From c999dcafa6c94c04f7063b6bd9983ba62a1bcf93 Mon Sep 17 00:00:00 2001 From: rugeli <91452427+rugeli@users.noreply.github.com> Date: Thu, 21 Mar 2024 17:53:59 +0000 Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20main=20@=20c?= =?UTF-8?q?78b89bbff70d10325155669ae5cf92e4cd32f64=20=F0=9F=9A=80?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- _modules/cellpack/autopack.html | 1 + _modules/cellpack/autopack/AWSHandler.html | 51 +++++++++++++----- .../cellpack/autopack/DBRecipeHandler.html | 18 ++++++- .../cellpack/autopack/FirebaseHandler.html | 28 ++++++++-- .../autopack/loaders/recipe_loader.html | 2 +- .../upy/simularium/simularium_helper.html | 4 +- cellpack.autopack.html | 29 ++++++++-- cellpack.html | 5 +- genindex.html | 8 ++- objects.inv | Bin 11818 -> 11852 bytes searchindex.js | 2 +- 11 files changed, 121 insertions(+), 27 deletions(-) diff --git a/_modules/cellpack/autopack.html b/_modules/cellpack/autopack.html index 9d6ed1b3..85f1f9d1 100644 --- a/_modules/cellpack/autopack.html +++ b/_modules/cellpack/autopack.html @@ -470,6 +470,7 @@
if database_name == "firebase":
db = DATABASE_IDS.handlers().get(database_name)
db_handler = DBRecipeLoader(db)
+ db_handler.validate_input_recipe_path(filename)
recipe_id = file_path.split("/")[-1]
db_doc, _ = db_handler.collect_docs_by_id(
collection="recipes", id=recipe_id
diff --git a/_modules/cellpack/autopack/AWSHandler.html b/_modules/cellpack/autopack/AWSHandler.html
index 96ead53c..284823ff 100644
--- a/_modules/cellpack/autopack/AWSHandler.html
+++ b/_modules/cellpack/autopack/AWSHandler.html
@@ -40,6 +40,7 @@ Navigation
Source code for cellpack.autopack.AWSHandler
import logging
from pathlib import Path
+from urllib.parse import parse_qs, urlparse, urlunparse
import boto3
from botocore.exceptions import ClientError
@@ -84,7 +85,7 @@ Source code for cellpack.autopack.AWSHandler
[docs]
def get_aws_object_key(self, object_name):
if self.folder_name is not None:
- object_name = self.folder_name + object_name
+ object_name = f"{self.folder_name}/{object_name}"
else:
object_name = object_name
return object_name
@@ -126,29 +127,55 @@ Source code for cellpack.autopack.AWSHandler
"""
object_name = self.get_aws_object_key(object_name)
# Generate a presigned URL for the S3 object
+ # The response contains the presigned URL
+ # https://{self.bucket_name}.s3.{region}.amazonaws.com/{object_key}
try:
url = self.s3_client.generate_presigned_url(
"get_object",
Params={"Bucket": self.bucket_name, "Key": object_name},
ExpiresIn=expiration,
)
+ base_url = urlunparse(urlparse(url)._replace(query="", fragment=""))
+ return base_url
except ClientError as e:
- logging.error(e)
- return None
- # The response contains the presigned URL
- # https://{self.bucket_name}.s3.{region}.amazonaws.com/{object_key}
- return url
+ logging.error(f"Error generating presigned URL: {e}")
+ return None
-
-[docs]
- def save_file(self, file_path):
+
+[docs]
+ def is_url_valid(self, url):
+ """
+ Validate the url's scheme, bucket name, and query parameters, etc.
+ """
+ parsed_url = urlparse(url)
+ # Check the scheme
+ if parsed_url.scheme != "https":
+ return False
+ # Check the bucket name
+ if not parsed_url.path.startswith(f"/{self.bucket_name}/"):
+ return False
+ # Check unwanted query parameters
+ unwanted_query_params = ["AWSAccessKeyId", "Signature", "Expires"]
+ if parsed_url.query:
+ query_params = parse_qs(parsed_url.query)
+ for param in unwanted_query_params:
+ if param in query_params:
+ return False
+ return True
+
+
+
+[docs]
+ def save_file_and_get_url(self, file_path):
"""
- Uploads a file to S3 and returns the presigned url
+ Uploads a file to S3 and returns the base url
"""
file_name = self.upload_file(file_path)
- if file_name:
- return file_name, self.create_presigned_url(file_name)
+ base_url = self.create_presigned_url(file_name)
+ if file_name and base_url:
+ if self.is_url_valid(base_url):
+ return file_name, base_url
Uploads a file to S3 and returns the presigned url
+Validate the url’s scheme, bucket name, and query parameters, etc.
