SetSpringOptions"], [2, 2, 1, "", "addMeshRBOrganelle"], [2, 2, 1, "", "addRB"], [2, 2, 1, "", "add_seed_number_to_base_name"], [2, 2, 1, "", "applyStep"], [2, 2, 1, "", "buildGrid"], [2, 2, 1, "", "build_compartment_grids"], [2, 2, 1, "", "calc_pairwise_distances"], [2, 2, 1, "", "callFunction"], [2, 2, 1, "", "check_new_placement"], [2, 2, 1, "", "clean_grid_cache"], [2, 2, 1, "", "clear"], [2, 2, 1, "", "clearRBingredient"], [2, 2, 1, "", "collectResultPerIngredient"], [2, 2, 1, "", "compartment_id_for_nearest_grid_point"], [2, 2, 1, "", "convertPickleToText"], [2, 2, 1, "", "create_compartment"], [2, 2, 1, "", "create_ingredient"], [2, 2, 1, "", "create_objects"], [2, 2, 1, "", "create_voxelization"], [2, 2, 1, "", "delRB"], [2, 2, 1, "", "distance_check_failed"], [2, 2, 1, "", "dropOneIngr"], [2, 2, 1, "", "dropOneIngrJson"], [2, 2, 1, "", "exportToBD_BOX"], [2, 2, 1, "", "exportToReaDDy"], [2, 2, 1, "", "exportToTEM"], [2, 2, 1, "", "exportToTEM_SIM"], [2, 2, 1, "", "extend_bounding_box_for_compartments"], [2, 2, 1, "", "extractMeshComponent"], [2, 2, 1, "", "finishWithWater"], [2, 2, 1, "", "getActiveIng"], [2, 2, 1, "", "getIngrFromNameInRecipe"], [2, 2, 1, "", "getOneIngr"], [2, 2, 1, "", "getOneIngrJson"], [2, 2, 1, "", "getPointToDrop"], [2, 2, 1, "", "getRotTransRB"], [2, 2, 1, "", "getSortedActiveIngredients"], [2, 2, 1, "", "getTotalNbObject"], [2, 2, 1, "", "get_all_distances"], [2, 2, 1, "", "get_attributes_to_update"], [2, 2, 1, "", "get_bounding_box_limits"], [2, 2, 1, "", "get_closest_ingredients"], [2, 2, 1, "", "get_compartment_object_by_name"], [2, 2, 1, "", "get_distances"], [2, 2, 1, "", "get_distances_and_angles"], [2, 2, 1, "", "get_dpad"], [2, 2, 1, "", "get_ingredient_angles"], [2, 2, 1, "", "get_ingredient_by_name"], [2, 2, 1, "", "get_ingredients_in_tree"], [2, 2, 1, "", "get_size_of_bounding_box"], [2, 2, 1, "", "includeIngrRecipe"], [2, 2, 1, "", "includeIngrRecipes"], [2, 2, 1, "", "includeIngredientRecipe"], [2, 2, 1, "", "is_two_d"], [2, 2, 1, "", "linkTraj"], [2, 2, 1, "", "loadFreePoint"], [2, 2, 1, "", "loadResult"], [2, 2, 1, "", "load_asJson"], [2, 2, 1, "", "load_asTxt"], [2, 2, 1, "", "loopThroughIngr"], [2, 2, 1, "", "moveRBnode"], [2, 2, 1, "", "onePrevIngredient"], [2, 2, 1, "", "pack_grid"], [2, 2, 1, "", "pickIngredient"], [2, 2, 1, "", "prep_molecules_for_save"], [2, 2, 1, "", "printFillInfo"], [2, 2, 1, "", "readArraysFromFile"], [2, 2, 1, "", "removeOnePoint"], [2, 2, 1, "", "reportprogress"], [2, 2, 1, "", "reset"], [2, 2, 1, "", "resetIngrRecip"], [2, 2, 1, "", "resolve_gradient_data_objects"], [2, 2, 1, "", "restore"], [2, 2, 1, "", "restoreFreePoints"], [2, 2, 1, "", "restoreGridFromFile"], [2, 2, 1, "", "restore_grids_from_pickle"], [2, 2, 1, "", "restore_molecules_array"], [2, 2, 1, "", "runBullet"], [2, 2, 1, "", "saveGridLogsAsJson"], [2, 2, 1, "", "saveGridToFile"], [2, 2, 1, "", "save_grids_to_pickle"], [2, 2, 1, "", "save_result"], [2, 2, 1, "", "setExteriorRecipe"], [2, 2, 1, "", "setGeomFaces"], [2, 2, 1, "", "setSeed"], [2, 2, 1, "", "set_gradient"], [2, 2, 1, "", "set_partners_ingredient"], [2, 2, 1, "", "set_result_file_name"], [2, 2, 1, "", "setupOctree"], [2, 2, 1, "", "setupRBOptions"], [2, 2, 1, "", "sortIngredient"], [2, 2, 1, "", "store"], [2, 2, 1, "", "store_asJson"], [2, 2, 1, "", "timeFunction"], [2, 2, 1, "", "unlinkTraj"], [2, 2, 1, "", "update_after_place"], [2, 2, 1, "", "update_largest_smallest_size"], [2, 2, 1, "", "update_variable_ingredient_attributes"], [2, 2, 1, "", "writeArraysToFile"]], "cellpack.autopack.FirebaseHandler": [[2, 1, 1, "", "FirebaseHandler"]], "cellpack.autopack.FirebaseHandler.FirebaseHandler": [[2, 2, 1, "", "create_path"], [2, 2, 1, "", "create_timestamp"], [2, 2, 1, "", "db_name"], [2, 2, 1, "", "delete_doc"], [2, 2, 1, "", "doc_id"], [2, 2, 1, "", "doc_to_dict"], [2, 2, 1, "", "get_all_docs"], [2, 2, 1, "", "get_collection_id_from_path"], [2, 2, 1, "", "get_creds"], [2, 2, 1, "", "get_dev_creds"], [2, 2, 1, "", "get_doc_by_id"], [2, 2, 1, "", "get_doc_by_name"], [2, 2, 1, "", "get_doc_by_ref"], [2, 2, 1, "", "get_path_from_ref"], [2, 2, 1, "", "get_staging_creds"], [2, 2, 1, "", "get_username"], [2, 2, 1, "", "get_value"], [2, 2, 1, "", "is_firebase_obj"], [2, 2, 1, "", "is_reference"], [2, 2, 1, "", "set_doc"], [2, 2, 1, "", "update_doc"], [2, 2, 1, "", "update_elements_in_array"], [2, 2, 1, "", "update_or_create"], [2, 2, 1, "", "update_reference_on_doc"], [2, 2, 1, "", "upload_doc"], [2, 2, 1, "", "which_db"], [2, 2, 1, "", "write_creds_path"]], "cellpack.autopack.GeometryTools": [[2, 1, 1, "", "GeometryTools"], [2, 1, 1, "", "Rectangle"]], "cellpack.autopack.GeometryTools.GeometryTools": [[2, 2, 1, "", "GetDistance"], [2, 2, 1, "", "LowerCircleFunction"], [2, 2, 1, "", "LowerRectangleFunction"], [2, 3, 1, "", "Resolution"], [2, 2, 1, "", "UpperCircleFunction"], [2, 2, 1, "", "UpperRectangleFunction"], [2, 2, 1, "", "calc_volume"], [2, 2, 1, "", "check_rectangle_oustide"], [2, 2, 1, "", "check_sphere_inside"], [2, 2, 1, "", "getBoundary"], [2, 2, 1, "", "get_rectangle_cercle_area"], [2, 2, 1, "", "region_1"], [2, 2, 1, "", "region_1_2_theta"], [2, 2, 1, "", "region_2"], [2, 2, 1, "", "region_2_integrand"], [2, 2, 1, "", "region_3"], [2, 2, 1, "", "region_3_integrand"]], "cellpack.autopack.Gradient": [[2, 1, 1, "", "Gradient"], [2, 4, 1, "", "random"]], "cellpack.autopack.Gradient.Gradient": [[2, 2, 1, "", "build_axis_weight_map"], [2, 2, 1, "", "build_directional_weight_map"], [2, 2, 1, "", "build_radial_weight_map"], [2, 2, 1, "", "build_surface_distance_weight_map"], [2, 2, 1, "", "build_weight_map"], [2, 2, 1, "", "create_voxelization"], [2, 2, 1, "", "defaultFunction"], [2, 2, 1, "", "getBinaryWeighted"], [2, 2, 1, "", "getForwWeight"], [2, 2, 1, "", "getLinearWeighted"], [2, 2, 1, "", "getMaxWeight"], [2, 2, 1, "", "getMinWeight"], [2, 2, 1, "", "getRndWeighted"], [2, 2, 1, "", "getSubWeighted"], [2, 2, 1, "", "get_center"], [2, 2, 1, "", "get_combined_gradient_weight"], [2, 2, 1, "", "get_gauss_weights"], [2, 2, 1, "", "normalize_vector"], [2, 2, 1, "", "pickPoint"], [2, 2, 1, "", "pick_point_for_ingredient"], [2, 2, 1, "", "pick_point_from_weight"], [2, 2, 1, "", "scale_between_0_and_1"], [2, 2, 1, "", "set_weights_by_mode"]], "cellpack.autopack.Graphics": [[2, 1, 1, "", "AutopackViewer"], [2, 1, 1, "", "ColladaExporter"]], "cellpack.autopack.Graphics.AutopackViewer": [[2, 2, 1, "", "SetHistoVol"], [2, 2, 1, "", "addCompartmentFromGeom"], [2, 2, 1, "", "addIngredientFromGeom"], [2, 2, 1, "", "addMasterIngr"], [2, 2, 1, "", "appendIngrInstance"], [2, 2, 1, "", "buildIngrPrimitive"], [2, 2, 1, "", "callFunction"], [2, 2, 1, "", "checkCreateEmpty"], [2, 2, 1, "", "checkIngrPartnerProperties"], [2, 2, 1, "", "checkIngrSpheres"], [2, 2, 1, "", "clearAll"], [2, 2, 1, "", "clearFill"], [2, 2, 1, "", "clearIngr"], [2, 2, 1, "", "clearRecipe"], [2, 2, 1, "", "collectResult"], [2, 2, 1, "", "color"], [2, 2, 1, "", "colorByDistanceFrom"], [2, 2, 1, "", "colorByOrder"], [2, 2, 1, "", "colorPT"], [2, 2, 1, "", "createIngrMesh"], [2, 2, 1, "", "createOrganelMesh"], [2, 2, 1, "", "createTemplate"], [2, 2, 1, "", "createTemplateCompartment"], [2, 2, 1, "", "delIngr"], [2, 2, 1, "", "delIngredientGrow"], [2, 2, 1, "", "displayCompartment"], [2, 2, 1, "", "displayCompartmentPoints"], [2, 2, 1, "", "displayCompartments"], [2, 2, 1, "", "displayCompartmentsIngredients"], [2, 2, 1, "", "displayCompartmentsPoints"], [2, 2, 1, "", "displayCytoplasmIngredients"], [2, 2, 1, "", "displayDistance"], [2, 2, 1, "", "displayEnv"], [2, 2, 1, "", "displayFill"], [2, 2, 1, "", "displayFillBox"], [2, 2, 1, "", "displayFreePoints"], [2, 2, 1, "", "displayFreePointsAsPS"], [2, 2, 1, "", "displayGradient"], [2, 2, 1, "", "displayIngrCylinders"], [2, 2, 1, "", "displayIngrGrow"], [2, 2, 1, "", "displayIngrGrows"], [2, 2, 1, "", "displayIngrMesh"], [2, 2, 1, "", "displayIngrResults"], [2, 2, 1, "", "displayIngrSpheres"], [2, 2, 1, "", "displayIngredients"], [2, 2, 1, "", "displayInstancesIngredient"], [2, 2, 1, "", "displayLeafOctree"], [2, 2, 1, "", "displayOctree"], [2, 2, 1, "", "displayOctreeLeaf"], [2, 2, 1, "", "displayOneNodeOctree"], [2, 2, 1, "", "displayParticleVolumeDistance"], [2, 2, 1, "", "displayPoints"], [2, 2, 1, "", "displayPreFill"], [2, 2, 1, "", "displayRoot"], [2, 2, 1, "", "displaysubnode"], [2, 2, 1, "", "dspMesh"], [2, 2, 1, "", "dspSph"], [2, 2, 1, "", "exportAsIndexedMeshs"], [2, 2, 1, "", "exportIngredient"], [2, 2, 1, "", "exportRecipeIngredients"], [2, 2, 1, "", "hideIngrPrimitive"], [2, 2, 1, "", "prepareDynamic"], [2, 2, 1, "", "prepareIngredient"], [2, 2, 1, "", "prepareMaster"], [2, 2, 1, "", "printIngredients"], [2, 2, 1, "", "printOneIngr"], [2, 2, 1, "", "replaceIngrMesh"], [2, 2, 1, "", "showHide"], [2, 2, 1, "", "showIngrPrimitive"], [2, 2, 1, "", "timeFunction"], [2, 2, 1, "", "toggleOrganelMatr"], [2, 2, 1, "", "toggleOrganelMesh"], [2, 2, 1, "", "toggleOrganelSurf"], [2, 2, 1, "", "undspMesh"], [2, 2, 1, "", "undspSph"]], "cellpack.autopack.Grid": [[2, 1, 1, "", "Grid"]], "cellpack.autopack.Grid.Grid": [[2, 2, 1, "", "create3DPointLookup"], [2, 2, 1, "", "getIJK"], [2, 2, 1, "", "reset"], [2, 2, 1, "", "restore"], [2, 2, 1, "", "save"]], "cellpack.autopack.IOutils": [[2, 1, 1, "", "ExportCollada"], [2, 1, 1, "", "GrabResult"], [2, 1, 1, "", "IOingredientTool"], [2, 4, 1, "", "addCompartments"], [2, 4, 1, "", "checkRotFormat"], [2, 4, 1, "", "gatherResult"], [2, 4, 1, "", "getAllPosRot"], [2, 4, 1, "", "getStringValueOptions"], [2, 4, 1, "", "load_Json"], [2, 4, 1, "", "load_JsonString"], [2, 4, 1, "", "load_MixedasJson"], [2, 4, 1, "", "saveResultBinary"], [2, 4, 1, "", "saveResultBinaryDic"], [2, 4, 1, "", "save_asPython"], [2, 4, 1, "", "serializedFromResult"], [2, 4, 1, "", "serializedRecipe"], [2, 4, 1, "", "serializedRecipe_group"], [2, 4, 1, "", "serializedRecipe_group_dic"], [2, 4, 1, "", "setValueToPythonStr"], [2, 4, 1, "", "setupFromJsonDic"], [2, 4, 1, "", "toBinary"], [2, 4, 1, "", "updatePositionsRadii"]], "cellpack.autopack.IOutils.GrabResult": [[2, 2, 1, "", "grab"], [2, 2, 1, "", "reset"]], "cellpack.autopack.IOutils.IOingredientTool": [[2, 2, 1, "", "clean_arguments"], [2, 2, 1, "", "ingrJsonNode"], [2, 2, 1, "", "ingrPythonNode"], [2, 2, 1, "", "makeIngredient"], [2, 2, 1, "", "makeIngredientFromJson"], [2, 2, 1, "", "read"], [2, 2, 1, "", "set_recipe_ingredient"]], "cellpack.autopack.MeshStore": [[2, 1, 1, "", "MeshStore"]], "cellpack.autopack.MeshStore.MeshStore": [[2, 2, 1, "", "add_mesh_to_scene"], [2, 2, 1, "", "build_mesh"], [2, 2, 1, "", "calc_scaled_distances_for_positions"], [2, 2, 1, "", "contains_point"], [2, 2, 1, "", "contains_points_mesh"], [2, 2, 1, "", "create_mesh"], [2, 2, 1, "", "create_sphere"], [2, 2, 1, "", "create_sphere_data"], [2, 2, 1, "", "decompose_mesh"], [2, 2, 1, "", "get_centroid"], [2, 2, 1, "", "get_collada_material"], [2, 2, 1, "", "get_mesh"], [2, 2, 1, "", "get_mesh_filepath_and_extension"], [2, 2, 1, "", "get_midpoint"], [2, 2, 1, "", "get_normal"], [2, 2, 1, "", "get_nsphere"], [2, 2, 1, "", "get_object"], [2, 2, 1, "", "get_scaled_distances_between_surfaces"], [2, 2, 1, "", "get_smallest_radius"], [2, 2, 1, "", "norm"], [2, 2, 1, "", "normal_array"], [2, 2, 1, "", "normalize"], [2, 2, 1, "", "normalize_v3"], [2, 2, 1, "", "read_mesh_file"]], "cellpack.autopack.Recipe": [[2, 1, 1, "", "Recipe"], [2, 4, 1, "", "random"]], "cellpack.autopack.Recipe.Recipe": [[2, 2, 1, "", "addIngredient"], [2, 2, 1, "", "delIngredient"], [2, 2, 1, "", "getMinMaxProteinSize"], [2, 2, 1, "", "is_key"], [2, 2, 1, "", "printFillInfo"], [2, 2, 1, "", "resetIngrs"], [2, 2, 1, "", "resolve_composition"], [2, 2, 1, "", "setCount"], [2, 2, 1, "", "sort"]], "cellpack.autopack.Serializable": [[2, 1, 1, "", "sCompartment"], [2, 1, 1, "", "sIngredient"], [2, 1, 1, "", "sIngredientFiber"], [2, 1, 1, "", "sIngredientGroup"]], "cellpack.autopack.Serializable.sCompartment": [[2, 2, 1, "", "addCompartment"], [2, 2, 1, "", "addIngredientGroup"], [2, 3, 1, "", "static_id"], [2, 2, 1, "", "to_JSON"]], "cellpack.autopack.Serializable.sIngredient": [[2, 3, 1, "", "static_id"], [2, 2, 1, "", "to_JSON"]], "cellpack.autopack.Serializable.sIngredientFiber": [[2, 3, 1, "", "static_id"], [2, 2, 1, "", "to_JSON"]], "cellpack.autopack.Serializable.sIngredientGroup": [[2, 2, 1, "", "addIngredient"], [2, 3, 1, "", "static_id"], [2, 2, 1, "", "to_JSON"]], "cellpack.autopack.binvox_rw": [[2, 1, 1, "", "Voxels"], [2, 4, 1, "", "dense_to_sparse"], [2, 4, 1, "", "read"], [2, 4, 1, "", "read_as_3d_array"], [2, 4, 1, "", "read_as_coord_array"], [2, 4, 1, "", "read_header"], [2, 4, 1, "", "sparse_to_dense"], [2, 4, 1, "", "write"]], "cellpack.autopack.binvox_rw.Voxels": [[2, 2, 1, "", "cartesian"], [2, 2, 1, "", "clone"], [2, 2, 1, "", "getIndex"], [2, 2, 1, "", "getIndexData"], [2, 2, 1, "", "ijkToIndex"], [2, 2, 1, "", "ijkToxyz"], [2, 2, 1, "", "write"], [2, 2, 1, "", "xyzToijk"]], "cellpack.autopack.ingredient": [[3, 0, 0, "-", "Ingredient"], [3, 0, 0, "-", "agent"], [3, 0, 0, "-", "grow"], [3, 0, 0, "-", "multi_cylinder"], [3, 0, 0, "-", "multi_sphere"], [3, 0, 0, "-", "single_cube"], [3, 0, 0, "-", "single_cylinder"], [3, 0, 0, "-", "single_sphere"], [3, 0, 0, "-", "utils"]], "cellpack.autopack.ingredient.Ingredient": [[3, 1, 1, "", "DistributionOptions"], [3, 1, 1, "", "DistributionTypes"], [3, 1, 1, "", "Ingredient"], [3, 1, 1, "", "IngredientInstanceDrop"], [3, 4, 1, "", "random"]], "cellpack.autopack.ingredient.Ingredient.DistributionOptions": [[3, 3, 1, "", "LIST_VALUES"], [3, 3, 1, "", "MAX"], [3, 3, 1, "", "MEAN"], [3, 3, 1, "", "MIN"], [3, 3, 1, "", "STD"]], "cellpack.autopack.ingredient.Ingredient.DistributionTypes": [[3, 3, 1, "", "LIST"], [3, 3, 1, "", "NORMAL"], [3, 3, 1, "", "UNIFORM"]], "cellpack.autopack.ingredient.Ingredient.Ingredient": [[3, 3, 1, "", "ARGUMENTS"], [3, 2, 1, "", "DecomposeMesh"], [3, 2, 1, "", "alignRotation"], [3, 2, 1, "", "apply_rotation"], [3, 2, 1, "", "attempt_to_pack_at_grid_location"], [3, 2, 1, "", "buildMesh"], [3, 2, 1, "", "checkDistance"], [3, 2, 1, "", "checkIfUpdate"], [3, 2, 1, "", "check_against_one_packed_ingr"], [3, 2, 1, "", "close_partner_check"], [3, 2, 1, "", "correctBB"], [3, 2, 1, "", "deleteblist"], [3, 2, 1, "", "far_enough_from_surfaces"], [3, 2, 1, "", "getAxisRotation"], [3, 2, 1, "", "getBiasedRotation"], [3, 2, 1, "", "getData"], [3, 2, 1, "", "getEncapsulatingRadius"], [3, 2, 1, "", "getIngredientsInBox"], [3, 2, 1, "", "getListCompFromMask"], [3, 2, 1, "", "getMaxJitter"], [3, 2, 1, "", "getMesh"], [3, 2, 1, "", "get_all_positions_to_check"], [3, 2, 1, "", "get_compartment"], [3, 2, 1, "", "get_cuttoff_value"], [3, 2, 1, "", "get_list_of_free_indices"], [3, 2, 1, "", "get_new_distances_and_inside_points"], [3, 2, 1, "", "get_new_jitter_location_and_rotation"], [3, 2, 1, "", "get_new_pos"], [3, 2, 1, "", "get_partners"], [3, 2, 1, "", "get_rbNodes"], [3, 2, 1, "", "get_rb_model"], [3, 2, 1, "", "get_rotation"], [3, 2, 1, "", "handle_real_time_visualization"], [3, 2, 1, "", "has_mesh"], [3, 2, 1, "", "has_pdb"], [3, 2, 1, "", "initialize_mesh"], [3, 2, 1, "", "is_point_in_correct_region"], [3, 2, 1, "", "jitterPosition"], [3, 2, 1, "", "jitter_place"], [3, 2, 1, "", "lookForNeighbours"], [3, 2, 1, "", "merge_place_results"], [3, 2, 1, "", "np_check_collision"], [3, 2, 1, "", "oneJitter"], [3, 2, 1, "", "pack_at_grid_pt_location"], [3, 2, 1, "", "perturbAxis"], [3, 2, 1, "", "place"], [3, 2, 1, "", "point_is_available"], [3, 2, 1, "", "randomize_rotation"], [3, 2, 1, "", "randomize_translation"], [3, 2, 1, "", "reject"], [3, 2, 1, "", "remove_from_realtime_display"], [3, 2, 1, "", "reset"], [3, 2, 1, "", "rigid_place"], [3, 2, 1, "", "setTilling"], [3, 2, 1, "", "spheres_SST_place"], [3, 3, 1, "", "static_id"], [3, 2, 1, "", "store_packed_object"], [3, 2, 1, "", "swap"], [3, 2, 1, "", "transformPoints"], [3, 2, 1, "", "transformPoints_mult"], [3, 2, 1, "", "update_data_tree"], [3, 2, 1, "", "update_display_rt"], [3, 2, 1, "", "update_ingredient_size"], [3, 2, 1, "", "use_mesh"], [3, 2, 1, "", "use_pdb"], [3, 2, 1, "", "validate_distribution_options"], [3, 2, 1, "", "validate_ingredient_info"]], "cellpack.autopack.ingredient.agent": [[3, 1, 1, "", "Agent"], [3, 4, 1, "", "random"]], "cellpack.autopack.ingredient.agent.Agent": [[3, 2, 1, "", "getSubWeighted"], [3, 2, 1, "", "get_weights_by_distance"], [3, 2, 1, "", "pick_partner_grid_index"]], "cellpack.autopack.ingredient.grow": [[3, 1, 1, "", "ActinIngredient"], [3, 1, 1, "", "GrowIngredient"], [3, 4, 1, "", "random"]], "cellpack.autopack.ingredient.grow.ActinIngredient": [[3, 2, 1, "", "updateFromBB"]], "cellpack.autopack.ingredient.grow.GrowIngredient": [[3, 3, 1, "", "ARGUMENTS"], [3, 2, 1, "", "getFirstPoint"], [3, 2, 1, "", "getInterpolatedSphere"], [3, 2, 1, "", "getJtransRot"], [3, 2, 1, "", "getJtransRot_r"], [3, 2, 1, "", "getNextPoint"], [3, 2, 1, "", "getNextPtIndCyl"], [3, 2, 1, "", "getV3"], [3, 2, 1, "", "get_alternate_position"], [3, 2, 1, "", "get_alternate_position_p"], [3, 2, 1, "", "get_new_distance_values"], [3, 2, 1, "", "get_signed_distance"], [3, 2, 1, "", "grow"], [3, 2, 1, "", "grow_place"], [3, 2, 1, "", "mask_sphere_points"], [3, 2, 1, "", "mask_sphere_points_angle"], [3, 2, 1, "", "mask_sphere_points_boundary"], [3, 2, 1, "", "mask_sphere_points_dihedral"], [3, 2, 1, "", "mask_sphere_points_ingredients"], [3, 2, 1, "", "mask_sphere_points_vector"], [3, 2, 1, "", "pickAlternateHalton"], [3, 2, 1, "", "pickHalton"], [3, 2, 1, "", "pickRandomSphere"], [3, 2, 1, "", "pick_alternate"], [3, 2, 1, "", "pick_random_alternate"], [3, 2, 1, "", "place_alternate"], [3, 2, 1, "", "place_alternate_p"], [3, 2, 1, "", "prepare_alternates"], [3, 2, 1, "", "prepare_alternates_proba"], [3, 2, 1, "", "reset"], [3, 2, 1, "", "resetLastPoint"], [3, 2, 1, "", "resetSphereDistribution"], [3, 2, 1, "", "updateGrid"], [3, 2, 1, "", "walkLattice"], [3, 2, 1, "", "walkLatticeSurface"], [3, 2, 1, "", "walkSphere"]], "cellpack.autopack.ingredient.multi_cylinder": [[3, 1, 1, "", "MultiCylindersIngr"]], "cellpack.autopack.ingredient.multi_cylinder.MultiCylindersIngr": [[3, 2, 1, "", "checkCylCollisions"], [3, 2, 1, "", "collides_with_compartment"], [3, 2, 1, "", "collision_jitter"], [3, 2, 1, "", "getBigBB"], [3, 2, 1, "", "get_cuttoff_value"], [3, 2, 1, "", "initialize_mesh"]], "cellpack.autopack.ingredient.multi_sphere": [[3, 1, 1, "", "MultiSphereIngr"]], "cellpack.autopack.ingredient.multi_sphere.MultiSphereIngr": [[3, 2, 1, "", "collides_with_compartment"], [3, 2, 1, "", "collision_jitter"], [3, 2, 1, "", "get_new_distance_values"], [3, 2, 1, "", "get_radius"], [3, 2, 1, "", "get_signed_distance"], [3, 2, 1, "", "pack_at_grid_pt_location"]], "cellpack.autopack.ingredient.single_cube": [[3, 1, 1, "", "SingleCubeIngr"]], "cellpack.autopack.ingredient.single_cube.SingleCubeIngr": [[3, 2, 1, "", "collides_with_compartment"], [3, 2, 1, "", "collision_jitter"], [3, 2, 1, "", "cube_surface_distance"], [3, 2, 1, "", "get_new_distance_values"], [3, 2, 1, "", "get_signed_distance"]], "cellpack.autopack.ingredient.single_cylinder": [[3, 1, 1, "", "SingleCylinderIngr"]], "cellpack.autopack.ingredient.single_cylinder.SingleCylinderIngr": [[3, 2, 1, "", "checkCylCollisions"], [3, 2, 1, "", "collides_with_compartment"], [3, 2, 1, "", "collision_jitter"], [3, 2, 1, "", "getBigBB"], [3, 2, 1, "", "get_cuttoff_value"], [3, 2, 1, "", "get_signed_distance"], [3, 2, 1, "", "initialize_mesh"]], "cellpack.autopack.ingredient.single_sphere": [[3, 1, 1, "", "SingleSphereIngr"]], "cellpack.autopack.ingredient.single_sphere.SingleSphereIngr": [[3, 2, 1, "", "collides_with_compartment"], [3, 2, 1, "", "collision_jitter"], [3, 2, 1, "", "create_circular_mask"], [3, 2, 1, "", "create_voxelization"], [3, 2, 1, "", "get_new_distance_values"], [3, 2, 1, "", "get_radius"], [3, 2, 1, "", "get_signed_distance"], [3, 2, 1, "", "initialize_mesh"]], "cellpack.autopack.ingredient.utils": [[3, 4, 1, "", "ApplyMatrix"], [3, 4, 1, "", "bullet_checkCollision_mp"], [3, 4, 1, "", "getDihedral"], [3, 4, 1, "", "getNormedVector"], [3, 4, 1, "", "getNormedVectorOnes"], [3, 4, 1, "", "getNormedVectorU"], [3, 4, 1, "", "get_reflected_point"], [3, 4, 1, "", "rotVectToVect"], [3, 4, 1, "", "rotax"]], "cellpack.autopack.interface_objects": [[4, 0, 0, "-", "database_ids"], [4, 0, 0, "-", "default_values"], [4, 0, 0, "-", "gradient_data"], [4, 0, 0, "-", "ingredient_types"], [4, 0, 0, "-", "meta_enum"], [4, 0, 0, "-", "packed_objects"], [4, 0, 0, "-", "partners"], [4, 0, 0, "-", "representations"]], "cellpack.autopack.interface_objects.database_ids": [[4, 1, 1, "", "DATABASE_IDS"]], "cellpack.autopack.interface_objects.database_ids.DATABASE_IDS": [[4, 3, 1, "", "AWS"], [4, 3, 1, "", "FIREBASE"], [4, 3, 1, "", "GITHUB"], [4, 2, 1, "", "handlers"], [4, 2, 1, "", "with_colon"]], "cellpack.autopack.interface_objects.gradient_data": [[4, 1, 1, "", "GradientData"], [4, 1, 1, "", "GradientModes"], [4, 1, 1, "", "InvertOptions"], [4, 1, 1, "", "ModeOptions"], [4, 1, 1, "", "PickModes"], [4, 1, 1, "", "WeightModeOptions"], [4, 1, 1, "", "WeightModes"]], "cellpack.autopack.interface_objects.gradient_data.GradientData": [[4, 3, 1, "", "default_values"], [4, 2, 1, "", "set_mode_properties"], [4, 2, 1, "", "validate_gradient_data"], [4, 2, 1, "", "validate_invert_settings"], [4, 2, 1, "", "validate_mode_settings"], [4, 2, 1, "", "validate_weight_mode_settings"]], "cellpack.autopack.interface_objects.gradient_data.GradientModes": [[4, 3, 1, "", "RADIAL"], [4, 3, 1, "", "SURFACE"], [4, 3, 1, "", "VECTOR"], [4, 3, 1, "", "X"], [4, 3, 1, "", "Y"], [4, 3, 1, "", "Z"]], "cellpack.autopack.interface_objects.gradient_data.InvertOptions": [[4, 3, 1, "", "distance"], [4, 3, 1, "", "weight"]], "cellpack.autopack.interface_objects.gradient_data.ModeOptions": [[4, 3, 1, "", "center"], [4, 3, 1, "", "direction"], [4, 3, 1, "", "gblob"], [4, 3, 1, "", "object"], [4, 3, 1, "", "radius"], [4, 3, 1, "", "scale_distance_between"]], "cellpack.autopack.interface_objects.gradient_data.PickModes": [[4, 3, 1, "", "BINARY"], [4, 3, 1, "", "LINEAR"], [4, 3, 1, "", "MAX"], [4, 3, 1, "", "MIN"], [4, 3, 1, "", "REG"], [4, 3, 1, "", "RND"], [4, 3, 1, "", "SUB"]], "cellpack.autopack.interface_objects.gradient_data.WeightModeOptions": [[4, 3, 1, "", "decay_length"], [4, 3, 1, "", "power"]], "cellpack.autopack.interface_objects.gradient_data.WeightModes": [[4, 3, 1, "", "CUBE"], [4, 3, 1, "", "EXPONENTIAL"], [4, 3, 1, "", "LINEAR"], [4, 3, 1, "", "POWER"], [4, 3, 1, "", "SQUARE"]], "cellpack.autopack.interface_objects.ingredient_types": [[4, 1, 1, "", "INGREDIENT_TYPE"]], "cellpack.autopack.interface_objects.ingredient_types.INGREDIENT_TYPE": [[4, 3, 1, "", "GROW"], [4, 3, 1, "", "MESH"], [4, 3, 1, "", "MULTI_CYLINDER"], [4, 3, 1, "", "MULTI_SPHERE"], [4, 3, 1, "", "SINGLE_CUBE"], [4, 3, 1, "", "SINGLE_CYLINDER"], [4, 3, 1, "", "SINGLE_SPHERE"]], "cellpack.autopack.interface_objects.meta_enum": [[4, 1, 1, "", "MetaEnum"]], "cellpack.autopack.interface_objects.meta_enum.MetaEnum": [[4, 2, 1, "", "is_member"], [4, 2, 1, "", "values"]], "cellpack.autopack.interface_objects.packed_objects": [[4, 1, 1, "", "PackedObject"], [4, 1, 1, "", "PackedObjects"]], "cellpack.autopack.interface_objects.packed_objects.PackedObjects": [[4, 2, 1, "", "add"], [4, 2, 1, "", "get_all"], [4, 2, 1, "", "get_compartment"], [4, 2, 1, "", "get_encapsulating_radii"], [4, 2, 1, "", "get_ingredients"], [4, 2, 1, "", "get_positions"], [4, 2, 1, "", "get_positions_for_ingredient"], [4, 2, 1, "", "get_radii"], [4, 2, 1, "", "get_rotations_for_ingredient"]], "cellpack.autopack.interface_objects.partners": [[4, 1, 1, "", "Partner"], [4, 1, 1, "", "Partners"]], "cellpack.autopack.interface_objects.partners.Partner": [[4, 2, 1, "", "distanceFunction"], [4, 2, 1, "", "get_point"], [4, 2, 1, "", "set_ingredient"]], "cellpack.autopack.interface_objects.partners.Partners": [[4, 2, 1, "", "add_partner"], [4, 2, 1, "", "get_partner_by_ingr_name"], [4, 2, 1, "", "is_partner"]], "cellpack.autopack.interface_objects.representations": [[4, 1, 1, "", "Representations"]], "cellpack.autopack.interface_objects.representations.Representations": [[4, 3, 1, "", "DATABASE"], [4, 2, 1, "", "get_active"], [4, 2, 1, "", "get_active_data"], [4, 2, 1, "", "get_adjusted_position"], [4, 2, 1, "", "get_deepest_level"], [4, 2, 1, "", "get_mesh_format"], [4, 2, 1, "", "get_mesh_name"], [4, 2, 1, "", "get_mesh_path"], [4, 2, 1, "", "get_min_max_radius"], [4, 2, 1, "", "get_pdb_path"], [4, 2, 1, "", "get_positions"], [4, 2, 1, "", "get_radii"], [4, 2, 1, "", "has_mesh"], [4, 2, 1, "", "has_pdb"], [4, 2, 1, "", "set_active"], [4, 2, 1, "", "set_sphere_positions"]], "cellpack.autopack.ldSequence": [[2, 1, 1, "", "HaltonSequence"], [2, 4, 1, "", "SphereHalton"], [2, 1, 1, "", "cHaltonSequence3"], [2, 4, 1, "", "halton"], [2, 4, 1, "", "halton2"], [2, 4, 1, "", "halton3"], [2, 4, 1, "", "halton_sequence"], [2, 4, 1, "", "haltonterm"]], "cellpack.autopack.ldSequence.cHaltonSequence3": [[2, 2, 1, "", "inc"], [2, 2, 1, "", "reset"]], "cellpack.autopack.loaders": [[5, 0, 0, "-", "analysis_config_loader"], [5, 0, 0, "-", "config_loader"], [5, 0, 0, "-", "migrate_v1_to_v2"], [5, 0, 0, "-", "migrate_v2_to_v2_1"], [5, 0, 0, "-", "recipe_loader"], [5, 0, 0, "-", "utils"], [5, 0, 0, "-", "v1_v2_attribute_changes"]], "cellpack.autopack.loaders.analysis_config_loader": [[5, 1, 1, "", "AnalysisConfigLoader"]], "cellpack.autopack.loaders.analysis_config_loader.AnalysisConfigLoader": [[5, 3, 1, "", "default_values"]], "cellpack.autopack.loaders.config_loader": [[5, 1, 1, "", "ConfigLoader"], [5, 1, 1, "", "Inner_Grid_Methods"], [5, 1, 1, "", "Place_Methods"]], "cellpack.autopack.loaders.config_loader.ConfigLoader": [[5, 3, 1, "", "default_values"]], "cellpack.autopack.loaders.config_loader.Inner_Grid_Methods": [[5, 3, 1, "", "RAYTRACE"], [5, 3, 1, "", "SCANLINE"], [5, 3, 1, "", "TRIMESH"]], "cellpack.autopack.loaders.config_loader.Place_Methods": [[5, 3, 1, "", "JITTER"], [5, 3, 1, "", "SPHERES_SST"]], "cellpack.autopack.loaders.migrate_v1_to_v2": [[5, 4, 1, "", "check_required_attributes"], [5, 4, 1, "", "convert"], [5, 4, 1, "", "convert_rotation_range"], [5, 4, 1, "", "get_and_store_v2_object"], [5, 4, 1, "", "get_representations"], [5, 4, 1, "", "migrate_ingredient"], [5, 4, 1, "", "split_ingredient_data"]], "cellpack.autopack.loaders.migrate_v2_to_v2_1": [[5, 4, 1, "", "convert"], [5, 4, 1, "", "convert_gradients"], [5, 4, 1, "", "convert_partners"]], "cellpack.autopack.loaders.recipe_loader": [[5, 1, 1, "", "RecipeLoader"]], "cellpack.autopack.loaders.recipe_loader.RecipeLoader": [[5, 3, 1, "", "default_values"], [5, 2, 1, "", "get_all_ingredients"], [5, 2, 1, "", "resolve_inheritance"]], "cellpack.autopack.loaders.utils": [[5, 4, 1, "", "create_file_info_object_from_full_path"], [5, 4, 1, "", "create_output_dir"], [5, 4, 1, "", "read_json_file"], [5, 4, 1, "", "write_json_file"]], "cellpack.autopack.octree": [[2, 1, 1, "", "OctNode"], [2, 1, 1, "", "Octree"]], "cellpack.autopack.octree.Octree": [[2, 2, 1, "", "addNode"], [2, 2, 1, "", "findBranch"], [2, 2, 1, "", "findPosition"], [2, 2, 1, "", "insertNode"]], "cellpack.autopack.plotly_result": [[2, 1, 1, "", "PlotlyAnalysis"]], "cellpack.autopack.plotly_result.PlotlyAnalysis": [[2, 2, 1, "", "add_circle"], [2, 2, 1, "", "add_ingredient_positions"], [2, 2, 1, "", "add_square"], [2, 2, 1, "", "format_color"], [2, 2, 1, "", "make_and_show_heatmap"], [2, 2, 1, "", "make_grid_heatmap"], [2, 2, 1, "", "show"], [2, 2, 1, "", "transformPoints2D"], [2, 2, 1, "", "update_title"]], "cellpack.autopack.randomRot": [[2, 1, 1, "", "RandomRot"]], "cellpack.autopack.randomRot.RandomRot": [[2, 2, 1, "", "get"], [2, 2, 1, "", "getOld"], [2, 2, 1, "", "quaternion_matrix"], [2, 2, 1, "", "random_quaternion"], [2, 2, 1, "", "random_rotation_matrix"], [2, 2, 1, "", "setSeed"]], "cellpack.autopack.ray": [[2, 4, 1, "", "dot"], [2, 4, 1, "", "f_dot_product"], [2, 4, 1, "", "f_ray_intersect_polyhedron"], [2, 4, 1, "", "findPointsCenter"], [2, 4, 1, "", "makeMarchingCube"], [2, 4, 1, "", "ray_intersect_polygon"], [2, 4, 1, "", "ray_intersect_polyhedron"], [2, 4, 1, "", "vcross"], [2, 4, 1, "", "vdiff"], [2, 4, 1, "", "vlen"], [2, 4, 1, "", "vnorm"]], "cellpack.autopack.trajectory": [[2, 1, 1, "", "Trajectory"], [2, 1, 1, "", "dcdTrajectory"], [2, 1, 1, "", "molbTrajectory"], [2, 1, 1, "", "xyzTrajectory"]], "cellpack.autopack.trajectory.Trajectory": [[2, 2, 1, "", "applyState"], [2, 2, 1, "", "applyState_cb"], [2, 2, 1, "", "applyState_name"], [2, 2, 1, "", "applyState_primitive_name"], [2, 2, 1, "", "completeMapping"], [2, 2, 1, "", "generalApply"], [2, 2, 1, "", "getIngredientInstancePos"], [2, 2, 1, "", "makeIngrMapping"], [2, 3, 1, "", "reg"], [2, 3, 1, "", "traj_type"]], "cellpack.autopack.trajectory.dcdTrajectory": [[2, 3, 1, "", "dcd"], [2, 2, 1, "", "getPosAt"], [2, 2, 1, "", "parse"], [2, 3, 1, "", "traj_type"]], "cellpack.autopack.trajectory.molbTrajectory": [[2, 2, 1, "", "applyState_name"], [2, 2, 1, "", "applyState_primitive_name"], [2, 2, 1, "", "getPosAt"], [2, 2, 1, "", "parse"], [2, 2, 1, "", "parse_one_mol"], [2, 3, 1, "", "traj_type"]], "cellpack.autopack.trajectory.xyzTrajectory": [[2, 2, 1, "", "getPosAt"], [2, 2, 1, "", "getPosLine"], [2, 2, 1, "", "parse"], [2, 3, 1, "", "traj_type"]], "cellpack.autopack.upy": [[6, 0, 0, "-", "colors"], [6, 4, 1, "", "getHClass"], [6, 4, 1, "", "getHelperClass"], [6, 0, 0, "-", "hostHelper"], [6, 4, 1, "", "retrieveHost"], [7, 0, 0, "-", "simularium"]], "cellpack.autopack.upy.colors": [[6, 4, 1, "", "RedWhiteBlueRamp"], [6, 4, 1, "", "ThreeColorRamp"], [6, 4, 1, "", "TwoColorRamp"], [6, 4, 1, "", "create_divergent_color_map_with_scaled_values"], [6, 4, 1, "", "getRamp"], [6, 4, 1, "", "hexToRgb"], [6, 4, 1, "", "map_colors"]], "cellpack.autopack.upy.hostHelper": [[6, 1, 1, "", "Helper"], [6, 4, 1, "", "dot"], [6, 4, 1, "", "vcross"], [6, 4, 1, "", "vdiff"], [6, 4, 1, "", "vdistance"], [6, 4, 1, "", "vlen"], [6, 4, 1, "", "vnorm"]], "cellpack.autopack.upy.hostHelper.Helper": [[6, 2, 1, "", "AddObject"], [6, 2, 1, "", "ApplyMatrix"], [6, 3, 1, "", "BONES"], [6, 3, 1, "", "CAM_OPTIONS"], [6, 2, 1, "", "Circle"], [6, 2, 1, "", "Cylinder"], [6, 2, 1, "", "CylinderHeadTails"], [6, 2, 1, "", "Decompose4x4"], [6, 2, 1, "", "Dodecahedron"], [6, 2, 1, "", "FixNormals"], [6, 2, 1, "", "Hexahedron"], [6, 3, 1, "", "IK"], [6, 2, 