+Validates if the input path corresponds to a recipe path in the database. +Format of a recipe path: firebase:recipes/[RECIPE-ID]
+AWSHandler
DBRecipeLoader.collect_docs_by_id()
DBRecipeLoader.compile_db_recipe_data()
DBRecipeLoader.prep_db_doc_for_download()
DBRecipeLoader.validate_input_recipe_path()
DBUploader
FirebaseHandler.get_path_from_ref()
FirebaseHandler.get_staging_creds()
FirebaseHandler.get_username()
FirebaseHandler.get_value()
FirebaseHandler.is_firebase_obj()
FirebaseHandler.is_reference()
FirebaseHandler.set_doc()
AWSHandler
DBRecipeLoader.collect_docs_by_id()
DBRecipeLoader.compile_db_recipe_data()
DBRecipeLoader.prep_db_doc_for_download()
DBRecipeLoader.validate_input_recipe_path()
DBUploader
FirebaseHandler.get_path_from_ref()
FirebaseHandler.get_staging_creds()
FirebaseHandler.get_username()
FirebaseHandler.get_value()
FirebaseHandler.is_firebase_obj()
FirebaseHandler.is_reference()
FirebaseHandler.set_doc()
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"cellpack.autopack.Analysis.Analysis.cartesian_to_sph"]], "cellpack.autopack": [[2, "module-cellpack.autopack"]], "cellpack.autopack.awshandler": [[2, "module-cellpack.autopack.AWSHandler"]], "cellpack.autopack.analysis": [[2, "module-cellpack.autopack.Analysis"]], "cellpack.autopack.basegrid": [[2, "module-cellpack.autopack.BaseGrid"]], "cellpack.autopack.compartment": [[2, "module-cellpack.autopack.Compartment"]], "cellpack.autopack.dbrecipehandler": [[2, "module-cellpack.autopack.DBRecipeHandler"]], "cellpack.autopack.environment": [[2, "module-cellpack.autopack.Environment"]], "cellpack.autopack.firebasehandler": [[2, "module-cellpack.autopack.FirebaseHandler"]], "cellpack.autopack.geometrytools": [[2, "module-cellpack.autopack.GeometryTools"]], "cellpack.autopack.gradient": [[2, "module-cellpack.autopack.Gradient"]], "cellpack.autopack.graphics": [[2, "module-cellpack.autopack.Graphics"]], "cellpack.autopack.grid": [[2, "module-cellpack.autopack.Grid"]], 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"clearall() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.clearAll"]], "clearcaches() (in module cellpack.autopack)": [[2, "cellpack.autopack.clearCaches"]], "clearfill() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.clearFill"]], "clearingr() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.clearIngr"]], "clearrbingredient() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.clearRBingredient"]], "clearrecipe() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.clearRecipe"]], "clone() (cellpack.autopack.binvox_rw.voxels method)": [[2, "cellpack.autopack.binvox_rw.Voxels.clone"]], "cmp_to_key() (in module cellpack.autopack.utils)": [[2, "cellpack.autopack.utils.cmp_to_key"]], "collectresult() 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"cellpack.autopack.Graphics.AutopackViewer.exportIngredient"]], "exportrecipeingredients() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.exportRecipeIngredients"]], "exporttobd_box() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.exportToBD_BOX"]], "exporttoreaddy() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.exportToReaDDy"]], "exporttotem() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.exportToTEM"]], "exporttotem_sim() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.exportToTEM_SIM"]], "extendgridarrays() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.extendGridArrays"]], "extend_bounding_box_for_compartments() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.extend_bounding_box_for_compartments"]], "extractmeshcomponent() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.extractMeshComponent"]], "f_dot_product() (in module cellpack.autopack.ray)": [[2, "cellpack.autopack.ray.f_dot_product"]], "f_ray_intersect_polyhedron() (in module cellpack.autopack.ray)": [[2, "cellpack.autopack.ray.f_ray_intersect_polyhedron"]], "filter_surface_pts_to_fill_box() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.filter_surface_pts_to_fill_box"]], "findbranch() (cellpack.autopack.octree.octree method)": [[2, "cellpack.autopack.octree.Octree.findBranch"]], "findpointscenter() (in module cellpack.autopack.ray)": [[2, "cellpack.autopack.ray.findPointsCenter"]], "findposition() (cellpack.autopack.octree.octree method)": [[2, "cellpack.autopack.octree.Octree.findPosition"]], "find_nearest() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.find_nearest"]], "finishwithwater() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.finishWithWater"]], "fixonepath() (in module cellpack.autopack)": [[2, "cellpack.autopack.fixOnePath"]], "fixpath() (in module cellpack.autopack)": [[2, "cellpack.autopack.fixPath"]], "flush() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.flush"]], "format_color() (cellpack.autopack.plotly_result.plotlyanalysis static method)": [[2, "cellpack.autopack.plotly_result.PlotlyAnalysis.format_color"]], "gatherresult() (in module cellpack.autopack.ioutils)": [[2, "cellpack.autopack.IOutils.gatherResult"]], "generalapply() (cellpack.autopack.trajectory.trajectory method)": [[2, "cellpack.autopack.trajectory.Trajectory.generalApply"]], "get() (cellpack.autopack.randomrot.randomrot method)": [[2, 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[[2, "cellpack.autopack.Compartment.Compartment.getCenter"]], "getclosestdistance() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.getClosestDistance"]], "getclosestfreegridpoint() (cellpack.autopack.basegrid.basegrid method)": [[2, "cellpack.autopack.BaseGrid.BaseGrid.getClosestFreeGridPoint"]], "getclosestgridpoint() (cellpack.autopack.basegrid.basegrid method)": [[2, "cellpack.autopack.BaseGrid.BaseGrid.getClosestGridPoint"]], "getdiagonal() (cellpack.autopack.basegrid.basegrid method)": [[2, "cellpack.autopack.BaseGrid.BaseGrid.getDiagonal"]], "getdistancefrom() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.getDistanceFrom"]], "getfacenormals() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.getFaceNormals"]], "getfacesnfromv() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.getFacesNfromV"]], "getforwweight() (cellpack.autopack.gradient.gradient method)": [[2, "cellpack.autopack.Gradient.Gradient.getForwWeight"]], "gethaltonunique() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.getHaltonUnique"]], "getijk() (cellpack.autopack.basegrid.basegrid method)": [[2, "cellpack.autopack.BaseGrid.BaseGrid.getIJK"]], "getijk() (cellpack.autopack.grid.grid method)": [[2, "cellpack.autopack.Grid.Grid.getIJK"]], "getindex() (cellpack.autopack.binvox_rw.voxels method)": [[2, "cellpack.autopack.binvox_rw.Voxels.getIndex"]], "getindexdata() (cellpack.autopack.binvox_rw.voxels method)": [[2, "cellpack.autopack.binvox_rw.Voxels.getIndexData"]], "getingrfromnameinrecipe() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.getIngrFromNameInRecipe"]], "getingredientinstancepos() (cellpack.autopack.trajectory.trajectory method)": [[2, "cellpack.autopack.trajectory.Trajectory.getIngredientInstancePos"]], "getinterpolatednormal() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.getInterpolatedNormal"]], "getlinearweighted() (cellpack.autopack.gradient.gradient method)": [[2, "cellpack.autopack.Gradient.Gradient.getLinearWeighted"]], "getmaxweight() (cellpack.autopack.gradient.gradient method)": [[2, "cellpack.autopack.Gradient.Gradient.getMaxWeight"]], "getmesh() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.getMesh"]], "getminmaxproteinsize() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.getMinMaxProteinSize"]], "getminmaxproteinsize() (cellpack.autopack.recipe.recipe method)": [[2, "cellpack.autopack.Recipe.Recipe.getMinMaxProteinSize"]], "getminweight() (cellpack.autopack.gradient.gradient method)": [[2, "cellpack.autopack.Gradient.Gradient.getMinWeight"]], "getnbgridpoints() (cellpack.autopack.basegrid.haltongrid method)": [[2, "cellpack.autopack.BaseGrid.HaltonGrid.getNBgridPoints"]], "getold() (cellpack.autopack.randomrot.randomrot method)": [[2, "cellpack.autopack.randomRot.RandomRot.getOld"]], "getoneingr() (cellpack.autopack.environment.environment class method)": [[2, "cellpack.autopack.Environment.Environment.getOneIngr"]], "getoneingrjson() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.getOneIngrJson"]], "getpointfrom3d() (cellpack.autopack.basegrid.basegrid method)": [[2, "cellpack.autopack.BaseGrid.BaseGrid.getPointFrom3D"]], "getpointfrom3d() (cellpack.autopack.basegrid.haltongrid method)": [[2, "cellpack.autopack.BaseGrid.HaltonGrid.getPointFrom3D"]], "getpointtodrop() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.getPointToDrop"]], "getpointsincube() (cellpack.autopack.basegrid.basegrid method)": [[2, "cellpack.autopack.BaseGrid.BaseGrid.getPointsInCube"]], "getpointsincubefillbb() (cellpack.autopack.basegrid.basegrid method)": [[2, "cellpack.autopack.BaseGrid.BaseGrid.getPointsInCubeFillBB"]], "getpointsinsphere() (cellpack.autopack.basegrid.basegrid method)": [[2, "cellpack.autopack.BaseGrid.BaseGrid.getPointsInSphere"]], "getposat() (cellpack.autopack.trajectory.dcdtrajectory method)": [[2, "cellpack.autopack.trajectory.dcdTrajectory.getPosAt"]], "getposat() (cellpack.autopack.trajectory.molbtrajectory method)": [[2, "cellpack.autopack.trajectory.molbTrajectory.getPosAt"]], "getposat() (cellpack.autopack.trajectory.xyztrajectory method)": [[2, "cellpack.autopack.trajectory.xyzTrajectory.getPosAt"]], "getposline() (cellpack.autopack.trajectory.xyztrajectory method)": [[2, "cellpack.autopack.trajectory.xyzTrajectory.getPosLine"]], "getpositionperidocity() (cellpack.autopack.basegrid.basegrid method)": [[2, "cellpack.autopack.BaseGrid.BaseGrid.getPositionPeridocity"]], "getpositionsfromobject() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.getPositionsFromObject"]], "getpositionsfromresfile() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.getPositionsFromResFile"]], "getradius() (cellpack.autopack.basegrid.basegrid method)": [[2, "cellpack.autopack.BaseGrid.BaseGrid.getRadius"]], "getradius() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.getRadius"]], "getrndweighted() (cellpack.autopack.gradient.gradient method)": [[2, "cellpack.autopack.Gradient.Gradient.getRndWeighted"]], "getrottransrb() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.getRotTransRB"]], "getscale() (cellpack.autopack.basegrid.haltongrid method)": [[2, "cellpack.autopack.BaseGrid.HaltonGrid.getScale"]], "getsizexyz() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.getSizeXYZ"]], "getsortedactiveingredients() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.getSortedActiveIngredients"]], "getstringvalueoptions() (in module cellpack.autopack.ioutils)": [[2, "cellpack.autopack.IOutils.getStringValueOptions"]], "getsubweighted() (cellpack.autopack.gradient.gradient method)": [[2, "cellpack.autopack.Gradient.Gradient.getSubWeighted"]], "getsurfaceinnerpoints() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.getSurfaceInnerPoints"]], "getsurfaceinnerpoints_kevin() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.getSurfaceInnerPoints_kevin"]], "getsurfaceinnerpoints_sdf() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.getSurfaceInnerPoints_sdf"]], "getsurfaceinnerpoints_sdf_interpolate() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.getSurfaceInnerPoints_sdf_interpolate"]], "getsurfacepoint() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.getSurfacePoint"]], "gettotalnbobject() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.getTotalNbObject"]], "getvnfromf() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.getVNfromF"]], "getvertexnormals() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.getVertexNormals"]], "getvolumeshell() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.getVolumeShell"]], "get_all_distances() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.get_all_distances"]], "get_attributes_to_update() (cellpack.autopack.environment.environment static method)": 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"cellpack.autopack.Environment.Environment.get_closest_ingredients"]], "get_collada_material() (cellpack.autopack.meshstore.meshstore static method)": [[2, "cellpack.autopack.MeshStore.MeshStore.get_collada_material"]], "get_collection_id_from_path() (cellpack.autopack.firebasehandler.firebasehandler static method)": [[2, "cellpack.autopack.FirebaseHandler.FirebaseHandler.get_collection_id_from_path"]], "get_compartment_object_by_name() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.get_compartment_object_by_name"]], "get_dev_creds() (cellpack.autopack.firebasehandler.firebasehandler static method)": [[2, "cellpack.autopack.FirebaseHandler.FirebaseHandler.get_dev_creds"]], "get_dict_from_glob() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.get_dict_from_glob"]], "get_distance() (in module cellpack.autopack.utils)": [[2, "cellpack.autopack.utils.get_distance"]], "get_distances() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.get_distances"]], "get_distances_and_angles() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.get_distances_and_angles"]], "get_distances_from_point() (in