1, "", "Icosahedron"], [6, 2, 1, "", "IndexedPolgonsToTriPoints"], [6, 2, 1, "", "JoinsObjects"], [6, 3, 1, "", "LIGHT_OPTIONS"], [6, 2, 1, "", "MidPoint"], [6, 2, 1, "", "ObjectsSelection"], [6, 2, 1, "", "Octahedron"], [6, 2, 1, "", "Platonic"], [6, 2, 1, "", "PointCloudObject"], [6, 2, 1, "", "Sphere"], [6, 2, 1, "", "Tetrahedron"], [6, 2, 1, "", "Text"], [6, 2, 1, "", "ToMat"], [6, 2, 1, "", "ToVec"], [6, 2, 1, "", "addBone"], [6, 2, 1, "", "addCameraToScene"], [6, 2, 1, "", "addConstraint"], [6, 2, 1, "", "addLampToScene"], [6, 2, 1, "", "addMaterial"], [6, 2, 1, "", "addMaterialFromDic"], [6, 2, 1, "", "addMeshEdge"], [6, 2, 1, "", "addMeshEdges"], [6, 2, 1, "", "addMeshFace"], [6, 2, 1, "", "addMeshFaces"], [6, 2, 1, "", "addMeshVertice"], [6, 2, 1, "", "addMeshVertices"], [6, 2, 1, "", "addObjectToScene"], [6, 2, 1, "", "advance_randpoint_onsphere"], [6, 2, 1, "", "angle_between_vectors"], [6, 2, 1, "", "animationStart"], [6, 2, 1, "", "animationStop"], [6, 2, 1, "", "armature"], [6, 2, 1, "", "assignMaterial"], [6, 2, 1, "", "assignNewMaterial"], [6, 2, 1, "", "box"], [6, 2, 1, "", "changeColor"], [6, 2, 1, "", "changeMaterialProperty"], [6, 2, 1, "", "changeObjColorMat"], [6, 2, 1, "", "checkIsMesh"], [6, 2, 1, "", "checkName"], [6, 2, 1, "", "colorMaterial"], [6, 2, 1, "", "colorObject"], [6, 2, 1, "", "combineDaeMeshData"], [6, 2, 1, "", "concatObjectMatrix"], [6, 2, 1, "", "constraintLookAt"], [6, 2, 1, "", "convertColor"], [6, 2, 1, "", "createColorsMat"], [6, 2, 1, "", "createMaterial"], [6, 2, 1, "", "createSpring"], [6, 2, 1, "", "createsNmesh"], [6, 2, 1, "", "deleteChildrens"], [6, 2, 1, "", "deleteMeshEdges"], [6, 2, 1, "", "deleteMeshFaces"], [6, 2, 1, "", "deleteMeshVertices"], [6, 2, 1, "", "dihedral"], [6, 2, 1, "", "dodecahedron"], [6, 2, 1, "", "drawGradientLine"], [6, 2, 1, "", "drawPtCol"], [6, 3, 1, "", "dupliVert"], [6, 2, 1, "", "eulerToMatrix"], [6, 2, 1, "", "fillTriangleColor"], [6, 2, 1, "", "findClosestPoint"], [6, 2, 1, "", "fit_view3D"], [6, 2, 1, "", "frameAdvanced"], [6, 2, 1, "", "getA"], [6, 2, 1, "", "getAllMaterials"], [6, 2, 1, "", "getAngleAxis"], [6, 2, 1, "", "getBoxSize"], [6, 2, 1, "", "getCenter"], [6, 2, 1, "", "getCornerPointCube"], [6, 2, 1, "", "getCurrentScene"], [6, 2, 1, "", "getCurrentSceneName"], [6, 2, 1, "", "getCurrentSelection"], [6, 2, 1, "", "getFace"], [6, 2, 1, "", "getFaceEdges"], [6, 2, 1, "", "getFaceNormalsArea"], [6, 2, 1, "", "getFaces"], [6, 2, 1, "", "getFacesfromV"], [6, 2, 1, "", "getImage"], [6, 2, 1, "", "getLayers"], [6, 2, 1, "", "getMasterInstance"], [6, 2, 1, "", "getMaterial"], [6, 2, 1, "", "getMaterialProperty"], [6, 2, 1, "", "getMesh"], [6, 2, 1, "", "getMeshEdge"], [6, 2, 1, "", "getMeshEdges"], [6, 2, 1, "", "getMeshFaces"], [6, 2, 1, "", "getMeshNormales"], [6, 2, 1, "", "getMeshVertice"], [6, 2, 1, "", "getMeshVertices"], [6, 2, 1, "", "getName"], [6, 2, 1, "", "getObject"], [6, 2, 1, "", "getObjectName"], [6, 2, 1, "", "getOrder"], [6, 2, 1, "", "getParticles"], [6, 2, 1, "", "getParticulesPosition"], [6, 2, 1, "", "getPosUntilRoot"], [6, 2, 1, "", "getProperty"], [6, 2, 1, "", "getPropertyObject"], [6, 2, 1, "", "getScale"], [6, 2, 1, "", "getSize"], [6, 2, 1, "", "getTranslation"], [6, 2, 1, "", "getTubeProperties"], [6, 2, 1, "", "getTubePropertiesMatrix"], [6, 2, 1, "", "getUV"], [6, 2, 1, "", "getUVs"], [6, 2, 1, "", "getVisibility"], [6, 2, 1, "", "get_noise"], [6, 2, 1, "", "hexahedron"], [6, 2, 1, "", "icosahedron"], [6, 2, 1, "", "instancesToCollada"], [6, 2, 1, "", "isSphere"], [6, 2, 1, "", "makeTexture"], [6, 2, 1, "", "matrixToFacesMesh"], [6, 2, 1, "", "matrixToVNMesh"], [6, 2, 1, "", "measure_distance"], [6, 2, 1, "", "metaballs"], [6, 2, 1, "", "newEmpty"], [6, 2, 1, "", "newInstance"], [6, 2, 1, "", "norm"], [6, 2, 1, "", "normal_array"], [6, 2, 1, "", "normalize"], [6, 2, 1, "", "normalize_v3"], [6, 2, 1, "", "octahedron"], [6, 2, 1, "", "oneMetaBall"], [6, 2, 1, "", "particle"], [6, 2, 1, "", "pathDeform"], [6, 2, 1, "", "plane"], [6, 2, 1, "", "progressBar"], [6, 2, 1, "", "randpoint_onsphere"], [6, 2, 1, "", "raycast"], [6, 2, 1, "", "reParent"], [6, 2, 1, "", "read"], [6, 2, 1, "", "readMeshFromFile"], [6, 2, 1, "", "recalc_normals"], [6, 2, 1, "", "reporthook"], [6, 2, 1, "", "rerieveAxis"], [6, 2, 1, "", "resetProgressBar"], [6, 2, 1, "", "resetTransformation"], [6, 2, 1, "", "restoreEditMode"], [6, 2, 1, "", "retrieveColorMat"], [6, 2, 1, "", "rotVectToVect"], [6, 2, 1, "", "rotateObj"], [6, 2, 1, "", "rotatePoint"], [6, 2, 1, "", "rotate_about_axis"], [6, 2, 1, "", "rotation_matrix"], [6, 2, 1, "", "saveDejaVuMesh"], [6, 2, 1, "", "saveObjMesh"], [6, 2, 1, "", "scalar"], [6, 2, 1, "", "scaleObj"], [6, 2, 1, "", "selectEdge"], [6, 2, 1, "", "selectEdges"], [6, 2, 1, "", "selectFace"], [6, 2, 1, "", "selectFaces"], [6, 2, 1, "", "selectVertice"], [6, 2, 1, "", "selectVertices"], [6, 2, 1, "", "setCurrentSelection"], [6, 2, 1, "", "setFrame"], [6, 2, 1, "", "setKeyFrame"], [6, 2, 1, "", "setLayers"], [6, 2, 1, "", "setMeshEdge"], [6, 2, 1, "", "setMeshEdges"], [6, 2, 1, "", "setMeshFace"], [6, 2, 1, "", "setMeshFaces"], [6, 2, 1, "", "setMeshVertice"], [6, 2, 1, "", "setMeshVertices"], [6, 2, 1, "", "setName"], [6, 2, 1, "", "setObjectMatrix"], [6, 2, 1, "", "setParticulesPosition"], [6, 2, 1, "", "setProperty"], [6, 2, 1, "", "setPropertyObject"], [6, 2, 1, "", "setRigidBody"], [6, 2, 1, "", "setSoftBody"], [6, 2, 1, "", "setTransformation"], [6, 2, 1, "", "setTranslation"], [6, 2, 1, "", "setUV"], [6, 2, 1, "", "setUVs"], [6, 2, 1, "", "setViewport"], [6, 2, 1, "", "spline"], [6, 2, 1, "", "testForEscape"], [6, 2, 1, "", "tetrahedron"], [6, 2, 1, "", "toggle"], [6, 2, 1, "", "toggleDisplay"], [6, 2, 1, "", "toggleEditMode"], [6, 2, 1, "", "toggleXray"], [6, 2, 1, "", "translateObj"], [6, 2, 1, "", "transposeMatrix"], [6, 2, 1, "", "triangulate"], [6, 2, 1, "", "triangulateFace"], [6, 2, 1, "", "triangulateFaceArray"], [6, 2, 1, "", "unit_vector"], [6, 2, 1, "", "update"], [6, 2, 1, "", "updateArmature"], [6, 2, 1, "", "updateBox"], [6, 2, 1, "", "updateMasterInstance"], [6, 2, 1, "", "updateParticles"], [6, 2, 1, "", "updatePathDeform"], [6, 2, 1, "", "updateSpring"], [6, 2, 1, "", "updateTubeObjs"], [6, 2, 1, "", "update_spline"], [6, 2, 1, "", "vector_norm"], [6, 2, 1, "", "write"], [6, 2, 1, "", "writeDX"], [6, 2, 1, "", "writeMeshToFile"], [6, 2, 1, "", "writeToFile"]], "cellpack.autopack.upy.simularium": [[7, 0, 0, "-", "plots"], [7, 0, 0, "-", "simularium_helper"]], "cellpack.autopack.upy.simularium.plots": [[7, 1, 1, "", "PlotData"]], "cellpack.autopack.upy.simularium.plots.PlotData": [[7, 2, 1, "", "add_histogram"], [7, 2, 1, "", "add_scatter"]], "cellpack.autopack.upy.simularium.simularium_helper": [[7, 1, 1, "", "Instance"], [7, 1, 1, "", "simulariumHelper"]], "cellpack.autopack.upy.simularium.simularium_helper.Instance": [[7, 2, 1, "", "increment_static"], [7, 2, 1, "", "move"], [7, 2, 1, "", "set_static"]], "cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper": [[7, 2, 1, "", "Box"], [7, 2, 1, "", "Cube"], [7, 2, 1, "", "Cylinders"], [7, 3, 1, "", "DATABASE"], [7, 3, 1, "", "DEBUG"], [7, 2, 1, "", "DecomposeMesh"], [7, 3, 1, "", "EMPTY"], [7, 2, 1, "", "FromVec"], [7, 2, 1, "", "Geom"], [7, 2, 1, "", "GetAbsPosUntilRoot"], [7, 3, 1, "", "INSTANCE"], [7, 2, 1, "", "IndexedPolygons"], [7, 2, 1, "", "Labels"], [7, 2, 1, "", "ObjectsSelection"], [7, 3, 1, "", "POLYGON"], [7, 2, 1, "", "Points"], [7, 2, 1, "", "Polylines"], [7, 3, 1, "", "SPHERE"], [7, 3, 1, "", "SPLINE"], [7, 2, 1, "", "Spheres"], [7, 2, 1, "", "TextureFaceCoordintesToVertexCoordinates"], [7, 2, 1, "", "ToVec"], [7, 3, 1, "", "VERBOSE"], [7, 2, 1, "", "addCameraToScene"], [7, 2, 1, "", "addLampToScene"], [7, 2, 1, "", "addMaterial"], [7, 2, 1, "", "add_compartment_to_scene"], [7, 2, 1, "", "add_grid_data_to_scene"], [7, 2, 1, "", "add_instance"], [7, 2, 1, "", "add_new_instance_and_update_time"], [7, 2, 1, "", "add_object_to_scene"], [7, 2, 1, "", "assignMaterial"], [7, 2, 1, "", "box"], [7, 2, 1, "", "changeColor"], [7, 2, 1, "", "changeColorO"], [7, 2, 1, "", "changeObjColorMat"], [7, 2, 1, "", "clear"], [7, 2, 1, "", "concatObjectMatrix"], [7, 2, 1, "", "createTexturedMaterial"], [7, 2, 1, "", "cylinder"], [7, 2, 1, "", "decomposeColladaGeom"], [7, 2, 1, "", "deleteInstance"], [7, 2, 1, "", "deleteObject"], [7, 2, 1, "", "format_rgb_color"], [7, 2, 1, "", "getAllMaterials"], [7, 2, 1, "", "getChilds"], [7, 2, 1, "", "getColladaMaterial"], [7, 2, 1, "", "getCornerPointCube"], [7, 2, 1, "", "getCurrentScene"], [7, 2, 1, "", "getCurrentSelection"], [7, 2, 1, "", "getFace"], [7, 2, 1, "", "getMaterial"], [7, 2, 1, "", "getMaterialName"], [7, 2, 1, "", "getMaterialObject"], [7, 2, 1, "", "getMesh"], [7, 2, 1, "", "getMeshEdges"], [7, 2, 1, "", "getMeshFaces"], [7, 2, 1, "", "getMeshNormales"], [7, 2, 1, "", "getMeshVertices"], [7, 2, 1, "", "getName"], [7, 2, 1, "", "getNormals"], [7, 2, 1, "", "getObject"], [7, 2, 1, "", "getTransformation"], [7, 2, 1, "", "getTranslation"], [7, 2, 1, "", "getType"], [7, 2, 1, "", "getVisibility"], [7, 2, 1, "", "get_display_data"], [7, 3, 1, "", "host"], [7, 2, 1, "", "increment_static_objects"], [7, 2, 1, "", "increment_time"], [7, 2, 1, "", "init_scene_with_objects"], [7, 2, 1, "", "instancePolygon"], [7, 2, 1, "", "instancesCylinder"], [7, 2, 1, "", "instancesSphere"], [7, 2, 1, "", "isIndexedPolyon"], [7, 2, 1, "", "is_fiber"], [7, 2, 1, "", "move_object"], [7, 2, 1, "", "newEmpty"], [7, 2, 1, "", "nodeToGeom"], [7, 2, 1, "", "oneColladaGeom"], [7, 2, 1, "", "oneCylinder"], [7, 2, 1, "", "open_in_simularium"], [7, 2, 1, "", "pathDeform"], [7, 3, 1, "", "pb"], [7, 2, 1, "", "place_object"], [7, 2, 1, "", "plane"], [7, 2, 1, "", "post_and_open_file"], [7, 2, 1, "", "progressBar"], [7, 2, 1, "", "raycast"], [7, 2, 1, "", "raycast_test"], [7, 2, 1, "", "reParent"], [7, 2, 1, "", "remove_nans"], [7, 2, 1, "", "resetProgressBar"], [7, 2, 1, "", "rotateObj"], [7, 2, 1, "", "scaleObj"], [7, 2, 1, "", "setInstance"], [7, 2, 1, "", "setObjectMatrix"], [7, 2, 1, "", "setRigidBody"], [7, 2, 1, "", "setTranslation"], [7, 2, 1, "", "setViewer"], [7, 2, 1, "", "set_object_static"], [7, 2, 1, "", "sort_values"], [7, 2, 1, "", "sphere"], [7, 2, 1, "", "spline"], [7, 2, 1, "", "store_metadata"], [7, 2, 1, "", "store_result_file"], [7, 2, 1, "", "toggleDisplay"], [7, 2, 1, "", "transformNode"], [7, 2, 1, "", "translateObj"], [7, 2, 1, "", "update"], [7, 2, 1, "", "updateAppli"], [7, 2, 1, "", "updateBox"], [7, 2, 1, "", "updateMasterInstance"], [7, 2, 1, "", "updateMesh"], [7, 2, 1, "", "updatePathDeform"], [7, 2, 1, "", "updatePoly"], [7, 2, 1, "", "updateTubeMesh"], [7, 2, 1, "", "update_instance_positions_and_rotations"], [7, 2, 1, "", "update_spline"], [7, 3, 1, "", "viewer"], [7, 2, 1, "", "write"], [7, 2, 1, "", "writeToFile"]], "cellpack.autopack.utils": [[2, 4, 1, "", "check_paired_key"], [2, 4, 1, "", "cmp_to_key"], [2, 4, 1, "", "deep_merge"], [2, 4, 1, "", "expand_object_using_key"], [2, 4, 1, "", "get_distance"], [2, 4, 1, "", "get_distances_from_point"], [2, 4, 1, "", "get_max_value_from_distribution"], [2, 4, 1, "", "get_min_value_from_distribution"], [2, 4, 1, "", "get_paired_key"], [2, 4, 1, "", "get_seed_list"], [2, 4, 1, "", "get_value_from_distribution"], [2, 4, 1, "", "ingredient_compare0"], [2, 4, 1, "", "ingredient_compare1"], [2, 4, 1, "", "ingredient_compare2"], [2, 4, 1, "", "load_object_from_pickle"]], "cellpack.autopack.writers": [[8, 1, 1, "", "IOingredientTool"], [8, 0, 0, "-", "ImageWriter"], [8, 1, 1, "", "NumpyArrayEncoder"], [8, 1, 1, "", "Writer"], [8, 4, 1, "", "updatePositionsRadii"]], "cellpack.autopack.writers.IOingredientTool": [[8, 2, 1, "", "ingrJsonNode"], [8, 2, 1, "", "write"]], "cellpack.autopack.writers.ImageWriter": [[8, 1, 1, "", "ImageWriter"]], "cellpack.autopack.writers.ImageWriter.ImageWriter": [[8, 2, 1, "", "concatenate_image_data"], [8, 2, 1, "", "convolve_channel"], [8, 2, 1, "", "convolve_image"], [8, 2, 1, "", "create_box_psf"], [8, 2, 1, "", "create_gaussian_psf"], [8, 2, 1, "", "export_image"], [8, 2, 1, "", "transpose_image_for_projection"]], "cellpack.autopack.writers.NumpyArrayEncoder": [[8, 2, 1, "", "default"]], "cellpack.autopack.writers.Writer": [[8, 2, 1, "", "return_object_value"], [8, 2, 1, "", "save"], [8, 2, 1, "", "save_Mixed_asJson"], [8, 2, 1, "", "save_as_simularium"], [8, 2, 1, "", "setValueToJsonNode"]], "cellpack.bin": [[9, 0, 0, "-", "analyze"], [9, 0, 0, "-", "clean"], [9, 0, 0, "-", "cleanup_tasks"], [9, 0, 0, "-", "pack"], [9, 0, 0, "-", "simularium_converter"], [9, 0, 0, "-", "upload"]], "cellpack.bin.analyze": [[9, 4, 1, "", "analyze"], [9, 4, 1, "", "main"]], "cellpack.bin.clean": [[9, 4, 1, "", "clean"], [9, 4, 1, "", "main"]], "cellpack.bin.cleanup_tasks": [[9, 4, 1, "", "run_cleanup"]], "cellpack.bin.pack": [[9, 4, 1, "", "main"], [9, 4, 1, "", "pack"]], "cellpack.bin.simularium_converter": [[9, 1, 1, "", "ConvertToSimularium"], [9, 4, 1, "", "main"]], "cellpack.bin.simularium_converter.ConvertToSimularium": [[9, 3, 1, "", "DEFAULT_GEO_TYPE"], [9, 3, 1, "", "DEFAULT_INPUT_RECIPE"], [9, 3, 1, "", "DEFAULT_OUTPUT_DIRECTORY"], [9, 3, 1, "", "DEFAULT_PACKING_RESULT"], [9, 3, 1, "", "DEFAULT_SCALE_FACTOR"], [9, 2, 1, "", "fill_in_empty_fiber_data"], [9, 2, 1, "", "get_bounding_box"], [9, 2, 1, "", "get_euler"], [9, 2, 1, "", "get_euler_from_matrix"], [9, 2, 1, "", "get_euler_from_quat"], [9, 2, 1, "", "get_ingredient_data"], [9, 2, 1, "", "get_ingredient_display_data"], [9, 2, 1, "", "get_mesh_data"], [9, 2, 1, "", "get_positions_per_ingredient"], [9, 2, 1, "", "is_matrix"], [9, 2, 1, "", "process_one_ingredient"], [9, 2, 1, "", "unpack_curve"], [9, 2, 1, "", "unpack_positions"]], "cellpack.bin.upload": [[9, 4, 1, "", "get_recipe_metadata"], [9, 4, 1, "", "main"], [9, 4, 1, "", "upload"]]}, "objnames": {"0": ["py", "module", "Python module"], "1": ["py", "class", "Python class"], "2": ["py", "method", "Python method"], "3": ["py", "attribute", "Python attribute"], "4": ["py", "function", "Python function"]}, "objtypes": {"0": "py:module", "1": "py:class", "2": "py:method", "3": "py:attribute", "4": "py:function"}, "terms": {"": [0, 2, 6, 10, 14], "0": [2, 3, 4, 5, 6, 7, 8, 9, 11], "00": 1, "0006022": 2, "0015926529164868282": 6, "01": [2, 3, 9], "01_04": 2, "022e23": 2, "022x10": 2, "04": 2, "06": 2, "06146124": 2, "09": 2, "0list": 2, "0x1e4fc4b0": [6, 7], "0x1e4fd3a0": 6, "0x1e4fd3d0": 6, "0x246c01a0": [6, 7], "1": [1, 3, 4, 5, 6, 7, 8, 9], "10": [0, 2, 3, 6, 7, 14], "100": [0, 2, 3, 5, 14], "1000": [0, 14], "10000": 2, "1000\u00e5": 2, "1024": 2, "1085": 2, "1087": 2, "10cm": 2, "10x": 2, "11": 2, "12": [6, 7], "1208118": 2, "123": 2, "124": 2, "130": 2, "132": 2, "133000000000003": 2, "14": 6, "141592653589793": [3, 6], "1415927": [0, 14], "15": [0, 2, 6, 7, 14], "16": [2, 6], "1660\u00e5": 2, "175": 2, "18": 2, "18nm": 2, "19": 2, "192": 2, "1978": 2, "1987": 2, "1990": 2, "1991": 2, "1992": 2, "1994": 2, "1cm": 2, "1d": 2, "1ing": 2, "1l": 2, "1m": 2, "1nm": 2, "1sphere": 6, "1\u00e5": 2, "2": [0, 2, 3, 6, 7, 14], "20": [1, 3, 6, 7], "200": [0, 2, 14], "2000": [2, 6], "2004": 2, "2005": 2, "2006": 2, "2009": 2, "2010": [2, 3, 6, 7], "2011": 