module cellpack.autopack.utils)": [[2, "cellpack.autopack.utils.get_distances_from_point"]], "get_doc_by_id() (cellpack.autopack.firebasehandler.firebasehandler method)": [[2, "cellpack.autopack.FirebaseHandler.FirebaseHandler.get_doc_by_id"]], "get_doc_by_name() (cellpack.autopack.firebasehandler.firebasehandler method)": [[2, "cellpack.autopack.FirebaseHandler.FirebaseHandler.get_doc_by_name"]], "get_doc_by_ref() (cellpack.autopack.firebasehandler.firebasehandler method)": [[2, "cellpack.autopack.FirebaseHandler.FirebaseHandler.get_doc_by_ref"]], "get_dpad() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.get_dpad"]], "get_gauss_weights() (cellpack.autopack.gradient.gradient method)": [[2, "cellpack.autopack.Gradient.Gradient.get_gauss_weights"]], "get_ingredient_angles() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.get_ingredient_angles"]], "get_ingredient_by_name() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.get_ingredient_by_name"]], "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"]], "get_ingredient_radii() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.get_ingredient_radii"]], "get_ingredients_in_tree() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.get_ingredients_in_tree"]], "get_list_of_dims() (cellpack.autopack.analysis.analysis static method)": [[2, "cellpack.autopack.Analysis.Analysis.get_list_of_dims"]], "get_local_file_location() (in module cellpack.autopack)": [[2, "cellpack.autopack.get_local_file_location"]], "get_max_value_from_distribution() (in module cellpack.autopack.utils)": [[2, "cellpack.autopack.utils.get_max_value_from_distribution"]], "get_mesh() (cellpack.autopack.meshstore.meshstore method)": [[2, "cellpack.autopack.MeshStore.MeshStore.get_mesh"]], "get_mesh_filepath_and_extension() (cellpack.autopack.meshstore.meshstore static method)": [[2, "cellpack.autopack.MeshStore.MeshStore.get_mesh_filepath_and_extension"]], "get_midpoint() (cellpack.autopack.meshstore.meshstore static method)": [[2, "cellpack.autopack.MeshStore.MeshStore.get_midpoint"]], "get_min_value_from_distribution() (in module cellpack.autopack.utils)": [[2, "cellpack.autopack.utils.get_min_value_from_distribution"]], "get_minimum_expected_distance_from_recipe() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.get_minimum_expected_distance_from_recipe"]], "get_normal() (cellpack.autopack.meshstore.meshstore method)": [[2, "cellpack.autopack.MeshStore.MeshStore.get_normal"]], "get_normal_for_point() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.get_normal_for_point"]], "get_normalized_values() (cellpack.autopack.gradient.gradient method)": [[2, "cellpack.autopack.Gradient.Gradient.get_normalized_values"]], "get_nsphere() (cellpack.autopack.meshstore.meshstore method)": [[2, "cellpack.autopack.MeshStore.MeshStore.get_nsphere"]], "get_number_of_ingredients_packed() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.get_number_of_ingredients_packed"]], "get_obj_dict() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.get_obj_dict"]], "get_object() (cellpack.autopack.meshstore.meshstore method)": [[2, "cellpack.autopack.MeshStore.MeshStore.get_object"]], "get_packed_minimum_distance() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.get_packed_minimum_distance"]], "get_paired_key() (in module cellpack.autopack.utils)": [[2, "cellpack.autopack.utils.get_paired_key"]], "get_parametrized_representation() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.get_parametrized_representation"]], "get_partner_pair_dict() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.get_partner_pair_dict"]], "get_path_from_ref() (cellpack.autopack.firebasehandler.firebasehandler static method)": [[2, "cellpack.autopack.FirebaseHandler.FirebaseHandler.get_path_from_ref"]], "get_rb_model() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.get_rb_model"]], "get_rectangle_cercle_area() (cellpack.autopack.geometrytools.geometrytools method)": [[2, "cellpack.autopack.GeometryTools.GeometryTools.get_rectangle_cercle_area"]], "get_reference_data() (cellpack.autopack.dbrecipehandler.compositiondoc static method)": [[2, "cellpack.autopack.DBRecipeHandler.CompositionDoc.get_reference_data"]], "get_reference_in_obj() (cellpack.autopack.dbrecipehandler.compositiondoc static method)": [[2, "cellpack.autopack.DBRecipeHandler.CompositionDoc.get_reference_in_obj"]], "get_scaled_distances_between_surfaces() (cellpack.autopack.meshstore.meshstore method)": [[2, "cellpack.autopack.MeshStore.MeshStore.get_scaled_distances_between_surfaces"]], "get_seed_list() (in module cellpack.autopack.utils)": [[2, "cellpack.autopack.utils.get_seed_list"]], "get_size_of_bounding_box() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.get_size_of_bounding_box"]], "get_smallest_radius() (cellpack.autopack.meshstore.meshstore method)": [[2, "cellpack.autopack.MeshStore.MeshStore.get_smallest_radius"]], "get_staging_creds() (cellpack.autopack.firebasehandler.firebasehandler static method)": [[2, "cellpack.autopack.FirebaseHandler.FirebaseHandler.get_staging_creds"]], "get_username() (cellpack.autopack.firebasehandler.firebasehandler static method)": [[2, "cellpack.autopack.FirebaseHandler.FirebaseHandler.get_username"]], "get_value_from_distribution() (in module cellpack.autopack.utils)": [[2, "cellpack.autopack.utils.get_value_from_distribution"]], "get_xyz_dict_from_all_pos_dict() (cellpack.autopack.analysis.analysis static method)": [[2, "cellpack.autopack.Analysis.Analysis.get_xyz_dict_from_all_pos_dict"]], "grab() (cellpack.autopack.ioutils.grabresult method)": [[2, "cellpack.autopack.IOutils.GrabResult.grab"]], "grabresultfromjson() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.grabResultFromJSON"]], "grabresultfromtxt() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.grabResultFromTXT"]], "gradient_list_to_dict() (cellpack.autopack.dbrecipehandler.compositiondoc static method)": [[2, "cellpack.autopack.DBRecipeHandler.CompositionDoc.gradient_list_to_dict"]], "gridpoint (class in cellpack.autopack.basegrid)": [[2, "cellpack.autopack.BaseGrid.gridPoint"]], "halton() (in module cellpack.autopack.ldsequence)": [[2, "cellpack.autopack.ldSequence.halton"]], "halton2() (in module cellpack.autopack.ldsequence)": [[2, "cellpack.autopack.ldSequence.halton2"]], "halton3() (in module cellpack.autopack.ldsequence)": [[2, "cellpack.autopack.ldSequence.halton3"]], "halton_sequence() (in module cellpack.autopack.ldsequence)": [[2, "cellpack.autopack.ldSequence.halton_sequence"]], "haltonterm() (in module cellpack.autopack.ldsequence)": [[2, "cellpack.autopack.ldSequence.haltonterm"]], "hideingrprimitive() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.hideIngrPrimitive"]], "histogram() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.histogram"]], "ijktoindex() (cellpack.autopack.binvox_rw.voxels method)": [[2, "cellpack.autopack.binvox_rw.Voxels.ijkToIndex"]], "ijktoxyz() (cellpack.autopack.binvox_rw.voxels method)": [[2, "cellpack.autopack.binvox_rw.Voxels.ijkToxyz"]], "inbox() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.inBox"]], "ingrid() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.inGrid"]], "inc() (cellpack.autopack.ldsequence.chaltonsequence3 method)": [[2, "cellpack.autopack.ldSequence.cHaltonSequence3.inc"]], "includeingrrecipe() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.includeIngrRecipe"]], "includeingrrecipes() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.includeIngrRecipes"]], "includeingredientrecipe() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.includeIngredientRecipe"]], "ingrjsonnode() (cellpack.autopack.ioutils.ioingredienttool method)": [[2, "cellpack.autopack.IOutils.IOingredientTool.ingrJsonNode"]], "ingrpythonnode() (cellpack.autopack.ioutils.ioingredienttool method)": [[2, "cellpack.autopack.IOutils.IOingredientTool.ingrPythonNode"]], "ingredient_compare0() (in module cellpack.autopack.utils)": [[2, "cellpack.autopack.utils.ingredient_compare0"]], "ingredient_compare1() (in module cellpack.autopack.utils)": [[2, "cellpack.autopack.utils.ingredient_compare1"]], "ingredient_compare2() (in module cellpack.autopack.utils)": [[2, "cellpack.autopack.utils.ingredient_compare2"]], "initialize_shape() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.initialize_shape"]], "insertnode() (cellpack.autopack.octree.octree method)": [[2, "cellpack.autopack.octree.Octree.insertNode"]], "is_db_dict() (cellpack.autopack.dbrecipehandler.datadoc static method)": [[2, "cellpack.autopack.DBRecipeHandler.DataDoc.is_db_dict"]], "is_firebase_obj() (cellpack.autopack.firebasehandler.firebasehandler static method)": [[2, "cellpack.autopack.FirebaseHandler.FirebaseHandler.is_firebase_obj"]], "is_full_url() (in module cellpack.autopack)": [[2, "cellpack.autopack.is_full_url"]], "is_key() (cellpack.autopack.dbrecipehandler.datadoc static method)": [[2, "cellpack.autopack.DBRecipeHandler.DataDoc.is_key"]], "is_key() (cellpack.autopack.recipe.recipe static method)": [[2, "cellpack.autopack.Recipe.Recipe.is_key"]], "is_nested_list() (cellpack.autopack.dbrecipehandler.datadoc static method)": [[2, "cellpack.autopack.DBRecipeHandler.DataDoc.is_nested_list"]], "is_obj() (cellpack.autopack.dbrecipehandler.datadoc static method)": [[2, "cellpack.autopack.DBRecipeHandler.DataDoc.is_obj"]], "is_point_inside_bb() (cellpack.autopack.basegrid.basegrid method)": [[2, "cellpack.autopack.BaseGrid.BaseGrid.is_point_inside_bb"]], "is_point_inside_mesh() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.is_point_inside_mesh"]], "is_reference() (cellpack.autopack.firebasehandler.firebasehandler static method)": [[2, "cellpack.autopack.FirebaseHandler.FirebaseHandler.is_reference"]], "is_remote_path() (in module cellpack.autopack)": [[2, "cellpack.autopack.is_remote_path"]], "is_two_d() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.is_two_d"]], "linktraj() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.linkTraj"]], "loadfreepoint() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.loadFreePoint"]], "loadjson() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.loadJSON"]], "loadresult() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.loadResult"]], "load_json() (in module cellpack.autopack.ioutils)": [[2, "cellpack.autopack.IOutils.load_Json"]], "load_jsonstring() (in module cellpack.autopack.ioutils)": [[2, "cellpack.autopack.IOutils.load_JsonString"]], "load_mixedasjson() (in module cellpack.autopack.ioutils)": [[2, "cellpack.autopack.IOutils.load_MixedasJson"]], "load_asjson() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.load_asJson"]], "load_astxt() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.load_asTxt"]], "load_file() (in module cellpack.autopack)": [[2, "cellpack.autopack.load_file"]], "load_object_from_pickle() (in module cellpack.autopack.utils)": [[2, "cellpack.autopack.utils.load_object_from_pickle"]], "loopthroughingr() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.loopThroughIngr"]], "makeingrmapping() (cellpack.autopack.trajectory.trajectory method)": [[2, "cellpack.autopack.trajectory.Trajectory.makeIngrMapping"]], "makeingredient() (cellpack.autopack.ioutils.ioingredienttool method)": [[2, "cellpack.autopack.IOutils.IOingredientTool.makeIngredient"]], "makeingredientfromjson() (cellpack.autopack.ioutils.ioingredienttool method)": [[2, "cellpack.autopack.IOutils.IOingredientTool.makeIngredientFromJson"]], "makemarchingcube() (in module cellpack.autopack.ray)": [[2, "cellpack.autopack.ray.makeMarchingCube"]], "make_and_show_heatmap() (cellpack.autopack.plotly_result.plotlyanalysis method)": [[2, "cellpack.autopack.plotly_result.PlotlyAnalysis.make_and_show_heatmap"]], "make_directory_if_needed() (in module cellpack.autopack)": [[2, "cellpack.autopack.make_directory_if_needed"]], "make_grid_heatmap() (cellpack.autopack.plotly_result.plotlyanalysis method)": [[2, "cellpack.autopack.plotly_result.PlotlyAnalysis.make_grid_heatmap"]], "merge() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.merge"]], "molbtrajectory (class in cellpack.autopack.trajectory)": [[2, "cellpack.autopack.trajectory.molbTrajectory"]], "moverbnode() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.moveRBnode"]], "norm() (cellpack.autopack.meshstore.meshstore static method)": [[2, "cellpack.autopack.MeshStore.MeshStore.norm"]], "normal_array() (cellpack.autopack.meshstore.meshstore static method)": [[2, "cellpack.autopack.MeshStore.MeshStore.normal_array"]], "normalize() (cellpack.autopack.meshstore.meshstore static method)": [[2, "cellpack.autopack.MeshStore.MeshStore.normalize"]], "normalize_similarity_df() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.normalize_similarity_df"]], "normalize_v3() (cellpack.autopack.meshstore.meshstore static method)": [[2, "cellpack.autopack.MeshStore.MeshStore.normalize_v3"]], "normalize_vector() (cellpack.autopack.gradient.gradient