2, "2012": 1, "2013": 2, "2014": 2, "2016": 2, "22": [2, 3], "222": [2, 6], "229": 2, "23": 1, "234": 2, "24": 2, "25": [2, 6], "255": [2, 6, 7], "256": [2, 6], "27": 2, "2831": [0, 3, 14], "29": 2, "29097116474265428": 6, "293748": 2, "29751650059422086": 6, "2d": [0, 2, 3, 6, 14], "2nd": 2, "2x": 2, "2x3": [6, 7], "3": [0, 2, 3, 6, 7, 11, 14], "30": [0, 3, 6, 7, 14], "32": 2, "320": 2, "323": 2, "324": 2, "32x32x32": 2, "331": 2, "345": 2, "35": [2, 3], "360": 6, "3600": 2, "3d": [2, 3, 6, 7], "4": [2, 6], "40": [6, 7], "41": 2, "41614630875957009": 6, "44": 2, "4492935982947064e": 6, "472": 2, "475": 2, "480": 6, "498": [0, 14], "49b": [6, 7], "4d": 6, "4x4": [2, 3, 6], "4x4arrai": [3, 6], "5": [0, 2, 3, 4, 6, 7, 8, 14], "50": [1, 3], "52": 2, "53": 1, "55": 2, "5708": 6, "58": 2, "595": 2, "6": [0, 2, 3, 6, 7, 14], "60": [0, 2, 14], "604": 2, "629": 2, "6330381706044601": 6, "642": 2, "65275180908484898": 6, "69670582573323303": 6, "6nm": 2, "7": [2, 11], "71735518109654839": 6, "7853981633974483": 2, "8": [2, 3, 6, 11], "827": 2, "828": 2, "8\u00e5": 2, "9": [2, 11], "90": [2, 3], "90929627358879683": 6, "95532": 6, "99810947": 2, "999": 3, "A": [0, 2, 6, 7, 10, 14], "AND": 2, "AS": 2, "As": [0, 14], "BE": 2, "BUT": 2, "BY": 2, "By": 2, "FOR": [2, 6, 7], "For": [2, 6, 8, 11], "IF": 2, "IN": 2, "IT": 11, "If": [0, 2, 3, 6, 7, 8, 11, 12, 14], "In": [0, 2, 6, 14], "It": [0, 2, 8, 10, 11, 14], "NO": 2, "NOT": 2, "No": 2, "OF": 2, "ON": 2, "OR": [2, 6], "One": [0, 6, 14], "Or": 12, "SUCH": 2, "THE": 2, "TO": [2, 6, 7], "The": [0, 3, 8, 9, 12, 14], "Then": 10, "These": 4, "To": [2, 6, 8, 11, 12], "Will": [0, 14], "__init__": [2, 7], "_also_": 2, "_analysi": 2, "_distance_dict": 2, "_not_": 3, "a34": 2, "a_norm": [2, 6], "ab": 2, "about": [2, 3, 6], "abov": 2, "absolu": [6, 7], "absolut": [2, 6, 7], "accept": [0, 14], "access": [2, 6, 7], "accompani": 2, "accord": [2, 6, 7], "according": 6, "account": [6, 11], "accum_result": 3, "accur": [0, 14], "across": [2, 3], "acta": 2, "actin": 3, "actiningredi": [2, 3], "action": 11, "activ": [2, 6, 7, 11], "activeingredi": 2, "actual": 2, "ad": [2, 3, 6, 7], "add": [2, 4, 6, 7, 10], "add_circl": [1, 2], "add_compart": [1, 2], "add_compartment_to_scen": [6, 7], "add_grid_data_to_scen": [6, 7], "add_histogram": [6, 7], "add_ingredient_posit": [1, 2], "add_ingredient_positions_to_plot": [1, 2], "add_inst": [6, 7], "add_mesh_to_scen": [1, 2], "add_new_instance_and_update_tim": [6, 7], "add_object_to_scen": [6, 7], "add_partn": [2, 4], "add_scatt": [6, 7], "add_seed_number_to_base_nam": [1, 2], "add_squar": [1, 2], "add_to_result": 2, "addbon": [2, 6], "addcameratoscen": [2, 6, 7], "addcompart": [1, 2], "addcompartmentfromgeom": [1, 2], "addconstraint": [2, 6], "addingredi": [1, 2], "addingredientfromgeom": [1, 2], "addingredientgroup": [1, 2], "addit": [0, 2, 6, 7, 14], "addlamptoscen": [2, 6, 7], "addmasteringr": [1, 2], "addmateri": [2, 6, 7], "addmaterialfromd": [2, 6], "addmeshedg": [2, 6], "addmeshfac": [2, 6], "addmeshrborganel": [1, 2], "addmeshvertic": [2, 6], "addnod": [1, 2], "addobject": [2, 6], "addobjecttoscen": [2, 6], "addrb": [1, 2], "addsp": 2, "adict": 2, "adjust": 3, "advance_randpoint_onspher": [2, 6], "advis": 2, "aeroplan": 6, "af": 2, "affili": 2, "afgui": 2, "after": [2, 3, 6, 7], "afvi": 3, "afview": 2, "against": [0, 2, 14], "agent": [1, 2], "agent_id": 9, "aic": 11, "al": 2, "algo": [0, 2, 14], "algorithm": [0, 2, 3, 11, 14], "alia": 6, "align": [3, 6], "alignrot": [2, 3], "all": [0, 2, 3, 4, 6, 7, 8, 10, 11, 14], "all_gradi": 2, "all_ingredi": 9, "all_ingredient_dist": 2, "all_object": 2, "all_po": 2, "all_pos_list": 2, "all_posit": 2, "all_rot": 2, "allclos": [2, 6], "allen": 9, "allencel": 11, "allingredi": 2, "allingrpt": 2, "allow": [0, 2, 14], "allow_nan": 8, "almost": 2, "along": [2, 6, 7], "alpha": [2, 6], "alreadi": 2, "also": [0, 2, 3, 10, 11, 14], "alt": 3, "altern": 3, "although": [2, 3], "alti": 3, "alusi": 2, "alwai": [0, 10, 12, 14], "am": 2, "amount": [0, 14], "amplitud": 3, "an": [0, 2, 3, 5, 6, 7, 8, 9, 11, 14], "anaconda": 10, "analys": [2, 9], "analyseap": 2, "analysi": [1, 9, 13], "analysis_config": 2, "analysis_config_load": [1, 2], "analysis_config_path": 9, "analysisconfigload": [2, 5], "analyz": [1, 2, 13], "andrew": 2, "angl": [2, 3, 6], "angle_between_vector": [2, 6], "ani": [2, 3, 6, 7, 11], "anim": 6, "animationstart": [2, 6], "animationstop": [2, 6], "anoth": [2, 3, 6], "anyth": 2, "apart": 2, "api": 2, "append": [2, 3], "appendingrinst": [1, 2], "applcabl": 6, "appli": [2, 3, 6, 7], "applic": [2, 6], "apply_rot": [2, 3], "applymatrix": [2, 3, 6], "applyst": [1, 2], "applystate_cb": [1, 2], "applystate_nam": [1, 2], "applystate_primitive_nam": [1, 2], "applystep": [1, 2], "appreci": 10, "approach": [2, 3], "appropri": 6, "apr": [0, 14], "april": 2, "ar": [0, 2, 3, 4, 6, 8, 10, 11, 14], "arai": 6, "arbitrari": [2, 8], "arcbal": 2, "area": [2, 6], "arg": [2, 6, 7, 9], "arguement": 6, "arguemt": 6, "argument": [2, 3, 6, 7, 9], "arguments_to_includ": 2, "aris": 2, "armatur": [2, 6], "armdata": 6, "around": [2, 6], "arr": [2, 6], "arrai": [0, 2, 3, 6, 7, 8, 14], "arrang": 2, "arthur": 2, "articl": 2, "as_dict": [1, 2], "ascii": 8, "asin": 6, "asmo": 2, "assign": [2, 3, 6, 7], "assignmateri": [2, 6, 7], "assignnewmateri": [2, 6], "assist": 2, "associ": 3, "assum": 2, "astr": 2, "atmost": 2, "atom": [4, 5, 11], "attempt": [0, 2, 3, 8, 14], "attempt_to_pack_at_grid_loc": [2, 3], "attenu": [6, 7], "attitud": [2, 6], "attractor": [0, 14], "attribut": [2, 3], "attrnam": [2, 8], "author": 2, "autin": [2, 6, 7], "auto": 6, "autofil": 2, "automat": 6, "autopack": [1, 9, 11, 13], "autopackserv": [0, 14], "autopackview": [1, 2], "avail": [2, 3, 4, 6, 7], "available_region": 3, "averag": 2, "avg_num_pack": 2, "avoid": [2, 6], "aw": [2, 4], "awai": [2, 3], "aws_access_key_id": 11, "aws_secret_access_kei": 11, "aws_url": 7, "awshandl": [1, 13], "ax": [2, 6], "axi": [2, 3, 6, 7], "axis_ord": 2, "az": 6, "azimuth": 6, "b": [2, 3, 6, 7, 10], "back": 2, "backward": 2, "bake": 6, "ball": [2, 6], "bank": 6, "bar": [2, 6, 7], "barycent": 2, "base": [0, 2, 3, 4, 5, 6, 7, 8, 9, 14], "base1": 2, "base2": 2, "base3": 2, "basedocu": [6, 7], "basegrid": [1, 13], "basenam": [2, 6], "baseobject": [6, 7], "basi": 8, "basic": [6, 7], "bb": [2, 3, 7], "bb_scale": 2, "bd_type": 2, "becam": 2, "becaus": [0, 2, 6, 14], "been": [2, 3], "befor": [0, 2, 3, 14], "begin": [2, 3], "behavior": [6, 8], "being": [0, 2, 6, 14], "believ": [0, 14], "belong": 3, "best": 2, "beta": 2, "better": 2, "between": [0, 2, 6, 14], "bezier": [6, 7], "bhtree": [0, 14], "bi": 2, "bia": 6, "bias": [3, 6], "bin": [1, 13], "binari": [2, 3, 4], "binding_prob": [2, 4], "binvox": [0, 2, 14], "binvox_rw": [1, 13], "biologi": 2, "bionumb": 2, "bisect": 2, "bit": 10, "bkp": 2, "blender": [2, 6, 7], "block": 2, "blockid_": 2, "blocksiz": 6, "blogspot": 2, "bodi": [2, 6, 7], "bond": 6, "bone": [2, 6], "bonepar": 6, "booelan": [6, 7], "book": 2, "bool": [2, 6, 7], "boolean": [0, 2, 3, 6, 7, 14], "both": [2, 11], "boto3": 11, "bottom": [2, 3, 6, 7], "bound": [0, 2, 3, 14], "bounding_box": [2, 3, 5], "boundingbox": [2, 3], "box": [0, 2, 3, 6, 7, 8, 14], "bpy_strct": [6, 7], "br": 10, "branch": [10, 11], "break": 11, "brep": 2, "brian": 3, "broadcast": 2, "browser": 11, "bucket": 2, "bucket_nam": 2, "buffer": 2, "bugfix": 10, "build": [0, 2, 3, 6, 10, 11, 14], "build_axis_weight_map": [1, 2], "build_compartment_grid": [1, 2], "build_directional_weight_map": [1, 2], "build_grid": [1, 2], "build_grid_spher": [1, 2], "build_mesh": [1, 2], "build_radial_weight_map": [1, 2], "build_surface_distance_weight_map": [1, 2], "build_weight_map": [1, 2], "buildcompartmentsgrid": [1, 2], "buildgrid": [1, 2], "buildgrid_bhtre": [1, 2], "buildgrid_binvox": [1, 2], "buildgrid_box": [1, 2], "buildgrid_kevin": [1, 2], "buildgrid_multisdf": [1, 2], "buildgrid_pyrai": [1, 2], "buildgrid_rai": [1, 2], "buildgrid_scanlin": [1, 2], "buildgrid_trimesh": [1, 2], "buildgrid_utsdf": [1, 2], "buildgridenviroonli": [1, 2], "buildingrprimit": [1, 2], "buildmesh": [1, 2, 3], "buildspher": [1, 2], "built": [0, 2, 14], "bullet_checkcollision_mp": [2, 3], "bump2vers": 10, "bumpvers": 11, "busi": 2, "byte": 2, "c": [2, 3, 6, 7, 11], "c0": 6, "c1": 6, "c4d": [2, 6, 7], "ca": 2, "cach": [2, 9], "calc_distance_between_surfac": 2, "calc_pairwise_dist": [1, 2], "calc_scaled_distances_for_posit": [1, 2], "calc_volum": [1, 2], "calcul": [0, 2, 3, 6, 14], "california": 2, "call": [2, 3, 6, 7, 8], "callbac": 6, "callback": [2, 6], "callfunct": [1, 2], "cam": [6, 7], "cam1": [6, 7], "cam_opt": [2, 6], "cambridg": 2, "came": 6, "camera": [6, 7], "cameratyp": [6, 7], "can": [0, 2, 3, 6, 7, 8, 10, 11, 12, 14], "cant": 6, "caract": 6, "card": 2, "carri": 2, "cartesian": [1, 2], "cartesian_to_sph": [1, 2], "carv": 2, "case": [0, 2, 6, 14], "caus": [2, 8], "cb": [2, 6], "cb_function": 2, "ccw": 2, "cd": [2, 10], "cellpack": [10, 12], "cellpack_data": [4, 7], "cellpack_database_1": [4, 7], "center": [2, 3, 4, 6, 7], "center_distance_dict": 2, "centerroot": 6, "centers1": 3, "centers2": 3, "cff": 2, "cgindex": 2, "chair": 2, "chair_out": 2, "chaltonsequence3": [1, 2], "chanc": 2, "chang": [2, 3, 6, 7, 10, 11], "changecolor": [2, 6, 7], "changecoloro": [6, 7], "changematerialproperti": [2, 6], "changeobjcolormat": [2, 6, 7], "channel": 8, "chapter": 2, "charact": [2, 8], "check": [0, 2, 3, 6, 8, 10, 14], "check_against_one_packed_ingr": [2, 3], "check_and_replace_refer": [1, 2], "check_circular": 8, "check_new_plac": [1, 2], "check_paired_kei": [1, 2], "check_rectangle_oustid": [1, 2], "check_required_attribut": [2, 5], "check_sphere_insid": [1, 2], "checkcollis": 3, "checkcreateempti": [1, 2], "checkcylcollis": [2, 3], "checkdist": [2, 3], "checkerrorinpath": [1, 2], "checkifupd": [2, 3], "checkingrpartnerproperti": [1, 2], "checkingrspher": [1, 2], "checkismesh": [2, 6], "checknam": [2, 6], "checkout": 10, "checkpath": [1, 2], "checkpointinsidebb": [1, 2], "checkrecipeavail": [1, 2], "checkrotformat": [1, 2], "child": 6, "children": [6, 7], "choic": 2, "chosen": 2, "christoph": 2, "chunk": [2, 3], "cid": 3, "ciff": 4, "cinema4d": [2, 6, 7], "circl": [2, 6], "circlespher": 2, "circular": [3, 8], "ckdtree": 2, "class": [3, 4, 5, 6, 8, 9], "classmethod": [2, 4, 6], "clean": [1, 2, 11, 13], "clean_argu": [1, 2], "clean_grid_cach": [1, 2, 5], "cleanup": 9, "cleanup_result": [1, 2], "cleanup_task": [1, 13], "clear": [1, 2, 6, 7], "clearal": [1, 2], "clearcach": [1, 2], "clearfil": [1, 2], "clearingr": [1, 2], "clearrbingredi": [1, 2], "clearrecip": [1, 2], "cli": 11, "clockwis": 3, "clone": [1, 2, 10, 12], "cloner": 6, "close": [0, 2, 3, 6, 7, 14], "close_indic": 3, "close_partner_check": [2, 3], "closepartn": [0, 14], "closest": [2, 6], "closest_ingredi": 2, "cloud": 2, "cmp": 2, "cmp_to_kei": [1, 2], "cmpt461": 2, "co": 6, "code": [2, 6, 9], "coffe": 2, "col": [2, 6, 7], "col1": 6, "col2": 6, "col3": 6, "colis": 2, "collada_xml": 6, "colladaexport": [1, 2], "collect": [2, 3], "collect_and_sort_data": [1, 2], "collect_docs_by_id": [1, 2], "collectresult": [1, 2], "collectresultperingredi": [1, 2], "collid": [0, 14], "collides_with_compart": [2, 3], "collinear": 6, "collis": [0, 3, 14], "collision_jitt": [2, 3], "collision_poss": 3, "collisiontre": 2, "color": [1, 2, 3, 7], "color_list": 6, "colorbydistancefrom": [1, 2], "colorbyord": [1, 2], "colormap": 6, "colormateri": [2, 6], "colorobject": [2, 6], "colorpt": [1, 2], "column": [2, 6], "com": [2, 4, 6, 7, 10, 11, 12], "combin": [2, 3], "combine_results_from_ingredi": [1, 2], "combine_results_from_se": [1, 2], "combined_pairwise_distance_dict": 2, "combinedaemeshdata": [2, 6], "come": 2, "command": [9, 12], "commen": 6, "commit": [10, 11], "common": 2, "comp": [2, 3], "comp_data": 2, "comp_dict": 2, "comp_id": [3, 9], "comp_or_obj": 2, "compact": 8, "compar": [2, 8], "compart": [0, 1, 3, 6, 7, 13, 14], "compartment_id": [2, 3], "compartment_id_for_nearest_grid_point": [1, 2], "compartment_kei": 2, "compartment_nam": 2, "compartmentlist": 1, "compdic": 2, "compid": 2, "compil": 2, "compile_db_recipe_data": [1, 2], "complet": [0, 2, 3, 14], "completemap": [1, 2], "completli": 2, "complex": [2, 3], "compliant": 8, "compmask": 3, "compon": [2, 6], "compose_matrix": 2, "composit": 2, "composition_dict": 2, "composition_id": 2, "compositiondoc": [1, 2], "comput": [2, 3, 6], "compute_volume_and_set_count": [1, 2], "computeexteriorvolum": [1, 2], "computegridnumberofpoint": [1, 2], "computevolum": [1, 2], "concaten": 2, "concatenate_image_data": [2, 8], "concatenate_matric": 2, "concatobjectmatrix": [2, 6, 7], "concentr": [0, 3, 14], "concept": [6, 7], "concert": 2, "conda": 11, "condit": 2, "config": [2, 9, 11], "config_load": [1, 2], "config_path": 9, "configload": [2, 5], "configur": [2, 11], "consequenti": 2, "consid": [0, 14], "consist": [3, 8], "constraint": 6, "constraintlookat": [2, 6], "constraintmarg": 3, "construct": 2, "constructor": [2, 8], "contact": 11, "contain": [2, 6, 8], "contains_point": [1, 2], "contains_points_mesh": [1, 2], "content": 13, "contigu": 2, "contr": 2, "contract": 2, "contributor": 2, "control": [2, 6], "control_point": 7, "convent": [2, 6], "conver": 6, "convers": [2, 6], "convert": [2, 5, 6, 7, 11], "convert_db_shortname_to_url": [1, 2], "convert_gradi": [2, 5], "convert_partn": [2, 5], "convert_positions_in_represent": [1, 2], "convert_represent": [1, 2], "convert_rotation_rang": [2, 5], "convertcolor": [2, 6], "convertpickletotext": [1, 2], "converttosimularium": [1, 9], "convolution_opt": 8, "convolv": 8, "convolve_channel": [2, 8], "convolve_imag": [2, 8], "coord": [3, 6, 7], "coord1": 6, "coord2": 6, "coordiant": 3, "coordin": [2, 6, 7], "copi": [2, 3, 6, 7, 12], "copyinggnugpl": 2, "copyright": [2, 6, 7], "corner": [0, 2, 3, 6, 7, 14], "cornerpoint": [3, 6, 7], "correct": [2, 6], "correctbb": [2, 3], "corrected_nam": 6, "correspond": [2, 6], "cosntraint": 6, "could": [2, 8], "count": [2, 3, 6], "count_opt": 3, "counter": 3, "cpython": 2, "cradiu": 7, "creat": [1, 3, 4, 6, 7, 8, 10, 11], "create3dpointlookup": [1, 2], "create_box_psf": [2, 8], "create_circular_mask": [2, 3], "create_compart": [1, 2], "create_divergent_color_map_with_scaled_valu": [2, 6], "create_file_info_object_from_full_path": [2, 5], "create_gaussian_psf": [2, 8], "create_grid_point_posit": [1, 2], "create_ingredi": [1, 2], "create_mesh": [1, 2], "create_object": [1, 2], "create_output_dir": [2, 5], "create_path": [1, 2], "create_presigned_url": [1, 2], "create_rbnod": [1, 2], "create_report": [1, 2], "create_spher": [1, 2], "create_sphere_data": [1, 2], "create_timestamp": [1, 2], "create_voxel": [1, 2, 3], "create_voxelized_mask": [1, 2], "createcolorsmat": [2, 6], "createingrmesh": [1, 2], "createmateri": [2, 6], "createorganelmesh": [1, 2], "createsnmesh": [2, 6], "createspr": [2, 6], "createsurfacepoint": [1, 2], "createtempl": [1, 2], "createtemplatecompart": [1, 2], "createtexturedmateri": [6, 7], "creation": [6, 7], "credenti": 11, "credit": 10, "crete": 6, "cron": 11, "cross": 2, "crowsandcat": 2, "cryst": 2, "csource2": 2, "ctree": 2, "cube": [2, 3, 4, 6, 7], "cube_surface_dist": [2, 3], "cubic": [2, 6, 7], "cumul": 6, "curl": 12, "curren": [6, 7], "current": [2, 6, 7, 8], "current_grid_dist": 3, "current_inst": 3, "current_object": 2, "current_packing_posit": 3, "currentpt": 3, "curret": 6, "curv": [6, 7], "custom": 8, "cutoff": [2, 3], "cutoff_boundari": 3, "cutoff_surfac": 3, "cw": 2, "cylind": [0, 2, 3, 6, 7, 14], "cylinderheadtail": [2, 6], "cytoplasm": [2, 3, 9], "d": [2, 3, 4], "dai": [8, 11], "damag": 2, "damp": 6, "dashboard": 11, "data": [2, 5, 6, 7, 8, 9], "data_d": 2, "data_in": 9, "data_sd": 2, "databas": [0, 2, 4, 6, 7, 9, 14], "database_id": [1, 2, 9], "database_nam": 2, "datadoc": [1, 2], "date": 11, "david": 2, "db": [2, 7], "db_choic": 2, "db_data": 2, "db_doc": 2, "db_handler": 2, "db_id": 9, "db_name": [1, 2], "db_recipe_data": 2, "dbmainten": [1, 2], "dbrecipehandl": [1, 13], "dbrecipeload": [1, 2], "dbupload": [1, 2], "dc": 2, "dcd": [1, 2], "dcdtrajectori": [1, 2], "dct": 2, "ddist": 6, "de": 2, "debug": [6, 7], "decay_length": [2, 4], "decid": 2, "declar": 2, "decod": 8, "decompos": [2, 6], "decompose4x4": [2, 6], "decompose_matrix": 2, "decompose_mesh": [1, 2], "decomposecolladageom": [6, 7], "decomposemesh": [2, 3, 6, 7], "decomposit": 6, "decreas": 2, "decres": 2, "deep_merg": [1, 2], "deepcopi": 2, "def": 8, "default": [0, 2, 3, 4, 5, 6, 8, 14], "default_db": 2, "default_geo_typ": [1, 9], "default_input_recip": [1, 9], "default_output_directori": [1, 9], "default_packing_result": [1, 9], "default_scale_factor": [1, 9], "default_valu": [1, 2, 5], "defaultfunct": [1, 2], "defin": [0, 2, 6, 9, 11, 14], "degre": 2, "deir": [6, 7], "dejavu": [2, 3, 6], "dejavutk": 7, "delet": [2, 6], "delete_doc": [1, 2], "deleteblist": [2, 3], "deletechildren": [2, 6], "deleteinst": [6, 7], "deletemeshedg": [2, 6], "deletemeshfac": [2, 6], "deletemeshvertic": [2, 6], "deleteobject": [6, 7], "delimit": 2, "delingr": [1, 2], "delingredi": [1, 2], "delingredientgrow": [1, 2], "delrb": [1, 2], "dens": 2, "dense_to_spars": [1, 2], "densiti": 3, "densityinmolar": 2, "depend": 11, "depnd": [6, 7], "deposit": 2, "deprec": [2, 6, 7], "deriv": [2, 6], "descend": [2, 3], "describ": [2, 6, 7], "descript": [4, 10], "design": 6, "desir": [6, 7], "destin": 2, "destinaon": 6, "detail": [2, 6, 7, 10], "detect": [0, 3, 14], "determin": [0, 2, 14], "dev": [2, 9, 10, 11], "develop": [0, 2, 10, 14], "diag": 2, "dic": 6, "dicgeom": 7, "dict": [2, 6, 8], "dictionari": [2, 3, 4, 6, 7, 8], "did": 2, "didnt": 6, "diebel": 2, "differ": [2, 6], "diffus": [6, 7], "dihedr": [2, 6], "dihedralgeometryerror": 6, "dilat": 2, "dim": 2, "dimens": [2, 6], "dimension": [2, 6], "direc": 6, "direct": [0, 2, 4, 6, 7, 14], "directli": [0, 11, 14], "directori": [2, 9], "diret": 3, "disclaim": 2, "discuss": 2, "displai": [0, 2, 6, 7, 14], "displaycompart": [1, 2], "displaycompartmentpoint": [1, 2], "displaycompartmentsingredi": [1, 2], "displaycompartmentspoint": [1, 2], "displaycytoplasmingredi": [1, 2], "displaydist": [1, 2], "displayenv": [1, 2], "displayfil": [1, 2], "displayfillbox": [1, 2], "displayfreepoint": [1, 2], "displayfreepointsasp": [1, 2], "displaygradi": [1, 2], "displayingrcylind": [1, 2], "displayingredi": [1, 2], "displayingrgrow": [1, 2], "displayingrmesh": [1, 2], "displayingrresult": [1, 2], "displayingrspher": [1, 2], "displayinstancesingredi": [1, 2], "displayleafoctre": [1, 2], "displayoctre": [1, 2], "displayoctreeleaf": [1, 2], "displayonenodeoctre": [1, 2], "displayparticlevolumedist": [1, 2], "displaypoint": [1, 2], "displayprefil": [1, 2], "displayroot": [1, 2], "displaysubnod": [1, 2], "dist": [2, 6, 7], "distanc": [0, 2, 3, 4, 6, 7, 14], "distance_check_fail": [1, 2], "distance_express": 3, "distance_funct": 3, "distancefunct": [2, 4], "distinct": 6, "distribut": [2, 3, 6, 7], "distribution_opt": [2, 3], "distributionopt": [2, 3], "distributiontyp": [2, 3], "disttoclosestsurf": 2, "distu": 6, "diverg": 6, "dmin": 2, "do": [0, 2, 3, 6, 7, 14], "doc": [2, 6, 7, 11], "doc_id": [1, 2], "doc_ref": 2, "doc_to_dict": [1, 2], "document": [2, 6, 7], "dodeca": 6, "dodecahedron": [2, 6], "doe": [0, 2, 6, 7, 14], "doesn": 2, "doesnt": [6, 7], "doloop": [1, 2], "domesh": 2, "don": [11, 12], "done": [2, 10], "dospher": 2, "dot": [1, 2, 6], "doubl": [2, 6], "down": [2, 6], "download": [2, 11, 12], "download_fil": [1, 2], "downloaded_data": 2, "downsampl": 2, "dpad": 3, "drastic": 6, "draw": [3, 6, 7], "drawgradientlin": [2, 6], "drawptcol": [2, 6], "drop": [0, 2, 3, 14], "dropbox": 9, "droponeingr": [1, 2], "droponeingrjson": [1, 2], "dropped_posit": 3, "dropped_rot": 3, "dspmesh": [1, 2], "dspsph": [1, 2], "dtype": [2, 6], "due": [2, 6], "duplic": 2, "duplifac": 6, "duplivert": [2, 6], "durat": 6, "dure": [3, 8], "dxf": 2, "dynam": 2, "dynamicsangulardamp": 6, "dynamicsbodi": 6, "dynamicslineardamp": 6, "e": [0, 2, 3, 6, 7, 10, 11, 14], "each": [0, 2, 3, 6, 7, 11, 14], "ed": 2, "edg": [0, 2, 3, 6, 7, 14], "edge_vertices_indic": 6, "edgeindc": 6, "edges_vertices_indic": 6, "edit": [2, 3, 6, 7, 10, 11], "editmod": 6, "editor": [6, 7], "edu": [2, 6], "eex": 2, "effect": 11, "effici": [0, 14], "egd": 6, "either": [2, 3, 6, 7, 12], "el": 6, "element": [2, 8], "elementari": 6, "elev": 6, "eli": [2, 3], "elimin": [3, 8], "els": [2, 6, 7, 8], "emanuel": 2, "emat": 6, "embed": 6, "emploi": 2, "empti": [2, 6, 7], "empty_child": [6, 7], "en": [6, 11], "encapsul": 2, "encapsulating_radiu": 2, "encod": [2, 8], "encourag": 11, "end": [2, 7], "endors": 2, "energi": [6, 7], "eng": 2, "enhanc": 2, "ensur": [8, 11], "ensure_ascii": 8, "enter": 11, "entir": [0, 2, 14], "entri": 9, "enum": [0, 4, 14], "enumer": [3, 4, 5], "env": [2, 3, 8, 11], "enviro": [0, 14], "environ": [1, 8, 10, 11, 13], "envum": 2, "epmv": [2, 6, 7], "epydoc": 2, "equal": 2, "error": 2, "esc": 6, "escap": 8, "essenti": 9, "establish": 4, "etc": [2, 6, 7], "eucledian": 6, "euclideanspac": 6, "euler": [2, 6], "euler_from_matrix": 2, "euler_matrix": 2, "eulertomatrix": [2, 6], "evalu": [0, 14], "even": [0, 2, 3, 6, 7, 11, 14], "event": 2, "everi": [2, 6, 10, 11], "everyth": 2, "ex": 10, "exact": 2, "exampl": [2, 6, 8, 9, 11], "except": [2, 8], "exclud": 2, "execut": [2, 6, 9], "exemplari": 2, "exist": [2, 11], "expand_dim": 6, "expand_object_using_kei": [1, 2], "expand_on": 2, "expect": [0, 2, 6, 14], "experi": 6, "expir": [2, 9], "exponenti": [2, 4], "export": [6, 8], "export_imag": [2, 8], "exportasindexedmesh": [1, 2], "exportcollada": [1, 2], "exportingredi": [1, 2], "exportrecipeingredi": [1, 2], "exporttobd_box": [1, 2], "exporttoreaddi": [1, 2], "exporttotem": [1, 2], "exporttotem_sim": [1, 2], "express": [2, 4], "ext": 2, "extend": 2, "extend_bounding_box_for_compart": [1, 2], "extendgridarrai": [1, 2], "exterior": 2, "extract": [2, 9], "extractmeshcompon": [1, 2], "extrem": [0, 2, 14], "f": [2, 6, 7], "f_dot_product": [1, 2], "f_ray_intersect_polyhedron": [1, 2], "face": [0, 2, 3, 6, 7, 14], "face_vertices_indic": 6, "faceindc": 6, "faceindex": 6, "faceindic": 6, "facemateri": [6, 7], "faces_vertices_indic": 6, "facesselect": [6, 7], "facilit": 2, "factor": 2, "fail": 3, "fals": [0, 2, 3, 4, 5, 6, 7, 8, 9, 14], "far_enough_from_surfac": [2, 3], "fast": [0, 2, 3, 14], "faster": [2, 3], "fbox_bb": 2, "featur": [6, 10], "field": [0, 2, 14], "figur": [2, 6], "figure_path": 2, "file": [0, 2, 3, 4, 6, 7, 8, 9, 10, 11, 14], "file_loc": 2, "file_nam": [2, 7], "file_path": [2, 7], "filenam": [2, 3, 6, 7, 8], "filepath": 6, "filespec": 2, "fill": [0, 2, 3, 14], "fill_in_empty_fiber_data": [1, 9], "fillbb": 2, "fillboxpseudocod": 2, "filltrianglecolor": [2, 6], "filter_surface_pts_to_fill_box": [1, 2], "final": 2, "find": [0, 2, 6, 14], "find_nearest": [1, 2], "findbranch": [1, 2], "findclosestpoint": [2, 6], "findpointscent": [1, 2], "findposit": [1, 2], "finishwithwat": [1, 2], "firebas": [2, 4, 9], "firebase_admin": 11, "firebasehandl": [1, 13], "first": [0, 2, 3, 6, 14], "fit": [2, 6, 7], "fit_view3d": [2, 6], "fix": 2, "fix_coord": 2, "fixnorm": [2, 6], "fixonepath": [1, 2], "fixpath": [1, 2], "flag": 2, "flex": 2, "float": [2, 3, 6, 7, 8], "float64": [2, 6], "flood": [0, 2, 14], "floodfil": [0, 14], "fluoresc": 2, "fn": 6, "fnorm": 6, "focal": [6, 7], "foce": 2, "folder": 2, "follow": [2, 3], "font": 6, "forc": [0, 2, 14], "force_random": 3, "foreach": 6, "forev": 2, "fork": 10, "form": [2, 3, 6], "format": [2, 5, 6, 7, 8], "format_color": [1, 2], "format_rgb_color": [6, 7], "format_vers": 5, "fortran": 3, "forward": 6, "forwhich": [6, 7], "found": [6, 10], "foundat": [2, 6, 7], "four": [2, 6], "fp": 2, "frame": [2, 6], "frameadvanc": [2, 6], "free": [0, 2, 3, 6, 7, 14], "free_point": [2, 3], "freepoint": 2, "fri": 1, "from": [0, 2, 3, 4, 6, 7, 9, 11, 14], "fromvec": [6, 7], "ftype": 2, "full": 11, "full_ingredient_nam": 4, "full_path": 5, "full_path_to_input_recipe_fil": 11, "full_path_to_packing_result": 11, "fulli": 2, "func": 2, "function": [0, 2, 3, 4, 6, 7, 8, 9, 14], "functon": 6, "futur": [6, 7], "g": [0, 2, 6, 7, 14], "ga": 2, "gain": 6, "gamma": 2, "gatherresult": [1, 2], "gauss": [2, 3], "gaussian": [2, 8], "gblob": [2, 4], "gem": 2, "gener": [2, 3, 6, 7, 11], "generalappli": [1, 2], "geom": [2, 6, 7], "geometri": [0, 2, 3, 6, 14], "geometrytool": [1, 13], "geomnam": [2, 3], "get": [0, 1, 2, 3, 6, 7, 8, 13, 14], "get_act": [2, 4], "get_active_data": [2, 4], "get_adjusted_posit": [2, 4], "get_al": [2, 4], "get_all_dist": [1, 2], "get_all_doc": [1, 2], "get_all_ingredi": [2, 5], "get_all_positions_to_check": [2, 3], "get_alternate_posit": [2, 3], "get_alternate_position_p": [2, 3], "get_and_store_v2_object": [2, 5], "get_angl": 2, "get_attributes_to_upd": [1, 2], "get_aws_object_kei": [1, 2], "get_bbox": [1, 2], "get_bounding_box": [1, 9], "get_bounding_box_limit": [1, 2], "get_cache_loc": [1, 2], "get_cent": [1, 2], "get_centroid": [1, 2], "get_closest_ingredi": [1, 2], "get_collada_materi": [1, 2], "get_collection_id_from_path": [1, 2], "get_combined_gradient_weight": [1, 2], "get_compart": [2, 3, 4], "get_compartment_object_by_nam": [1, 2], "get_cr": [1, 2], "get_cuttoff_valu": [2, 3], "get_deepest_level": [2, 4], "get_dev_cr": [1, 2], "get_display_data": [6, 7], "get_dist": [1, 2], "get_distance_distribut": 2, "get_distances_and_angl": [1, 2], "get_distances_from_point": [1, 2], "get_doc_by_id": [1, 2], "get_doc_by_nam": [1, 2], "get_doc_by_ref": [1, 2], "get_dpad": [1, 2], "get_encapsulating_radii": [2, 4], "get_eul": [1, 9], "get_euler_from_matrix": [1, 9], "get_euler_from_quat": [1, 9], "get_gauss_weight": [1, 2], "get_ingredi": [2, 4], "get_ingredient_angl": [1, 2], "get_ingredient_by_nam": [1, 2], "get_ingredient_data": [1, 9], "get_ingredient_display_data": [1, 9], "get_ingredient_key_from_object_or_comp_nam": [1, 2], "get_ingredient_radii": [1, 2], "get_ingredients_in_tre": [1, 2], "get_list_of_dim": [1, 2], "get_list_of_free_indic": [2, 3], "get_local_file_loc": [1, 2], "get_max_value_from_distribut": [1, 2], "get_mesh": [1, 2], "get_mesh_data": [1, 9], "get_mesh_filepath_and_extens": [1, 2], "get_mesh_format": [2, 4], "get_mesh_nam": [2, 4], "get_mesh_path": [2, 4], "get_midpoint": [1, 2], "get_min_max_radiu": [2, 4], "get_min_value_from_distribut": [1, 2], "get_minimum_expected_distance_from_recip": [1, 2], "get_module_vers": [1, 13], "get_new_distance_valu": [2, 3], "get_new_distances_and_inside_point": [2, 3], "get_new_jitter_location_and_rot": [2, 3], "get_new_po": [2, 3], "get_nois": [2, 6], "get_norm": [1, 2], "get_normal_for_point": [1, 2], "get_nspher": [1, 2], "get_number_of_ingredients_pack": [1, 2], "get_obj_dict": [1, 2], "get_object": [1, 2], "get_packed_minimum_dist": [1, 2], "get_paired_kei": [1, 2], "get_partn": [2, 3], "get_partner_by_ingr_nam": [2, 4], "get_partner_pair_dict": [1, 2], "get_path_from_ref": [1, 2], "get_pdb_path": [2, 4], "get_point": [2, 4], "get_posit": [2, 4], "get_positions_for_ingredi": [2, 4], "get_positions_per_ingredi": [1, 9], "get_radii": [2, 4], "get_radiu": [2, 3], "get_rb_model": [1, 2, 3], "get_rbnod": [2, 3], "get_recipe_metadata": [1, 9], "get_rectangle_cercle_area": [1, 2], "get_reference_data": [1, 2], "get_reference_in_obj": [1, 2], "get_reflected_point": [2, 3], "get_represent": [2, 5], "get_rot": [2, 3], "get_rotations_for_ingredi": [2, 4], "get_scaled_distances_between_surfac": [1, 2], "get_seed_list": [1, 2], "get_signed_dist": [2, 3], "get_size_of_bounding_box": [1, 2], "get_smallest_radiu": [1, 2], "get_staging_cr": [1, 2], "get_usernam": [1, 2], "get_valu": [1, 2], "get_value_from_distribut": [1, 2], "get_weights_by_dist": [2, 3], "geta": [2, 6], "getabsposuntilroot": [6, 7], "getact": [1, 2], "getallmateri": [2, 6, 7], "getallposrot": [1, 2], "getangleaxi": [2, 6], "getaxisrot": [2, 3], "getbiasedrot": [2, 3], "getbigbb": [2, 3], "getbinaryweight": [1, 2], "getboundari": [1, 2], "getboundingbox": [1, 2], "getboxs": [2, 6], "getcent": [1, 2, 6], "getchild": [6, 7], "getclosestfreegridpoint": [1, 2], "getclosestgridpoint": [1, 2], "getcolladamateri": [6, 7], "getcornerpointcub": [2, 6, 7], "getcurrentscen": [2, 6, 7], "getcurrentscenenam": [2, 6], "getcurrentselect": [2, 6, 7], "getdata": [2, 3], "getdiagon": [1, 2], "getdihedr": [2, 3], "getdist": [1, 2], "getencapsulatingradiu": [2, 3], "getfac": [2, 6, 7], "getfaceedg": [2, 6], "getfacenorm": [1, 2], "getfacenormalsarea": [2, 6], "getfacesfromv": [2, 6], "getfacesnfromv": [1, 2], "getfirstpoint": [2, 3], "getforwweight": [1, 2], "gethaltonuniqu": [1, 2], "gethclass": [2, 6], "gethelperclass": [2, 6], "getijk": [1, 2], "getimag": [2, 6], "getindex": [1, 2], "getindexdata": [1, 2], "getinfo": 3, "getingredientinstancepo": [1, 2], "getingredientsinbox": [2, 3], "getingrfromnameinrecip": [1, 2], "getinterpolatednorm": [1, 2], "getinterpolatedspher": [2, 3], "getjtransrot": [2, 3], "getjtransrot_r": [2, 3], "getlay": [2, 6], "getlinearweight": [1, 2], "getlistcompfrommask": [2, 3], "getmasterinst": [2, 6], "getmateri": [2, 6, 7], "getmaterialnam": [6, 7], "getmaterialobject": [6, 7], "getmaterialproperti": [2, 6], "getmaxjitt": [2, 3], "getmaxweight": [1, 2], "getmesh": [1, 2, 3, 6, 7], "getmeshedg": [2, 6, 7], "getmeshfac": [2, 6, 7], "getmeshnormal": [2, 6, 7], "getmeshvertic": [2, 6, 7], "getminmaxproteins": [1, 2], "getminweight": [1, 2], "getnam": [2, 6, 7], "getnbgridpoint": [1, 2], "getnextpoint": [2, 3], "getnextptindcyl": [2, 3], "getnorm": [6, 7], "getnormedvector": [2, 3], "getnormedvectoron": [2, 3], "getnormedvectoru": [2, 3], "getobjecnam": [6, 7], "getobject": [2, 6, 7], "getobjectnam": [2, 6, 7], "getold": [1, 2], "getoneingr": [1, 2], "getoneingrjson": [1, 2], "getord": [2, 6], "getparticl": [2, 6], "getparticulesposit": [2, 6], "getpointfrom3d": [1, 2], "getpointsincub": [1, 2], "getpointsincubefillbb": [1, 2], "getpointsinspher": [1, 2], "getpointtodrop": [1, 2], "getposat": [1, 2], "getpositionperidoc": [1, 2], "getposlin": [1, 2], "getposuntilroot": [2, 6], "getproperti": [2, 6], "getpropertyobject": [2, 6], "getradiu": [1, 2], "getramp": [2, 6], "getrndweight": [1, 2], "getrottransrb": [1, 2], "getscal": [1, 2, 6], "getsiz": [2, 6], "getsizexyz": [1, 2], "getsortedactiveingredi": [1, 2], "getstringvalueopt": [1, 2], "getsubweight": [1, 2, 3], "getsurfaceinnerpoint": [1, 2], "getsurfaceinnerpoints_kevin": [1, 2], "getsurfaceinnerpoints_sdf": [1, 