method)": [[2, "cellpack.autopack.Gradient.Gradient.normalize_vector"]], "oneprevingredient() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.onePrevIngredient"]], "one_exp() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.one_exp"]], "pack() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.pack"]], "pack_grid() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.pack_grid"]], "pack_one_seed() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.pack_one_seed"]], "parse() (cellpack.autopack.trajectory.dcdtrajectory method)": [[2, "cellpack.autopack.trajectory.dcdTrajectory.parse"]], "parse() (cellpack.autopack.trajectory.molbtrajectory method)": [[2, "cellpack.autopack.trajectory.molbTrajectory.parse"]], "parse() (cellpack.autopack.trajectory.xyztrajectory method)": [[2, "cellpack.autopack.trajectory.xyzTrajectory.parse"]], "parse_one_mol() (cellpack.autopack.trajectory.molbtrajectory method)": [[2, "cellpack.autopack.trajectory.molbTrajectory.parse_one_mol"]], "pickingredient() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.pickIngredient"]], "pickpoint() (cellpack.autopack.gradient.gradient method)": [[2, "cellpack.autopack.Gradient.Gradient.pickPoint"]], "plot() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.plot"]], "plotnresult2d() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.plotNResult2D"]], "plot_and_save_similarity_heatmaps() 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method)": [[2, "cellpack.autopack.Environment.Environment.runBullet"]], "run_analysis_workflow() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.run_analysis_workflow"]], "run_distance_analysis() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.run_distance_analysis"]], "run_partner_analysis() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.run_partner_analysis"]], "run_similarity_analysis() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.run_similarity_analysis"]], "scompartment (class in cellpack.autopack.serializable)": [[2, "cellpack.autopack.Serializable.sCompartment"]], "singredient (class in cellpack.autopack.serializable)": [[2, "cellpack.autopack.Serializable.sIngredient"]], "singredientfiber (class in cellpack.autopack.serializable)": [[2, "cellpack.autopack.Serializable.sIngredientFiber"]], "singredientgroup (class 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method)": [[2, "cellpack.autopack.Analysis.Analysis.save_spilr_heatmap"]], "serializedfromresult() (in module cellpack.autopack.ioutils)": [[2, "cellpack.autopack.IOutils.serializedFromResult"]], "serializedrecipe() (in module cellpack.autopack.ioutils)": [[2, "cellpack.autopack.IOutils.serializedRecipe"]], "serializedrecipe_group() (in module cellpack.autopack.ioutils)": [[2, "cellpack.autopack.IOutils.serializedRecipe_group"]], "serializedrecipe_group_dic() (in module cellpack.autopack.ioutils)": [[2, "cellpack.autopack.IOutils.serializedRecipe_group_dic"]], "setcount() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.setCount"]], "setcount() (cellpack.autopack.recipe.recipe method)": [[2, "cellpack.autopack.Recipe.Recipe.setCount"]], "setexteriorrecipe() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.setExteriorRecipe"]], "setgeomfaces() 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"cellpack.autopack.Environment.Environment.set_result_file_name"]], "set_surfptsbht() (cellpack.autopack.basegrid.basegrid method)": [[2, "cellpack.autopack.BaseGrid.BaseGrid.set_surfPtsBht"]], "set_surfptscht() (cellpack.autopack.basegrid.basegrid method)": [[2, "cellpack.autopack.BaseGrid.BaseGrid.set_surfPtscht"]], "set_surface_distances() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.set_surface_distances"]], "set_weights_by_mode() (cellpack.autopack.gradient.gradient method)": [[2, "cellpack.autopack.Gradient.Gradient.set_weights_by_mode"]], "setup() (cellpack.autopack.basegrid.basegrid method)": [[2, "cellpack.autopack.BaseGrid.BaseGrid.setup"]], "setupboundaryperiodicity() (cellpack.autopack.basegrid.basegrid method)": [[2, "cellpack.autopack.BaseGrid.BaseGrid.setupBoundaryPeriodicity"]], "setupfromjsondic() (in module cellpack.autopack.ioutils)": [[2, "cellpack.autopack.IOutils.setupFromJsonDic"]], "setupoctree() 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method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.showHide"]], "showingrprimitive() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.showIngrPrimitive"]], "simpleplot() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.simpleplot"]], "slow_box_fill() (cellpack.autopack.basegrid.basegrid method)": [[2, "cellpack.autopack.BaseGrid.BaseGrid.slow_box_fill"]], "sort() (cellpack.autopack.recipe.recipe method)": [[2, "cellpack.autopack.Recipe.Recipe.sort"]], "sortingredient() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.sortIngredient"]], "sparse_to_dense() (in module cellpack.autopack.binvox_rw)": [[2, "cellpack.autopack.binvox_rw.sparse_to_dense"]], "static_id (cellpack.autopack.serializable.scompartment attribute)": [[2, "cellpack.autopack.Serializable.sCompartment.static_id"]], "static_id (cellpack.autopack.serializable.singredient attribute)": [[2, "cellpack.autopack.Serializable.sIngredient.static_id"]], "static_id (cellpack.autopack.serializable.singredientfiber attribute)": [[2, "cellpack.autopack.Serializable.sIngredientFiber.static_id"]], "static_id (cellpack.autopack.serializable.singredientgroup attribute)": [[2, "cellpack.autopack.Serializable.sIngredientGroup.static_id"]], "store() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.store"]], "store_asjson() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.store_asJson"]], "store_packed_object() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.store_packed_object"]], "test_points_in_bb() (cellpack.autopack.basegrid.basegrid method)": [[2, "cellpack.autopack.BaseGrid.BaseGrid.test_points_in_bb"]], "timefunction() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.timeFunction"]], "timefunction() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.timeFunction"]], "tobinary() (in module cellpack.autopack.ioutils)": [[2, "cellpack.autopack.IOutils.toBinary"]], "to_json() (cellpack.autopack.serializable.scompartment method)": [[2, "cellpack.autopack.Serializable.sCompartment.to_JSON"]], "to_json() (cellpack.autopack.serializable.singredient method)": [[2, "cellpack.autopack.Serializable.sIngredient.to_JSON"]], "to_json() (cellpack.autopack.serializable.singredientfiber method)": [[2, "cellpack.autopack.Serializable.sIngredientFiber.to_JSON"]], "to_json() (cellpack.autopack.serializable.singredientgroup