2], "getsurfaceinnerpoints_sdf_interpol": [1, 2], "getsurfacepoint": [1, 2], "gettotalnbobject": [1, 2], "gettransform": [6, 7], "gettransl": [2, 6, 7], "gettubeproperti": [2, 6], "gettubepropertiesmatrix": [2, 6], "gettyp": [6, 7], "getuv": [2, 6], "getv3": [2, 3], "getvertexnorm": [1, 2], "getvis": [2, 6, 7], "getvnfromf": [1, 2], "gh": 10, "git": [10, 11, 12], "git_upi": [6, 7], "github": [2, 4, 9, 10, 11, 12], "githubusercont": [4, 7], "give": [2, 6, 7], "given": [2, 3, 6, 7, 10], "gj": [0, 14], "gl": [6, 7], "glmultmatrixd": 2, "glob_str": 2, "global": [2, 6, 7], "globalc": 2, "glowingpython": 2, "gnu": [2, 6, 7], "go": [2, 6], "gohlk": [2, 6], "goldman": 2, "good": 2, "googl": 11, "gov": 2, "gpl": [6, 7], "grab": [1, 2], "grabresult": [1, 2], "grad_dict": 2, "grad_nam": 2, "gradient": [1, 3, 4, 6, 13], "gradient_data": [1, 2], "gradient_list": 2, "gradient_list_to_dict": [1, 2], "gradient_nam": 4, "gradient_opt": 4, "gradientdata": [2, 4], "gradientdoc": [1, 2], "gradientmod": [2, 4], "graham": 2, "graph": 2, "graphic": [1, 13], "grd": 2, "grdaient": 2, "grdpo": 2, "greatest": 2, "greatli": 10, "grid": [0, 1, 3, 8, 13, 14], "grid_distance_valu": 3, "grid_file_nam": 2, "grid_file_path": 2, "grid_point_compartment_id": 7, "grid_point_dist": 3, "grid_point_index": [2, 3], "grid_point_loc": 3, "grid_point_posit": 7, "grid_pt_radiu": 7, "gridcent": 6, "gridfilenam": 2, "gridfileout": 2, "gridpoint": [1, 2], "gridpointscoord": 3, "gridspac": 2, "gridstep": 6, "gridvalu": 6, "grisiz": 6, "group": 3, "group_nam": 6, "grouptyp": 2, "grow": [0, 1, 2, 4, 14], "grow_plac": [2, 3], "growingredi": [2, 3], "guarante": 8, "guess": 6, "guid": [2, 11, 12], "h": 2, "ha": [0, 2, 3, 14], "hack": [2, 3], "halton": [1, 2], "halton2": [1, 2], "halton3": [1, 2], "halton_sequ": [1, 2], "haltongrid": [1, 2], "haltonsequ": [1, 2], "haltonterm": [1, 2], "ham": 3, "hand": [2, 6], "handl": [2, 6, 7, 10], "handle_expired_result": [1, 2], "handle_real_time_visu": [2, 3], "handler": [2, 4], "hartlei": 2, "has_mesh": [2, 3, 4], "has_pdb": [2, 3, 4], "have": [2, 6, 7, 12], "hclass": 6, "he": 6, "head": [6, 7, 11], "headcoord": 6, "header": 2, "height": 6, "help": [2, 10], "helper": [2, 3], "hemisph": 6, "here": [2, 3, 10], "hexa": 6, "hexahedron": [2, 6], "hexatil": [0, 14], "hextorgb": [2, 6], "hi": [2, 6, 7], "hide": [6, 7], "hideingrprimit": [1, 2], "hierarchi": [2, 6], "high": [0, 2, 3, 14], "hip": 2, "histo": 2, "histogram": [1, 2], "histovol": [2, 3], "histovolum": 2, "hold": 2, "holder": 2, "hollasch": 2, "hollow": [2, 8], "home": 6, "homogen": [2, 3], "hope": [2, 6, 7], "horn": 2, "host": [0, 2, 6, 7, 14], "hostap": 6, "hostapp": [2, 6, 7], "hostdo": 6, "hostedg": 6, "hostfac": [6, 7], "hosthelp": [1, 2], "hostmateri": [6, 7], "hostmatric": [6, 7], "hostmesh": [6, 7], "hostobj": [6, 7], "hostobjec": 3, "hostobject": [2, 6, 7], "hostscen": 6, "hosttyp": [6, 7], "how": [0, 3, 6, 10, 14], "howev": 2, "hr": 6, "htm": [2, 6], "html": [2, 6, 7, 10, 11], "http": [2, 3, 4, 6, 7, 11, 12], "hybrid": 2, "i": [0, 2, 3, 6, 7, 8, 9, 10, 11, 12, 14], "ico": 6, "icosahedron": [2, 6], "id": [0, 2, 3, 9, 14], "idarrai": 2, "ideal": 2, "ident": [2, 6], "identity_matrix": 2, "ie": [0, 2, 6, 7, 14], "ii": 2, "iii": 2, "ijk": 2, "ijktoindex": [1, 2], "ijktoxyz": [1, 2], "ik": [2, 6], "imag": [2, 6, 8], "image_data": [2, 3], "image_export_opt": 2, "image_s": [2, 3], "image_writ": 2, "imagewrit": [1, 2], "imdraw": 6, "img": 6, "implement": [2, 6, 8], "impli": [2, 6, 7], "import": [2, 6], "improv": 3, "inbox": [1, 2], "inc": [1, 2], "incident": 2, "includ": [0, 2, 10, 11, 14], "includeingredientrecip": [1, 2], "includeingrrecip": [1, 2], "incom": [3, 8], "incoming_nam": 7, "increas": 2, "increment": 6, "increment_stat": [6, 7], "increment_static_object": [6, 7], "increment_tim": [6, 7], "ind": 2, "indent": [2, 8], "independ": 2, "index": [2, 3, 4, 6, 9, 11], "indexedpolgonstotripoint": [2, 6], "indexedpolygon": [3, 6, 7], "indexpolygon": 6, "indic": [2, 6], "indicesinsid": 2, "indirect": 2, "individu": 4, "indpolfac": 6, "indpolvert": 6, "infin": 8, "infinit": [2, 8], "influenc": 2, "influencerad": 3, "info": [2, 3, 4], "inform": [2, 11], "ing": 2, "ingr": [2, 3, 8], "ingr1nam": 2, "ingr2nam": 2, "ingr_format": 8, "ingr_result": 2, "ingr_typ": 7, "ingrcompnum": 2, "ingrdic": 2, "ingred": 2, "ingredi": [1, 2, 7, 9], "ingredient_angle_dict": 2, "ingredient_compare0": [1, 2], "ingredient_compare1": [1, 2], "ingredient_compare2": [1, 2], "ingredient_data": [5, 9], "ingredient_info": 3, "ingredient_kei": [2, 5], "ingredient_key_dict": 2, "ingredient_nam": [2, 4, 9], "ingredient_occurence_dict": 2, "ingredient_posit": 2, "ingredient_position_dict": 2, "ingredient_radii": 2, "ingredient_typ": [1, 2], "ingredientinstancedrop": [2, 3], "ingrgroup": 2, "ingrid": [1, 2], "ingrjsonnod": [1, 2, 8], "ingrnam": 2, "ingrobj": 2, "ingrpythonnod": [1, 2], "inherit": [2, 6], "init_scene_with_object": [6, 7], "initi": [2, 9], "initialize_mesh": [2, 3], "initialize_shap": [1, 2], "inner": 2, "inner_grid_method": [2, 5], "inner_mesh": 2, "inner_mesh_nam": 2, "inod": 2, "input": [0, 2, 3, 6, 14], "input_dict": 2, "input_file_loc": 2, "input_file_path": 5, "insert": [2, 6, 8], "insertnod": [1, 2], "insid": [0, 2, 6, 14], "inside_point": 3, "insidepoint": 2, "inst": 9, "instal": [2, 10, 11], "instanc": [2, 4, 6, 7], "instance_id": [2, 7], "instance_nod": 6, "instance_sph": [6, 7], "instancepolygon": [6, 7], "instancescylind": [6, 7], "instancesspher": [6, 7], "instancestocollada": [2, 6], "instanci": 6, "instanti": 2, "instead": [0, 2, 6, 7, 14], "instruct": 11, "int": [2, 6, 7, 8], "intact": 2, "integ": [6, 8], "integr": 2, "intel": 2, "intens": [6, 7], "interest": [2, 3], "interfac": [2, 4], "interface_object": [1, 2], "interior": [2, 3], "intermedi": 6, "intern": 2, "interpol": [2, 6], "interpret": [2, 6, 7], "interrupt": 2, "intersect": 2, "interv": [2, 3], "inv": 2, "invalid": 6, "invert": [2, 4, 6], "invert_opt": 4, "invertopt": [2, 4], "involv": 2, "io": 11, "io_ingr": 2, "ioingredienttool": [1, 2, 8], "ioutil": [1, 13], "irvin": 2, "is_attractor": 3, "is_compart": 4, "is_db_dict": [1, 2], "is_fib": [6, 7], "is_firebase_obj": [1, 2], "is_full_url": [1, 2], "is_kei": [1, 2], "is_matrix": [1, 9], "is_memb": [2, 4], "is_nested_list": [1, 2], "is_obj": [1, 2], "is_partn": [2, 4], "is_point_in_correct_region": [2, 3], "is_point_inside_bb": [1, 2], "is_point_inside_mesh": [1, 2], "is_refer": [1, 2], "is_remote_path": [1, 2], "is_s3_url": [1, 2], "is_same_transform": [2, 6], "is_stat": 7, "is_two_d": [1, 2], "is_url_valid": [1, 2], "isindexedpolyon": [6, 7], "isn": [0, 3, 14], "isph1": [6, 7], "ispolyhedron": 2, "isspher": [2, 6], "item": [2, 4, 8], "item_separ": 8, "iter": [2, 8], "its": [2, 6], "itzhack": 2, "iv": 2, "ix": 2, "j": [2, 6, 7], "jame": 2, "jan": 2, "javascript": 8, "jitter": [0, 2, 3, 5, 14], "jitter_attempt": 3, "jitter_plac": [2, 3], "jitterposit": [2, 3], "jmp": 2, "johnson": 2, "join": [6, 7], "joinsobject": [2, 6], "jot": 2, "json": [0, 2, 8, 9, 11, 14], "jsonencod": 8, "jtran": 3, "jul": 1, "juli": 2, "jun": 2, "just": [2, 3, 11], "jwa3": 2, "jy": 2, "j\u00f6bstl": 2, "k": [2, 6, 7], "kabsch": 2, "karnei": 2, "kaufmann": 2, "keep": 2, "kei": [2, 6, 8, 11], "ken": 2, "kevin": [0, 2, 14], "key1": 2, "key2": 2, "key_from_pairwise_distance_dict": 2, "key_or_dict": 2, "key_separ": 8, "key_to_dict_map": [1, 2], "keyfram": 6, "keyword": [2, 6, 7], "known": [0, 2, 14], "knurbscurv": 7, "kw": [2, 3, 6, 7], "kwarg": [2, 3], "kwd": [2, 8], "kz": 2, "l": [2, 6, 7], "la": [0, 14], "lab": 2, "label": [2, 6, 7], "laboratori": 2, "lacunar": 6, "lai": 2, "larg": 2, "larger": [2, 3], "largest": [0, 2, 14], "last": 2, "later": [2, 6, 7], "latest": 11, "latitud": 6, "latter": 6, "launch": 11, "layer": 6, "ldsequenc": [1, 13], "leakag": [0, 2, 14], "leakproof": [0, 2, 14], "leas": 2, "leav": 2, "left": [0, 2, 3, 6, 7, 14], "left_hand": 9, "leftbound": 2, "lefthand": 2, "len": 2, "length": [3, 6, 7], "less": 2, "let": 8, "level": [0, 1, 3, 6, 8, 14], "lexic": 2, "lexsort": 2, "lfd": [2, 6], "liabil": 2, "liabl": 2, "librari": 2, "licens": [2, 6, 7, 11], "light": [6, 7], "light1": [6, 7], "light_opt": [2, 6], "like": [2, 8], "limit": 2, "linalg": [2, 6], "line": [2, 9], "linear": [2, 4, 6, 7], "link": 2, "linktraj": [1, 2], "lint": [10, 11], "linux": 6, "list": [2, 3, 6, 7, 8], "list_of_pt": 2, "list_valu": [2, 3], "liste_nod": 3, "liste_object": 6, "listeclosest": 3, "listeind": 6, "listenam": 6, "listeobj": 6, "listeobject": [6, 7], "listept": 6, "listeptcurv": 3, "listeptlinear": 3, "lister": 6, "listingredi": 2, "listobj": 7, "listorganel": 2, "listpt": 2, "littl": 10, "live_pack": 5, "load_asjson": [1, 2], "load_astxt": [1, 2], "load_fil": [1, 2], "load_from_grid_fil": 5, "load_json": [1, 2], "load_jsonstr": [1, 2], "load_mixedasjson": [1, 2], "load_object_from_pickl": [1, 2], "loader": [1, 2, 9], "loadfreepoint": [1, 2], "loadjson": [1, 2], "loadresult": [1, 2], "local": [2, 6, 7, 9, 10], "local_data": 2, "local_file_path": 2, "locat": [0, 2, 3, 6, 7, 14], "loevel": 6, "log": 2, "logic": 2, "long": 6, "longitud": 6, "look": [0, 2, 6, 14], "lookat": 6, "lookforneighbour": [2, 3], "lookup_dict": 2, "loop": 2, "loopthroughingr": [1, 2], "loss": 2, "lot": 2, "low": [0, 2, 3, 14], "lower": 3, "lowercirclefunct": [1, 2], "lowerrectanglefunct": [1, 2], "ludo": 2, "ludov": 2, "lue": 2, "m": [0, 2, 6, 7, 10, 14], "m0": 2, "m00": 6, "m01": 6, "m02": 6, "m1": 2, "m10": 6, "m11": 6, "m12": 6, "m2": 2, "m20": 6, "m21": 6, "m22": 6, "m2r": 10, "made": 2, "maerial": [6, 7], "mai": [2, 6], "main": [1, 2, 6, 9, 11, 12], "main_contain": 9, "mainli": 2, "maintain": 10, "mainten": 2, "major": [2, 3, 10], "make": [2, 6, 10, 11], "make_and_show_heatmap": [1, 2], "make_directory_if_need": [1, 2], "make_grid_heatmap": [1, 2], "makeingredi": [1, 2], "makeingredientfromjson": [1, 2], "makeingrmap": [1, 2], "makemarchingcub": [1, 2], "makenurbsphere1": 6, "maketextur": [2, 6], "manag": [2, 3], "mani": [0, 3, 14], "map": [2, 6], "map_color": [2, 6], "mar": 2, "march": 2, "marg": [2, 3, 6], "marge_diedr": 3, "marge_in": 3, "marge_out": 3, "markdown": 2, "marrai": 2, "mask": [0, 2, 3, 14], "mask_sphere_point": [2, 3], "mask_sphere_points_angl": [2, 3], "mask_sphere_points_boundari": [2, 3], "mask_sphere_points_dihedr": [2, 3], "mask_sphere_points_ingredi": [2, 3], "mask_sphere_points_vector": [2, 3], "mass": [2, 6], "massclamp": 6, "master": [2, 4, 7], "master_grid_posit": 2, "mat": [3, 6, 7], "mat1": 6, "mat2": 6, "mat_to_quat": 3, "match": 2, "matdic": 6, "mater": 6, "materi": [2, 6, 7], "math": [2, 6], "matnam": [6, 7], "matric": [2, 6, 7], "matrix": [2, 3, 6, 7], "matrixtofacesmesh": [2, 6], "matrixtovnmesh": [2, 6], "max": [2, 3, 4, 6], "max_jitt": 3, "max_radiu": 3, "max_valu": 6, "maxi": [2, 6], "maximum": [2, 6], "maxl": 2, "maxx": 2, "maxz": 2, "maya": [2, 6, 7], "mb": 2, "md": [2, 11], "mean": [2, 3], "meant": 2, "measur": [2, 6], "measure_dist": [2, 6], "meganriel": 9, "mehan": 9, "member": [2, 8], "memori": 2, "merchant": [2, 6, 7], "merg": [2, 6, 11], "merge_dct": 2, "merge_place_result": [2, 3], "mesh": [0, 2, 3, 4, 5, 6, 7, 14], "mesh_nam": 2, "mesh_stor": [2, 3], "meshfil": 3, "meshobject": 3, "meshspher": 7, "meshstor": [1, 13], "mesoscal": 2, "mesoscop": [4, 7, 11, 12], "messag": [6, 7], "mesur": 2, "met": 2, "meta_enum": [1, 2], "metab": 6, "metabal": [2, 6], "metadata": [2, 9], "metaenum": [2, 3, 4, 5], "meteri": 6, "method": [0, 2, 3, 6, 7, 8, 12, 14], "michel": 2, "midpoint": [2, 6], "might": 2, "migrate_ingredi": [2, 5], "migrate_v1_to_v2": [1, 2], "migrate_v2_to_v2_1": [1, 2], "min": [2, 3, 4, 6], "min_radiu": 2, "min_valu": 6, "mingr": 2, "mini": [2, 6], "minim": 6, "minimum": 2, "minor": [2, 10], "minx": 2, "minz": 2, "mira": 2, "miss": 2, "mit": 11, "mix": 2, "mod": 2, "mode": [2, 4, 6, 10, 11], "mode_nam": 4, "mode_set": 4, "mode_settings_dict": 4, "model": [2, 6], "model_typ": 3, "modeltyp": 3, "modeopt": [2, 4], "modif": [2, 6, 7], "modifi": [2, 6, 7], "modifierfor": [6, 7], "modul": [11, 13], "mol": 2, "molar": [2, 3], "molb": 2, "molbiol": 2, "molbtrajectori": [1, 2], "mole": 2, "molecul": [2, 6], "molecular": [2, 11], "mon": 2, "more": [2, 6, 7], "morgan": 2, "most": [6, 8, 11, 12], "mostafa": 2, "mostli": 2, "move": [0, 2, 3, 6, 7, 14], "move_object": [6, 7], "moverbnod": [1, 2], "msh": 2, "much": 3, "multi_bound": 3, "multi_cylind": [1, 2, 4], "multi_spher": [1, 2, 4], "multicylind": [0, 14], "multicylindersingr": [2, 3], "multipl": 2, "multisdf": 2, "multispher": [0, 3, 14], "multisphereingr": [2, 3], "must": [2, 3], "mutat": 2, "mx": 3, "mycmp": 2, "myspher": [6, 7], "myspinningspher": 6, "n": [2, 3, 6, 7, 11], "n_pick": 2, "na": 2, "name": [2, 3, 4, 5, 6, 7, 8], "namespac": 9, "nan": 8, "nasa": 6, "natur": 11, "navig": 11, "nbasi": 6, "nbfreepoint": [2, 3], "nbgridpoint": 2, "nbingredi": 2, "nbinstanc": 2, "nbr": 2, "ncbi": 2, "ndarrai": [2, 6, 8], "near_by_ingredi": 3, "nearbi": [0, 2, 14], "nearest": 2, "necessari": [0, 2, 6, 11, 14], "need": [2, 3, 6, 7], "neg": [0, 3, 6, 8, 14], "neglig": 2, "neighbor": [0, 14], "neither": 2, "nest": 2, "net": [2, 3], "never": [0, 14], "new": [2, 3, 6, 7, 10, 11], "new_dist": 2, "new_dist_point": 3, "new_inside_point": 3, "new_item_ref": 2, "new_object": 4, "new_point": 7, "new_posit": [2, 3], "new_result": 3, "newdistpoint": 2, "newempti": [2, 6, 7], "newinst": [2, 6, 7], "newli": 2, "newlin": 8, "newmesh": [2, 7], "newpath": 2, "newpo": 6, "newpt": 3, "next": 2, "ni": 7, "nih": 2, "nlm": 2, "nm_analysis_c_rapid": 9, "nm_analysis_figurea": [0, 14], "nm_analysis_figurea1": [0, 14], "nm_analysis_figureb1": 11, "nm_analysis_figurec1": 9, "node": [2, 7], "node1": 3, "node2": 3, "nodetogeom": [6, 7], "nodexml": 7, "non": [3, 6, 8], "none": [2, 3, 4, 5, 6, 7, 8, 9], "nonzero": 2, "nor": 2, "norga": 2, "norm": [1, 2, 6], "normal": [1, 2, 3, 6, 7], "normal_arrai": [1, 2, 6], "normalize_v3": [1, 2, 6], "normalize_vector": [1, 2], "normalizedprior": 2, "note": [2, 3, 6], "notic": 2, "novo": 2, "now": [2, 3, 10], "np": [2, 8], "np_array_of_pt": 2, "np_check_collis": [2, 3], "nr": 2, "ntype": 6, "null": [0, 6, 7, 14], "null1": [6, 7], "null2": [6, 7], "num": 2, "number": [0, 2, 3, 6, 14], "number_of_pack": 5, "number_of_point": 2, "numberingredientstopack": 2, "numer": 6, "numpi": [2, 6, 7, 8], "numpyarrayencod": [2, 8], "o": [2, 6, 7, 8, 11], "obj": [2, 4, 6, 7, 8], "obj1": 6, "obj2": 6, "obj_data": 2, "obj_dict": 2, "obj_id": 2, "obj_nam": 2, "objdata": 2, "objec": [6, 7], "object": [0, 2, 3, 5, 7, 8, 14], "object_data": [2, 5], "object_info": 2, "object_kei": [2, 5], "object_nam": [2, 3], "objectdoc": [1, 2], "objects_dict": 5, "objects_to_path_map": 2, "objectsselect": [2, 6, 7], "obtain": [6, 11], "ocata": 6, "occur": 2, "octahedron": [2, 6], "octav": 6, "octnod": [1, 2], "octre": [1, 13], "odd": 2, "off": [2, 6, 7], "off_grid_po": 2, "off_grid_surface_point": 2, "off_grid_surface_pt": 2, "offset": [1, 3, 6, 13], "ol": 12, "old_gradients_dict": 5, "old_ingredi": 5, "old_ingredient_data": 5, "old_recip": 5, "olson": 2, "omit": 3, "omni": [6, 7], "onam": [6, 7], "onc": [2, 3, 12], "one": [2, 3, 6, 7], "one_spher": 11, "onecolladageom": [6, 7], "onecylind": [6, 7], "onejitt": [2, 3], "onemetabal": [2, 6], "oneprevingredi": [1, 2], "ones": 2, "onli": [0, 2, 3, 6, 7, 8, 14], "opac": 2, "open": 2, "open_in_simularium": [6, 7], "open_results_in_brows": [5, 7], "opengl": [2, 3, 6], "openvdb": 2, "oper": [2, 9], "opposit": [0, 3, 14], "opt": 2, "optim": 2, "option": [2, 3, 4, 6, 7], "optionli": 6, "order": [0, 2, 3, 6, 7, 14], "ordered_pack": 5, "org": [2, 6, 7, 11], "orga": 2, "organ": 2, "organam": 2, "organel": [2, 3], "orgaresult": 2, "orient": [2, 3, 6], "orient_bias_rang": 3, "origin": [0, 2, 3, 10, 14], "ortho": 6, "orthogon": 2, "orthogonal": [6, 7], "otat": 2, "other": [0, 2, 10, 11, 14], "otherwis": [2, 8], "our": 2, "out": [2, 3, 5, 6, 8, 11], "out_base_fold": 5, "outer": 2, "outer_mesh": 2, "outer_mesh_nam": 2, "output": [2, 3, 5, 8], "output_image_loc": 2, "output_path": [2, 8, 9, 11], "outputsimularium": [1, 13], "outsid": [0, 2, 6, 14], "overal": [2, 3], "overrid": [0, 14], "overwrit": [0, 6, 7, 14], "overwrite_distance_funct": 3, "overwrite_place_method": 5, "overwriten": 6, "own": [6, 7], "owner": [2, 11], "p": [2, 6, 11], "p1": [2, 3, 6], "p2": [2, 3, 6], "pack": [0, 1, 2, 3, 4, 5, 13, 14], "pack_at_grid_pt_loc": [2, 3], "pack_grid": [1, 2], "pack_one_se": [1, 2], "packag": [0, 10, 11, 13, 14], "packed_object": [1, 2], "packed_posit": 3, "packed_rot": 3, "packedobject": [2, 4], "packignprior": 3, "packing_config_data": 2, "packing_loc": 3, "packing_mod": 3, "packing_opt": 8, "packing_result_path": 5, "packing_results_path": [2, 9], "packingradiu": [0, 14], "packingweight": [0, 14], "pad": 2, "pade": 2, "page": [6, 11], "pair": 2, "pairwis": 2, "pairwise_distance_dict": 2, "parallel": 5, "param": [2, 3, 6, 7, 9], "paramet": [0, 2, 6, 8, 14], "parent": [2, 6, 7], "parent_object": 6, "parentcent": [6, 7], "parentnod": 2, "parentxml": 7, "parentxmlnod": 7, "pariti": 2, "parrallelpip": 3, "pars": [1, 2, 6], "parse_one_mol": [1, 2], "parse_s3_uri": [1, 2], "part": [2, 3, 6, 7, 9], "particl": [2, 6], "particul": 6, "particular": [2, 6, 7], "partner": [0, 1, 2, 3, 14], "pass": [2, 3, 6, 7, 8, 10], "patch": 10, "path": [2, 5, 6, 7, 9], "pathdeform": [2, 6, 7], "paulbourk": 2, "pb": [6, 7], "pdb": [1, 3, 4, 13], "pdf": 2, "per": [0, 2, 3, 6, 7, 14], "perform": [0, 2, 9, 14], "period": [0, 2, 14], "permiss": 2, "permit": [2, 6], "persp": [2, 6, 7], "perspect": [2, 6, 7], "perturb_axis_amplitud": 3, "perturbaxi": [2, 3], "pervertex": [6, 7], "pervertic": 6, "pgridspac": 2, "phi": 6, "phong": 6, "php": 2, "physic": 6, "pi": [0, 6, 14], "pick": [0, 2, 4, 14], "pick_altern": [2, 3], "pick_mod": 4, "pick_partner_grid_index": [2, 3], "pick_point_for_ingredi": [1, 2], "pick_point_from_weight": [1, 2], "pick_random_altern": [2, 3], "pickalternatehalton": [2, 3], "pickhalton": [2, 3], "pickingredi": [1, 2], "pickl": 2, "pickle_file_object": 2, "pickmod": [2, 4], "pickpoint": [1, 2], "pickrandomspher": [2, 3], "pil": 6, "pip": [10, 11, 12], "piror": 2, "place": [0, 2, 3, 8, 14], "place_altern": [2, 3], "place_alternate_p": [2, 3], "place_method": [2, 3, 5], "place_object": [6, 7], "placed_partn": 3, "placer": 2, "plai": 6, "plane": [2, 6, 7], "platon": [2, 6], "pleas": 11, "plot": [1, 2, 6], "plot_distance_distribut": [1, 2], "plot_figur": 2, "plot_occurence_distribut": [1, 2], "plot_position_distribut": [1, 2], "plot_position_distribution_tot": [1, 2], "plotdata": [6, 7], "plotly_result": [1, 13], "plotlyanalysi": [1, 2], "plu": 3, "plug": 2, "ply": 2, "pmc": 2, "pmc3910158": 2, "png": 2, "po": [2, 3, 6, 7], "point": [0, 2, 3, 6, 7, 14], "point2": 6, "point_is_avail": [2, 3], "point_po": 2, "pointcloud": [2, 6], "pointcloudobject": [2, 6], "poli": [2, 3, 6, 7], "polygon": [2, 3, 6, 7], "polygone1": [6, 7], "polyhedr": 2, "polyhedron": [0, 2, 14], "polylin": [6, 7], "posit": [2, 3, 4, 6, 7], "position2": 3, "position_list": 2, "positions2": 3, "positions_to_adjust": 3, "possibl": [2, 10], "post_and_open_fil": [6, 7], "potenti": [0, 14], "pov": 2, "power": [2, 4], "pp": 2, "pquadranglepointlist": 2, "pquadranglepointposit": 2, "pr": 11, "prayendpo": 2, "praystartpo": 2, "pre": 11, "precis": 2, "precomput": 2, "prefer": 12, "prep_data_for_db": [1, 2], "prep_db_doc_for_download": [1, 2], "prep_molecules_for_sav": [1, 2], "prep_recipe_data": 2, "prepar": 2, "prepare_altern": [2, 3], "prepare_alternates_proba": [2, 3], "prepare_buildgrid_box": [1, 2], "preparedynam": [1, 2], "prepareingredi": [1, 2], "preparemast": [1, 2], "presign": 2, "press": [2, 6], "pretti": 8, "prevent": 8, "previous": 2, "previouspoint": 3, "prevpoint": 3, "prim": [0, 14], "primit": [0, 14], "princip": 3, "principal_vector": 3, "print": [2, 6, 7, 8], "printfillinfo": [1, 2], "printingredi": [1, 2], "printoneingr": [1, 2], "prior": 2, "priorit": [0, 14], "prioriti": [2, 3], "privat": 11, "probability_bind": 4, "probabl": 2, "process": [2, 12], "process_ingredients_in_recip": [1, 2], "process_one_ingredi": [1, 9], "procur": 2, "produc": [2, 6, 7], "product": [2, 6], "profit": 2, "progress": [2, 6, 7], "progressbar": [2, 6, 7], "project": [0, 2, 10, 11, 14], "projection_axi": 8, "promot": 2, "prompt": 11, "properti": [2, 3, 6], "protein": [0, 2, 14], "provid": [0, 2, 3, 6, 7, 14], "proxycol": 6, "proxyobject": [6, 7], "pseudo": 2, "psf": 8, "psf_paramet": 8, "pt": [2, 3, 6], "pt1": [2, 3, 6], "pt2": [2, 3, 6], "pt3d": 2, "pt_ind": 3, "pt_index": [3, 4], "pti": 2, "ptid": 3, "ptind": [2, 3], "ptruncatetoseg": 2, "ptsinspher": 3, "pub": 6, "public": [2, 6, 7, 12], "publicli": [0, 14], "publish": [2, 6, 7, 10], "pull": [10, 11], "purpos": [2, 6, 7], "push": [2, 10, 11], "put": [6, 7], "pv": 3, "px": [6, 7], "py": [2, 3, 6, 7, 11, 12], "pyembre": 2, "pypi": [10, 11], "pyrai": [0, 14], "python": [2, 3, 6, 7, 10, 11, 12], "pz": [6, 7], "q": 2, "quad": 6, "qualiti": [6, 7], "quaternion": [2, 8], "quaternion_about_axi": 2, "quaternion_matrix": [1, 2], "quaternion_multipli": 2, "quatut": 2, "queri": 2, "question": 2, "qx": 2, "qy": 2, "qz": 2, "r": [2, 3, 6, 7, 11], "r0": 6, "r1": 6, "rad": [2, 6], "radc": 3, "radial": [2, 4], "radian": [2, 3, 6], "radii": [2, 3, 7], "radiu": [0, 2, 3, 4, 6, 7, 14], "rai": [1, 13], "rais": [6, 8], "ramp": 2, "ramp_color1": 2, "ramp_color2": 2, "ramp_color3": 2, "rand": [2, 6], "random": [0, 1, 2, 3, 6, 14], "random_quaternion": [1, 2], "random_rotation_matrix": [1, 2], "random_vector": 2, "randomis": 6, "randomize_rot": [2, 3], "randomize_transl": [2, 3], "randomli": [0, 2, 14], "randomness_se": 5, "randompartn": [0, 14], "randomrot": [1, 13], "randpoint_onspher": [2, 6], "rang": [2, 6], "rare": 11, "rather": 2, "ratio": 3, "raw": [2, 4, 7, 10], "ray_intersect_polygon": [1, 2], "ray_intersect_polyhedron": [1, 2], "raycast": [0, 2, 6, 7, 14], "raycast_test": [6, 7], "raytrac": [0, 2, 5, 14], "rb": [2, 3], "rdf": 2, "rdic": 2, "re": [2, 6, 7, 10], "reach": [2, 6, 11], "read": [1, 2, 6, 10], "read_as_3d_arrai": [1, 2], "read_as_coord_arrai": [1, 2], "read_dict_from_glob_fil": [1, 2], "read_head": [1, 2], "read_json_fil": [2, 5], "read_mesh_fil": [1, 2], "read_text_fil": [1, 2], "readarraysfromfil": [1, 2], "readgridfromfil": [1, 2], "readi": [2, 10], "readm": 2, "readme_url": [1, 2], "readmeshfromfil": [2, 6], "realtim": [0, 14], "reativ": 2, "rebuild": 2, "recal": [0, 14], "recalc_norm": [2, 6], "recalcul": 6, "receiv": [2, 6, 7], "recent": [6, 12], "reciev": 2, "recip": [1, 3, 4, 8, 9, 11, 13], "recipe_data": [2, 9], "recipe_data_2_0": 5, "recipe_dictionari": 2, "recipe_load": [1, 2], "recipe_meta_data": 2, "recipe_nam": [5, 7], "recipe_path": 9, "recipe_to_sav": 2, "recipefil": 2, "recipeload": [2, 5], "recipesfil": 2, "recommend": [2, 10, 11], "recov": 2, "recreat": 2, "rect": 2, "rectangl": [1, 2, 6], "rectilinear": 6, "recurs": [2, 6, 8], "recursionerror": 8, "red": 6, "redistribut": [2, 6, 7], "redund": [6, 7], "redwhiteblueramp": [2, 6], "refer": [2, 6, 7, 8], "referenc": 2, "references_to_upd": 2, "referring_comp_id": 2, "reflect": 2, "reg": [1, 2, 4], "regent": 2, "region": 2, "region_1": [1, 2], "region_1_2_theta": [1, 2], "region_2": [1, 2], "region_2_integrand": [1, 2], "region_3": [1, 2], "region_3_integrand": [1, 2], "region_list": 5, "region_nam": 2, "regress": 8, "reject": [0, 2, 3, 14], "rejection_threshold": 3, "rejectioncount": 3, "rel": 3, "relat": [2, 11], "releas": [10, 11], "remain": 2, "remind": 10, "remov": [2, 6, 7], "remove_comp_nam": 2, "remove_from_realtime_displai": [2, 3], "remove_item": 2, "remove_nan": [6, 7], "removefreepoint": [1, 2], "removelast": 3, "removeonepoint": [1, 2], "renam": 6, "render": [2, 6, 7], "rendermod": [6, 7], "renedr": [6, 7], "reorder": 2, "reorder_free_point": [1, 2], "rep": 2, "repar": [2, 6, 7], "repetit": 2, "replac": 2, "replaceingrmesh": [1, 2], "repo": [6, 10, 12], "report": 2, "report_md": 2, "report_output_path": 2, "reporthook": [2, 6], "reportprogress": [1, 2], "repositori": [11, 12], "repres": [2, 3], "represent": [1, 2, 3, 5, 8], "reproduc": 2, "request": [6, 7, 10, 11], "requir": [0, 1, 3, 11, 14], "requisit": 11, "rerieveaxi": [2, 6], "res_filenam": 2, "reserv": 2, "reset": [1, 2, 3, 6, 7], "resetdefault": [1, 2], "resetingr": [1, 2], "resetingrrecip": [1, 2], "resetlastpoint": [2, 3], "resetprogressbar": [2, 6, 7], "resetspheredistribut": [2, 3], "resettransform": [2, 6], "resolut": [1, 2, 6], "resolution_dictionari": 3, "resolv": [2, 10], "resolve_composit": [1, 2], "resolve_db_region": [1, 2], "resolve_gradient_data_object": [1, 2], "resolve_inherit": [2, 5], "resolve_local_region": [1, 2], "resolve_object_data": [1, 2], "respect": [2, 6], "restor": [1, 2, 6], "restore_grid": 2, "restore_grids_from_pickl": [1, 2], "restore_molecules_arrai": [1, 2], "restoreeditmod": [2, 6], "restorefreepoint": [1, 2], "restoregridfromfil": [1, 2], "restructur": 2, "result": [0, 2, 3, 6, 7, 8, 9, 14], "resultdoc": [1, 2], "resultfilenam": 2, "results_data_in": [5, 9], "results_seed_0": 9, "retain": 2, "retriev": [2, 6, 7], "retrievecolormat": [2, 6], "retrievehost": [2, 6], "return": [0, 2, 3, 6, 7, 8, 9, 14], "return_int": 2, "return_object_valu": [2, 8], "revers": [4, 6, 7], "revis": 2, "rg": 3, "rgb": [6, 7], "rho": 2, "ri": 2, "rid": 2, "right": [0, 2, 6, 7, 14], "rightbound": 2, "rightmost": 2, "rigid": [2, 6, 7], "rigid_plac": [2, 3], "rlength": 6, "rnd": [2, 4], "roll": 6, "ronald": 2, "root": [2, 6], "rot": [2, 3, 6, 7], "rot_mat": 3, "rotat": [2, 3, 4, 6, 7], "rotate_about_axi": [2, 6], "rotateobj": [2, 6, 7], "rotatepoint": [2, 6], "rotatio_i": [6, 7], "rotation_axi": 3, "rotation_matrix": [2, 3, 6], "rotation_rang": 3, "rotation_x": [6, 7], "rotation_z": [6, 7], "rotax": [2, 3], "rotmassclamp": 6, "rotmat": [2, 3], "rotmatj": 3, "rotvecttovect": [2, 3, 6], "rotx": 2, "rotz": 2, "row": [2, 6], "rq": 2, "rsz": 6, "rtype": [2, 3, 6, 7], "ru": 2, "rule": 2, "run": [2, 3, 6, 9, 10, 12], "run_": 2, "run_analysis_workflow": [1, 2], "run_cleanup": [1, 9], "run_distance_analysi": [1, 2], "run_partner_analysi": [1, 2], "runbullet": [1, 2], "runtim": [2, 3], "runtimedisplai": 2, "rx": 2, "rxyz": 2, "ry": 2, "ryxi": 2, "rz": [2, 6], "s3": 2, "s3_uri": 2, "safeguard": [0, 2, 14], "sagenb": 6, "said": 2, "same": [2, 3], "sampl": 2, "sane": 2, "sanner": 2, "saturdai": 1, "save": [0, 1, 2, 8, 14], "save_analyze_result": 5, "save_as_simularium": [2, 8], "save_aspython": [1, 2], "save_converted_recip": 5, "save_file_and_get_url": [1, 2], "save_gradient_data_as_imag": [2, 5], "save_grid_log": 2, "save_grids_to_pickl": [1, 2], "save_mixed_asjson": [2, 8], "save_png": 2, "save_result": [1, 2], "save_result_as_fil": 2, "savedejavumesh": [2, 6], "savegridlogsasjson": [1, 2], "savegridtofil": [1, 2], "saveobjmesh": [2, 6], "saverecipeavail": [1, 2], "saverecipeavailablejson": [1, 2], "saveresultbinari": [1, 2], "saveresultbinaryd": [1, 2], "saw": 3, "sc": [6, 7], "scalar": [2, 6], "scale": [2, 6, 7], "scale_between_0_and_1": [1, 2], "scale_distance_between": [2, 4], "scale_matrix": 2, "scaleobj": [2, 6, 7], "scan": 6, "scanlin": [0, 2, 5, 14], "scene": [6, 7, 8], "schedul": 9, "schemat": 2, "scheme": 2, "scientif": 6, "scn": 6, "scname": 6, "scompart": [1, 2], "script": [2, 6, 9], "sdf": [0, 14], "sdk": 11, "search": [2, 3, 11], "search_nam": 2, "search_tre": 3, "second": [2, 6], "secondpoint": 3, "section": [2, 11], "see": [2, 6, 7, 11], "seed": [2, 3], "seed_basenam": 2, "seed_index": 2, "seed_list": 2, "seed_numb": 2, "seed_to_results_map": 8, "seednum": 2, "segment": 2, "sel": 2, "selecion": [6, 7], "select": [0, 2, 6, 7, 11, 14], "selectedg": [2, 6], "selectfac": [2, 6], "selectvertic": [2, 6], "self": [2, 3, 8], "sensibl": 8, "separ": [2, 8, 11], "sept": 2, "septemb": 1, "sequenc": [2, 3], "sequenti": 6, "serial": 8, "serializ": [1, 8, 13], "serializedfromresult": [1, 2], "serializedrecip": [1, 2], "serializedrecipe_group": [1, 2], "serializedrecipe_group_d": [1, 2], "servic": [2, 11], "set": [0, 2, 3, 6, 7, 10, 11, 14], "set_act": [2, 4], "set_doc": [1, 2], "set_gradi": [1, 2], "set_ingredi": [2, 4], "set_ingredient_color": [1, 2], "set_mode_properti": [2, 4], "set_object_stat": [6, 7], "set_partners_ingredi": [1, 2], "set_recipe_ingredi": [1, 2], "set_result_file_nam": [1, 2], "set_sphere_posit": [2, 4], "set_stat": [6, 7], "set_surface_dist": [1, 2], "set_surfptsbht": [1, 2], "set_surfptscht": [1, 2], "set_weights_by_mod": [1, 2], "setcount": [1, 2], "setcurrentselect": [2, 6], "setexteriorrecip": [1, 2], "setfram": [2, 6], "setgeomfac": [1, 2], "sethistovol": [1, 2], "setinnerrecip": [1, 2], "setinst": [6, 7], "setkeyfram": [2, 6], "setlay": [2, 6], "setmesh": [1, 2], "setmeshedg": [2, 6], "setmeshfac": [2, 6], "setmeshvertic": [2, 6], "setnam": [2, 6], "setnumb": [1, 2], "setobjectmatrix": [2, 6, 7], "setparticulesposit": [2, 6], "setproperti": [2, 6], "setpropertyobject": [2, 6], "setrbopt": [1, 2], "setrigidbodi": [2, 6, 7], "setse": [1, 2], "setsoftbodi": [2, 6], "setspringopt": [1, 2], "setsurfacerecip": [1, 2], "settil": [2, 3], "settransform": [2, 6], "settransl": [2, 6, 7], "setup": [0, 1, 2, 8, 12, 14], "setupboundaryperiod": [1, 2], "setupfil": 2, "setupfromjsond": [1, 2], "setupoctre": [1, 2], "setuprbopt": [1, 2], "setuv": [2, 6], "setvaluetojsonnod": [2, 8], "setvaluetopythonstr": [1, 2], "setview": [6, 7], "setviewport": [2, 6], "sfu": 2, "shadow": [6, 7], "shall": 2, "shallow_match": [1, 2], "shape": [2, 3, 6], "share": 2, "sharealik": 2, "shear": 2, "shear_matrix": 2, "shoemak": 2, "short": [2, 10], "shoud": 6, "should": [2, 3, 6, 7, 8, 11], "should_writ": [1, 2], "show": [1, 2], "show_grid": 2, "show_grid_plot": 5, "show_plotly_plot": 2, "show_progress_bar": 5, "show_sphere_tre": [5, 7], "showhid": [1, 2], "showingrprimit": [1, 2], "shown": 2, "side": [0, 3, 11, 14], "side_length": 2, "sigma": 8, "sign": [0, 2, 6, 14], "signed_distance_to_surfac": 3, "similar": 2, "simpl": [0, 2, 14], "simpleplot": [1, 2], "simpli": [0, 2, 6, 8, 14], "simularium": [2, 5, 6, 8, 11], "simularium_convert": [1, 13], "simularium_help": [2, 6], "simulariumhelp": [6, 7], "simulationtim": 2, "sin": 6, "sinc": [2, 3], "singl": [0, 3, 14], "single_cub": [1, 2, 4], "single_cylind": [1, 2, 4], "single_spher": [1, 2, 4], "singlecub": [0, 14], "singlecubeingr": [2, 3], "singlecylinderingr": [2, 3], "singlespher": [0, 14], "singlesphereingr": [2, 3], "singredi": [1, 2], "singredientfib": [1, 