method)": [[2, "cellpack.autopack.Serializable.sIngredientGroup.to_JSON"]], "toggleorganelmatr() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.toggleOrganelMatr"]], "toggleorganelmesh() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.toggleOrganelMesh"]], "toggleorganelsurf() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.toggleOrganelSurf"]], "traj_type (cellpack.autopack.trajectory.trajectory attribute)": [[2, "cellpack.autopack.trajectory.Trajectory.traj_type"]], "traj_type (cellpack.autopack.trajectory.dcdtrajectory attribute)": [[2, "cellpack.autopack.trajectory.dcdTrajectory.traj_type"]], "traj_type (cellpack.autopack.trajectory.molbtrajectory attribute)": [[2, "cellpack.autopack.trajectory.molbTrajectory.traj_type"]], "traj_type (cellpack.autopack.trajectory.xyztrajectory attribute)": [[2, "cellpack.autopack.trajectory.xyzTrajectory.traj_type"]], "transformmesh() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.transformMesh"]], "transformpoints2d() (cellpack.autopack.plotly_result.plotlyanalysis method)": [[2, "cellpack.autopack.plotly_result.PlotlyAnalysis.transformPoints2D"]], "undspmesh() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.undspMesh"]], "undspsph() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.undspSph"]], "unlinktraj() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.unlinkTraj"]], "updatedistances() (cellpack.autopack.basegrid.basegrid static method)": [[2, "cellpack.autopack.BaseGrid.BaseGrid.updateDistances"]], "updatepath() (in module cellpack.autopack)": [[2, "cellpack.autopack.updatePath"]], "updatepathjson() (in module cellpack.autopack)": [[2, "cellpack.autopack.updatePathJSON"]], "updatepositionsradii() (in module cellpack.autopack.ioutils)": [[2, "cellpack.autopack.IOutils.updatePositionsRadii"]], "updaterecipavailablexml() (in module cellpack.autopack)": [[2, "cellpack.autopack.updateRecipAvailableXML"]], "updatereplacepath() (in module cellpack.autopack)": [[2, "cellpack.autopack.updateReplacePath"]], "update_after_place() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.update_after_place"]], "update_crosswise_distances() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.update_crosswise_distances"]], "update_distance_distribution_dictionaries() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.update_distance_distribution_dictionaries"]], "update_doc() (cellpack.autopack.firebasehandler.firebasehandler method)": [[2, "cellpack.autopack.FirebaseHandler.FirebaseHandler.update_doc"]], "update_elements_in_array() (cellpack.autopack.firebasehandler.firebasehandler static method)": [[2, "cellpack.autopack.FirebaseHandler.FirebaseHandler.update_elements_in_array"]], "update_largest_smallest_size() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.update_largest_smallest_size"]], "update_or_create() (cellpack.autopack.firebasehandler.firebasehandler method)": [[2, "cellpack.autopack.FirebaseHandler.FirebaseHandler.update_or_create"]], "update_reference() (cellpack.autopack.dbrecipehandler.compositiondoc static method)": [[2, "cellpack.autopack.DBRecipeHandler.CompositionDoc.update_reference"]], "update_reference_on_doc() (cellpack.autopack.firebasehandler.firebasehandler static method)": [[2, "cellpack.autopack.FirebaseHandler.FirebaseHandler.update_reference_on_doc"]], "update_title() (cellpack.autopack.plotly_result.plotlyanalysis method)": [[2, "cellpack.autopack.plotly_result.PlotlyAnalysis.update_title"]], "update_variable_ingredient_attributes() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.update_variable_ingredient_attributes"]], "upload_collections() (cellpack.autopack.dbrecipehandler.dbuploader method)": [[2, "cellpack.autopack.DBRecipeHandler.DBUploader.upload_collections"]], "upload_compositions() (cellpack.autopack.dbrecipehandler.dbuploader method)": [[2, "cellpack.autopack.DBRecipeHandler.DBUploader.upload_compositions"]], "upload_data() (cellpack.autopack.dbrecipehandler.dbuploader method)": [[2, "cellpack.autopack.DBRecipeHandler.DBUploader.upload_data"]], "upload_doc() (cellpack.autopack.firebasehandler.firebasehandler method)": [[2, "cellpack.autopack.FirebaseHandler.FirebaseHandler.upload_doc"]], "upload_file() (cellpack.autopack.awshandler.awshandler method)": [[2, "cellpack.autopack.AWSHandler.AWSHandler.upload_file"]], "upload_gradients() (cellpack.autopack.dbrecipehandler.dbuploader method)": [[2, "cellpack.autopack.DBRecipeHandler.DBUploader.upload_gradients"]], "upload_objects() (cellpack.autopack.dbrecipehandler.dbuploader method)": [[2, "cellpack.autopack.DBRecipeHandler.DBUploader.upload_objects"]], "upload_recipe() (cellpack.autopack.dbrecipehandler.dbuploader method)": [[2, "cellpack.autopack.DBRecipeHandler.DBUploader.upload_recipe"]], "upload_result_metadata() (cellpack.autopack.dbrecipehandler.dbuploader method)": [[2, "cellpack.autopack.DBRecipeHandler.DBUploader.upload_result_metadata"]], "upload_single_object() (cellpack.autopack.dbrecipehandler.dbuploader method)": [[2, "cellpack.autopack.DBRecipeHandler.DBUploader.upload_single_object"]], "url_exists() (in module cellpack.autopack)": [[2, "cellpack.autopack.url_exists"]], "vcross() (in module cellpack.autopack.ray)": [[2, "cellpack.autopack.ray.vcross"]], "vdiff() (in module cellpack.autopack.ray)": [[2, "cellpack.autopack.ray.vdiff"]], "vlen() (in module cellpack.autopack.ray)": [[2, "cellpack.autopack.ray.vlen"]], "vnorm() (in module cellpack.autopack.ray)": [[2, "cellpack.autopack.ray.vnorm"]], "which_db() (cellpack.autopack.firebasehandler.firebasehandler static method)": [[2, "cellpack.autopack.FirebaseHandler.FirebaseHandler.which_db"]], "write() (cellpack.autopack.binvox_rw.voxels method)": [[2, "cellpack.autopack.binvox_rw.Voxels.write"]], "write() (in module cellpack.autopack.binvox_rw)": [[2, "cellpack.autopack.binvox_rw.write"]], "writearraystofile() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.writeArraysToFile"]], "writejson() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.writeJSON"]], "write_creds_path() (cellpack.autopack.firebasehandler.firebasehandler static method)": [[2, "cellpack.autopack.FirebaseHandler.FirebaseHandler.write_creds_path"]], "write_username_to_creds() (in module cellpack.autopack)": [[2, "cellpack.autopack.write_username_to_creds"]], "xyztoijk() (cellpack.autopack.binvox_rw.voxels method)": [[2, "cellpack.autopack.binvox_rw.Voxels.xyzToijk"]], "xyztrajectory (class in