2], "singredientgroup": [1, 2], "size": [2, 3, 6, 7, 8], "size_opt": 3, "sizei": 6, "sizex": 6, "skip": [2, 3, 8], "skipkei": 8, "slow": [0, 14], "slow_box_fil": [1, 2], "small": 11, "smallest": [0, 2, 14], "smooth": [6, 7], "so": [2, 3, 6, 11], "soc": 2, "soft": [6, 7], "softwar": [2, 6, 7], "solid": 6, "solut": 2, "some": [2, 6], "sort": [1, 2, 3, 8], "sort_kei": 8, "sort_valu": [6, 7], "sortingredi": [1, 2], "sourc": [1, 2, 3, 4, 5, 6, 7, 8, 9], "space": [2, 3, 5], "spars": 2, "sparse_to_dens": [1, 2], "spec": 2, "special": [2, 6, 7], "specif": [2, 6, 8], "specifi": [2, 3, 6, 7, 8, 9], "specifii": 6, "specular": 6, "speed": 2, "speedup": 2, "spencer": 2, "sph": [6, 7], "sph1": [6, 7], "sphee": 2, "sphere": [0, 2, 3, 4, 6, 7, 14], "sphere_mesh": 6, "sphere_obj": 6, "sphere_radius_100": [0, 14], "spherehalton": [1, 2], "spheres_sst": [2, 5], "spheres_sst_plac": [2, 3], "spheressst": [0, 5, 14], "spheretre": [0, 14], "spheric": [2, 6], "spline": [0, 2, 6, 7, 14], "split_ingredient_data": [2, 5], "spot": [6, 7], "sprin": 6, "spring": [2, 6], "sqrt": 6, "squar": [2, 4], "squaretil": [0, 14], "squash": 11, "srfpt": 2, "stabl": [2, 11], "stackoverflow": 2, "stage": 11, "stamp": 2, "standard": 6, "stare": 3, "start": [3, 6, 7], "starting_po": 3, "starting_rot": 3, "startingpoint": 3, "state": [2, 3, 6, 7], "static": [2, 3, 5, 7, 8, 9], "static_id": [1, 2, 3], "statu": [6, 7], "std": [2, 3], "step": [2, 6, 11], "stepbystep": 3, "stepsiz": 3, "steve": 2, "stif": 6, "still": 11, "stop": [2, 6], "storag": [2, 7], "store": [1, 2], "store_asjson": [1, 2], "store_metadata": [6, 7], "store_packed_object": [1, 2, 3], "store_result_fil": [6, 7], "str": [2, 4, 6, 8, 9], "strict": 2, "string": [0, 2, 3, 6, 7, 9, 14], "string_or_dict": 2, "strng": 6, "structur": [2, 4], "style": [2, 3], "sub": [2, 4], "sub_dir": 5, "sub_folder_nam": 2, "sub_point": 7, "subclass": 8, "subdivis": [6, 7], "submit": 10, "submodul": [1, 13], "subpackag": 13, "substitut": 2, "success": [2, 3], "suitabl": 2, "sum": [2, 6], "sun": [2, 6, 7], "super": [0, 2, 14], "superfin": [0, 2, 14], "superimpos": 2, "support": [2, 6, 7, 8], "sure": [2, 10], "surfac": [0, 2, 3, 4, 14], "surfacepoint": 2, "surfacepointsnorm": 2, "surfanc": 3, "surfptsbbnorm": 2, "surpris": 6, "surround": 2, "swap": [2, 3], "sxyz": 2, "system": [2, 6], "t": [0, 2, 3, 6, 7, 8, 11, 12, 14], "tag": [10, 11], "tail": [6, 7], "tailcoord": 6, "take": [0, 2, 3, 4, 6, 7, 8, 14], "tan": 2, "tarbal": 12, "target": [2, 3, 6], "target_grid_point_posit": 3, "target_point": 3, "targeta": 6, "targeted_master_grid_point": 3, "task": [2, 9], "tatic": 2, "tau": 3, "te": 2, "team": 11, "techniqu": [2, 3], "temporari": [2, 3], "term": [2, 6, 7], "termin": [2, 12], "terminologi": 2, "test": [0, 2, 3, 5, 8, 10, 11, 14], "test_partner_pack": 5, "test_points_in_bb": [1, 2], "testforescap": [2, 6], "testwhen": 3, "tetha": 6, "tetra": 6, "tetrahedron": [2, 6], "text": [2, 6], "textu": [6, 7], "textur": [6, 7], "texturefacecoordintestovertexcoordin": [6, 7], "than": 2, "thegreenplac": [2, 3], "thei": [0, 2, 6, 10, 14], "them": [2, 3], "theori": 2, "therefor": [2, 6], "theses": 2, "thesi": 2, "theta": [2, 6], "thi": [0, 2, 3, 6, 7, 8, 9, 10, 11, 12, 14], "thin": 2, "third": [2, 6], "thoma": 2, "though": [2, 6], "thread": [6, 7], "three": [2, 6], "threecolorramp": [2, 6], "threshold": 3, "thresholdprior": 2, "through": [2, 6, 10, 12], "thu": 2, "ti": [2, 7], "tiff": [8, 10], "time": [0, 2, 3, 7, 14], "time_point": 7, "time_step_index": 9, "timefunct": [1, 2], "titl": [2, 7], "title_str": 2, "to_json": [1, 2], "tobinari": [1, 2], "todo": [2, 3], "toggl": [2, 6, 7], "toggledisplai": [2, 6, 7], "toggleeditmod": [2, 6], "toggleorganelmatr": [1, 2], "toggleorganelmesh": [1, 2], "toggleorganelsurf": [1, 2], "togglexrai": [2, 6], "toint": 6, "tomat": [2, 6], "too": 3, "tool": 2, "top": [1, 2, 3, 6], "toreplac": 2, "torsion": 6, "tort": 2, "total": [2, 3], "total_step": 9, "totals": 6, "touching_radiu": 2, "tovec": [2, 6, 7], "tox": 11, "tr": 6, "trace": [6, 7], "tragetb": 6, "traj_typ": [1, 2], "trajectori": [1, 13], "tran": [2, 3, 6], "transform": [1, 3, 6, 7, 13], "transformatio": 6, "transformmesh": [1, 2], "transformnod": [6, 7], "transformpoint": [2, 3], "transformpoints2d": [1, 2], "transformpoints_mult": [2, 3], "translat": [2, 3, 6, 7], "translateobj": [2, 6, 7], "translation_matrix": 2, "transpos": [2, 3, 6, 8], "transpose_image_for_project": [2, 8], "transposematrix": [2, 6], "tree": [0, 2, 3, 4, 14], "tri": [2, 3, 7], "triangl": [2, 6], "triangletil": [0, 14], "triangul": [2, 6], "triangulatefac": [2, 6], "triangulatefacearrai": [2, 6], "trimesh": [0, 2, 5, 14], "tripl": 2, "true": [0, 2, 3, 5, 6, 7, 8, 14], "try": [2, 8], "tsri": [6, 7], "tube": 6, "tue": 2, "tupe": 6, "tupl": [2, 6, 8], "tuppl": 6, "turn": [2, 3, 6], "tutori": 11, "twice": [2, 3], "two": [0, 2, 3, 6, 14], "two_d": 2, "twocolorramp": [2, 6], "type": [2, 3, 6, 7, 8], "typeerror": 8, "typesel": [6, 7], "u": [2, 6], "u_length": 3, "uci": [2, 6], "ug": 2, "ui": [6, 7], "ulength": 3, "unallow": [0, 14], "under": [2, 6, 7], "undirect": 6, "undspmesh": [1, 2], "undspsph": [1, 2], "uniform": [2, 3, 6], "uniformli": [2, 3], "uniq": [2, 7], "uniqu": [0, 6, 14], "unique_id": 7, "unit": [2, 3], "unit_length": 3, "unit_vector": [2, 6], "univers": 2, "unless": 2, "unlinktraj": [1, 2], "unpack_curv": [1, 9], "unpack_posit": [1, 9], "until": 6, "untitl": 6, "unus": 2, "up": [2, 6, 10, 11], "updat": [0, 2, 3, 6, 7, 14], "update_after_plac": [1, 2], "update_data_tre": [2, 3], "update_display_rt": [2, 3], "update_distance_distribution_dictionari": [1, 2], "update_doc": [1, 2], "update_elements_in_arrai": [1, 2], "update_in_arrai": 2, "update_ingredient_s": [2, 3], "update_instance_positions_and_rot": [6, 7], "update_largest_smallest_s": [1, 2], "update_or_cr": [1, 2], "update_pairwise_dist": [1, 2], "update_partn": 2, "update_refer": [1, 2], "update_reference_on_doc": [1, 2], "update_splin": [2, 6, 7], "update_titl": [1, 2], "update_variable_ingredient_attribut": [1, 2], "updateappli": [6, 7], "updatearmatur": [2, 6], "updatebox": [2, 6, 7], "updatedist": [1, 2], "updatefrombb": [2, 3], "updategrid": [2, 3], "updatemasterinst": [2, 6, 7], "updatemesh": [6, 7], "updateparticl": [2, 6], "updatepath": [1, 2], "updatepathdeform": [2, 6, 7], "updatepathjson": [1, 2], "updatepoli": [6, 7], "updatepositionsradii": [1, 2, 8], "updaterecipavailablexml": [1, 2], "updatereplacepath": [1, 2], "updatespr": [2, 6], "updatetre": 2, "updatetubemesh": [6, 7], "updatetubeobj": [2, 6], "upi": [1, 2], "upload": [1, 2, 13], "upload_collect": [1, 2], "upload_composit": [1, 2], "upload_data": [1, 2], "upload_doc": [1, 2], "upload_fil": [1, 2], "upload_gradi": [1, 2], "upload_object": [1, 2], "upload_recip": [1, 2], "upload_result": 5, "upload_result_metadata": [1, 2], "upload_single_object": [1, 2], "upper": [3, 6, 7], "uppercirclefunct": [1, 2], "upperrectanglefunct": [1, 2], "upward": 6, "url": [2, 7], "url_exist": [1, 2], "us": [0, 2, 3, 6, 7, 8, 9, 11, 14], "usag": 2, "use_mesh": [2, 3], "use_orient_bia": 3, "use_par": [6, 7], "use_pdb": [2, 3], "use_period": 5, "use_quaternion": 2, "use_rbspher": 3, "use_rotation_axi": 3, "usecylind": 3, "usefix": 2, "useful": 2, "usehalton": 3, "uselength": 3, "usemateri": 6, "usemtl": 2, "useobjectcolor": 6, "usepp": 3, "user": [9, 11], "usexref": [2, 8], "usual": [0, 2, 14], "usus": [6, 7], "ut": [0, 2, 14], "utf": 2, "util": [1, 13], "uv": [2, 6], "v": [2, 3, 6, 7], "v0": [2, 6], "v1": [2, 3, 6, 9, 11], "v1_v2_attribute_chang": [1, 2], "v2": [2, 3, 6, 11], "v3": [3, 6], "v4": 6, "val_dict": 2, "vale": 6, "valid": [2, 3, 6], "validate_distribution_opt": [2, 3], "validate_exist": [1, 2], "validate_gradient_data": [2, 4], "validate_ingredient_info": [2, 3], "validate_input_recipe_path": [1, 2], "validate_invert_set": [2, 4], "validate_mode_set": [2, 4], "validate_weight_mode_set": [2, 4], "valu": [0, 2, 3, 4, 5, 6, 7, 8, 14], "valueerror": 8, "van": 2, "variabl": [2, 6], "variou": [2, 11], "vcross": [1, 2, 6], "vdebug": 2, "vdiff": [1, 2, 6], "vdistanc": [2, 6], "vec": [2, 6], "vec1": 6, "vec2": 6, "vec4": 6, "vecor": [2, 6], "vect1": [3, 6], "vect2": [3, 6], "vector": [2, 3, 4, 6, 7], "vector1": 2, "vector2": 2, "vector_a_to_b": 6, "vector_norm": [2, 6], "vector_product": 2, "verbos": [2, 6, 7], "veri": [2, 11], "verifi": 6, "versa": 6, "version": [2, 5, 6, 7, 8, 10], "vert": [2, 3, 6], "vert_list": 2, "vertex": [2, 6, 7], "vertex_indic": 6, "vertex_point": 2, "vertexindex": 6, "vertic": [2, 6, 7], "vertice_coordin": 6, "vertice_indic": 6, "vertices_coordin": 6, "vertices_indic": 6, "vetor": 6, "vi": 7, "vice": 6, "view": [2, 6, 11], "viewer": [2, 6, 7, 11], "viewertyp": 2, "viewport": [2, 6, 7], "vindic": [2, 6], "virtual": 11, "virtualenv": 10, "visibl": [2, 6, 7], "vision": 2, "visit": 11, "viz_typ": 7, "vlen": [1, 2, 6], "vn": 6, "vnorm": [1, 2, 6], "vnormal": [2, 6], "void": 9, "volum": [0, 2, 14], "vote": 2, "voxel": [0, 1, 2, 3, 8, 14], "voxel_data": 2, "voxel_model": 2, "voxel_s": [2, 3, 8], "vrangestart": 2, "vrml": 2, "vsurfacearea": 2, "vtestid": 2, "vthreshstart": 2, "vtk": 2, "w": 2, "w1": 2, "w2": 2, "wa": 2, "wai": [2, 3, 6], "walkignmod": 3, "walkingmod": 3, "walklattic": [2, 3], "walklatticesurfac": [2, 3], "walkspher": [2, 3], "want": [2, 6, 7], "warranti": [2, 6, 7], "waveren": 2, "wb": 2, "we": [2, 3, 6, 7], "weakref": [2, 3], "web": 11, "websit": 10, "wed": 2, "weight": [2, 3, 4], "weight_mod": 4, "weight_mode_nam": 4, "weight_mode_set": 4, "weight_mode_settings_dict": 4, "weighted_choice_sub": [2, 3], "weightmod": [2, 4], "weightmodeopt": [2, 4], "welcom": 10, "well": [2, 11], "what": 3, "when": [0, 2, 3, 10, 11, 14], "where": [2, 6], "whether": [0, 2, 14], "which": [0, 2, 3, 6, 7, 8, 11, 14], "which_db": [1, 2], "while": [0, 14], "white": [2, 3], "whitespac": 8, "who": [6, 7], "whole": 6, "width": 2, "window": 6, "wirefram": 2, "with_colon": [2, 4], "within": 2, "without": [2, 6, 7], "work": [2, 6, 7, 10, 11], "workflow": [2, 9], "world": [3, 6, 7], "worldsiz": 2, "would": 8, "wrap": [0, 2, 14], "write": [1, 2, 6, 7, 8], "write_creds_path": [1, 2], "write_json_fil": [2, 5], "write_username_to_cr": [1, 2], "writearraystofil": [1, 2], "writedx": [2, 6], "writejson": [1, 2], "writemeshtofil": [2, 6], "writer": [1, 2], "writetofil": [2, 6, 7], "written": 2, "wrl": 2, "wu": 2, "www": [2, 6, 7], "x": [0, 2, 3, 4, 6, 7, 14], "x_label": 2, "x_n": 2, "x_width": [2, 3], "xaxi": 2, "xaxis_titl": 7, "xgl": 2, "xml": [2, 8], "xmlnode": 2, "xrai": 6, "xtrace": 7, "xy": 6, "xyz": [2, 6, 7], "xyztoijk": [1, 2], "xyztrajectori": [1, 2], "y": [0, 2, 3, 4, 6, 7, 14], "y_label": 2, "y_n": 2, "y_width": [2, 3], "yaxi": 2, "yaxis_titl": 7, "yet": 2, "yml": 9, "you": [2, 6, 7, 8, 10, 11, 12], "your": [2, 6, 7, 10, 11, 12], "your_development_typ": 10, "your_name_her": 10, "yourself": 11, "ytrace": 7, "z": [0, 2, 3, 4, 6, 7, 8, 14], "z_n": 2, "z_width": [2, 3], "zaxi": 2, "zissermann": 2, "\u00e5": 2}, "titles": ["Cellpack Recipe Schema 1.0", "cellpack package", "cellpack.autopack package", "cellpack.autopack.ingredient package", "cellpack.autopack.interface_objects package", "cellpack.autopack.loaders package", "cellpack.autopack.upy package", "cellpack.autopack.upy.simularium package", "cellpack.autopack.writers package", "cellpack.bin package", "Contributing", "Welcome to cellPack\u2019s documentation!", "Installation", "cellpack", "Cellpack Recipe Schema 1.0"], "titleterms": {"": 11, "0": [0, 14], "00": 2, "1": [0, 2, 14], "20": 2, "2012": 2, "23": 2, "50": 2, "53": 2, "The": [2, 6, 7], "_hackfreept": [0, 14], "_timer": [0, 14], "abstract": [6, 7], "agent": 3, "an": 4, "analysi": 2, "analysis_config_load": 5, "analyz": 9, "autopack": [2, 3, 4, 5, 6, 7, 8], "aw": 11, "awshandl": 2, "basegrid": 2, "bin": 9, "binvox_rw": 2, "boundingbox": [0, 14], "canceldialog": [0, 14], "cellpack": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 13, 14], "cheat": 11, "class": [2, 7], "clean": 9, "cleanup_task": 9, "code": 11, "color": [0, 6, 14], "compart": 2, "compartmentlist": 2, "computegridparam": [0, 14], "config_load": 5, "content": [1, 2, 3, 4, 5, 6, 7, 8, 9], "contribut": [10, 11], "convers": 11, "coordsystem": [0, 14], "count": [0, 14], "creat": 2, "cutoff_boundari": [0, 14], "cutoff_surfac": [0, 14], "data": 4, "databas": 11, "database_id": 4, "dbrecipehandl": 2, "default_valu": 4, "definit": [0, 14], "deploi": 10, "develop": 11, "differ": 4, "document": 11, "encapsulating_radiu": [0, 14], "environ": 2, "enviroonli": [0, 14], "exampl": [0, 14], "excluded_partners_nam": [0, 14], "firebas": 11, "firebasehandl": 2, "firestor": 11, "freeptsupdatethreshold": [0, 14], "fri": 2, "from": 12, "geometrytool": 2, "get": [9, 10], "gradient": [0, 2, 14], "gradient_data": 4, "graphic": 2, "grid": 2, "grow": 3, "helper": [6, 7], "hold": 4, "hosthelp": 6, "imagewrit": 8, "indic": 11, "ingredi": [0, 3, 4, 14], "ingredient_typ": 4, "ingrlookforneighbour": [0, 14], "innergridmethod": [0, 14], "instal": 12, "interface_object": 4, "introduct": 11, "ioutil": 2, "is_attractor": [0, 14], "jitter_attempt": [0, 14], "jul": 2, "largestproteins": [0, 14], "ldsequenc": 2, "loader": 5, "max_jitt": [0, 14], "meshfil": [0, 14], "meshnam": [0, 14], "meshstor": 2, "meta_enum": 4, "migrate_v1_to_v2": 5, "migrate_v2_to_v2_1": 5, "modul": [1, 2, 3, 4, 5, 6, 7, 8, 9], "molar": [0, 14], "multi_cylind": 3, "multi_spher": 3, "name": [0, 14], "object": [4, 6], "octre": 2, "offset": [0, 9, 14], "option": [0, 14], "organ": [0, 14], "orientbiasrotrangemax": [0, 14], "orientbiasrotrangemin": [0, 14], "outputsimularium": 2, "overwriteplacemethod": [0, 14], "pack": [9, 11], "packag": [1, 2, 3, 4, 5, 6, 7, 8, 9], "packed_object": 4, "packing_mod": [0, 14], "partner": 4, "partners_nam": [0, 14], "partners_posit": [0, 14], "partners_weight": [0, 14], "pdb": [0, 9, 14], "perturb_axis_amplitud": [0, 14], "pickrandpt": [0, 14], "pickweightedingr": [0, 14], "place_method": [0, 14], "plot": 7, "plotly_result": 2, "posit": [0, 14], "positions2": [0, 14], "prerequisit": 11, "principal_vector": [0, 14], "prioriti": [0, 14], "proba_bind": [0, 14], "proba_not_bind": [0, 14], "properti": [0, 14], "radii": [0, 14], "rai": 2, "randomrot": 2, "recip": [0, 2, 14], "recipe_load": 5, "rejection_threshold": [0, 14], "releas": 12, "remot": 11, "represent": 4, "requir": 2, "result_fil": [0, 14], "rotation_axi": [0, 14], "rotation_rang": [0, 14], "run": 11, "runtimedisplai": [0, 14], "s3": 11, "saturdai": 2, "saveresult": [0, 14], "schema": [0, 14], "score": [0, 14], "septemb": 2, "serializ": 2, "setup": 11, "sheet": 11, "simularium": 7, "simularium_convert": 9, "simularium_help": 7, "single_cub": 3, "single_cylind": 3, "single_spher": 3, "smallestproteins": [0, 14], "sourc": 12, "spherefil": [0, 14], "stabl": 12, "start": 10, "submodul": [2, 3, 4, 5, 6, 7, 8, 9], "subpackag": [1, 2, 6], "tabl": 11, "thi": 4, "trajectori": 2, "transform": 2, "type": [0, 4, 14], "upi": [6, 7], "upload": 9, "use_gradi": [0, 14], "use_orient_bia": [0, 14], "use_period": [0, 14], "use_rotation_axi": [0, 14], "util": [2, 3, 5], "v1_v2_attribute_chang": 5, "version": [0, 14], "weight": [0, 14], "welcom": 11, "windowss": [0, 14], "writer": 8}})
\ No newline at end of file