cellpack.autopack.trajectory)": [[2, "cellpack.autopack.trajectory.xyzTrajectory"]], "arguments (cellpack.autopack.ingredient.ingredient.ingredient attribute)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.ARGUMENTS"]], "arguments (cellpack.autopack.ingredient.grow.growingredient attribute)": [[3, "cellpack.autopack.ingredient.grow.GrowIngredient.ARGUMENTS"]], "actiningredient (class in cellpack.autopack.ingredient.grow)": [[3, "cellpack.autopack.ingredient.grow.ActinIngredient"]], "agent (class in cellpack.autopack.ingredient.agent)": [[3, "cellpack.autopack.ingredient.agent.Agent"]], "applymatrix() (in module cellpack.autopack.ingredient.utils)": [[3, "cellpack.autopack.ingredient.utils.ApplyMatrix"]], "decomposemesh() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.DecomposeMesh"]], "distributionoptions (class in cellpack.autopack.ingredient.ingredient)": [[3, "cellpack.autopack.ingredient.Ingredient.DistributionOptions"]], "distributiontypes (class in cellpack.autopack.ingredient.ingredient)": [[3, "cellpack.autopack.ingredient.Ingredient.DistributionTypes"]], "growingredient (class in cellpack.autopack.ingredient.grow)": [[3, "cellpack.autopack.ingredient.grow.GrowIngredient"]], "ingredient (class in cellpack.autopack.ingredient.ingredient)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient"]], "ingredientinstancedrop (class in cellpack.autopack.ingredient.ingredient)": [[3, "cellpack.autopack.ingredient.Ingredient.IngredientInstanceDrop"]], "list (cellpack.autopack.ingredient.ingredient.distributiontypes attribute)": [[3, "cellpack.autopack.ingredient.Ingredient.DistributionTypes.LIST"]], "list_values (cellpack.autopack.ingredient.ingredient.distributionoptions attribute)": [[3, "cellpack.autopack.ingredient.Ingredient.DistributionOptions.LIST_VALUES"]], "max (cellpack.autopack.ingredient.ingredient.distributionoptions attribute)": [[3, "cellpack.autopack.ingredient.Ingredient.DistributionOptions.MAX"]], "mean (cellpack.autopack.ingredient.ingredient.distributionoptions attribute)": [[3, "cellpack.autopack.ingredient.Ingredient.DistributionOptions.MEAN"]], "min (cellpack.autopack.ingredient.ingredient.distributionoptions attribute)": [[3, "cellpack.autopack.ingredient.Ingredient.DistributionOptions.MIN"]], "multicylindersingr (class in cellpack.autopack.ingredient.multi_cylinder)": [[3, "cellpack.autopack.ingredient.multi_cylinder.MultiCylindersIngr"]], "multisphereingr (class in cellpack.autopack.ingredient.multi_sphere)": [[3, "cellpack.autopack.ingredient.multi_sphere.MultiSphereIngr"]], "normal (cellpack.autopack.ingredient.ingredient.distributiontypes attribute)": [[3, "cellpack.autopack.ingredient.Ingredient.DistributionTypes.NORMAL"]], "std (cellpack.autopack.ingredient.ingredient.distributionoptions attribute)": [[3, "cellpack.autopack.ingredient.Ingredient.DistributionOptions.STD"]], "singlecubeingr (class in cellpack.autopack.ingredient.single_cube)": [[3, "cellpack.autopack.ingredient.single_cube.SingleCubeIngr"]], "singlecylinderingr (class in cellpack.autopack.ingredient.single_cylinder)": [[3, "cellpack.autopack.ingredient.single_cylinder.SingleCylinderIngr"]], "singlesphereingr (class in cellpack.autopack.ingredient.single_sphere)": [[3, "cellpack.autopack.ingredient.single_sphere.SingleSphereIngr"]], "uniform (cellpack.autopack.ingredient.ingredient.distributiontypes attribute)": [[3, "cellpack.autopack.ingredient.Ingredient.DistributionTypes.UNIFORM"]], "alignrotation() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.alignRotation"]], "apply_rotation() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.apply_rotation"]], "attempt_to_pack_at_grid_location() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.attempt_to_pack_at_grid_location"]], "buildmesh() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.buildMesh"]], "bullet_checkcollision_mp() (in module cellpack.autopack.ingredient.utils)": [[3, "cellpack.autopack.ingredient.utils.bullet_checkCollision_mp"]], "cellpack.autopack.ingredient": [[3, "module-cellpack.autopack.ingredient"]], "cellpack.autopack.ingredient.ingredient": [[3, "module-cellpack.autopack.ingredient.Ingredient"]], "cellpack.autopack.ingredient.agent": [[3, "module-cellpack.autopack.ingredient.agent"]], "cellpack.autopack.ingredient.grow": [[3, "module-cellpack.autopack.ingredient.grow"]], "cellpack.autopack.ingredient.multi_cylinder": [[3, "module-cellpack.autopack.ingredient.multi_cylinder"]], "cellpack.autopack.ingredient.multi_sphere": [[3, "module-cellpack.autopack.ingredient.multi_sphere"]], "cellpack.autopack.ingredient.single_cube": [[3, "module-cellpack.autopack.ingredient.single_cube"]], "cellpack.autopack.ingredient.single_cylinder": [[3, "module-cellpack.autopack.ingredient.single_cylinder"]], "cellpack.autopack.ingredient.single_sphere": [[3, "module-cellpack.autopack.ingredient.single_sphere"]], "cellpack.autopack.ingredient.utils": [[3, "module-cellpack.autopack.ingredient.utils"]], "checkcylcollisions() (cellpack.autopack.ingredient.multi_cylinder.multicylindersingr method)": [[3, "cellpack.autopack.ingredient.multi_cylinder.MultiCylindersIngr.checkCylCollisions"]], "checkcylcollisions() (cellpack.autopack.ingredient.single_cylinder.singlecylinderingr method)": [[3, "cellpack.autopack.ingredient.single_cylinder.SingleCylinderIngr.checkCylCollisions"]], "checkdistance() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.checkDistance"]], "checkifupdate() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.checkIfUpdate"]], "check_against_one_packed_ingr() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.check_against_one_packed_ingr"]], "close_partner_check() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.close_partner_check"]], "collides_with_compartment() (cellpack.autopack.ingredient.multi_cylinder.multicylindersingr method)": [[3, "cellpack.autopack.ingredient.multi_cylinder.MultiCylindersIngr.collides_with_compartment"]], "collides_with_compartment() (cellpack.autopack.ingredient.multi_sphere.multisphereingr method)": [[3, "cellpack.autopack.ingredient.multi_sphere.MultiSphereIngr.collides_with_compartment"]], "collides_with_compartment() (cellpack.autopack.ingredient.single_cube.singlecubeingr method)": [[3, "cellpack.autopack.ingredient.single_cube.SingleCubeIngr.collides_with_compartment"]], "collides_with_compartment() (cellpack.autopack.ingredient.single_cylinder.singlecylinderingr method)": [[3, "cellpack.autopack.ingredient.single_cylinder.SingleCylinderIngr.collides_with_compartment"]], "collides_with_compartment() (cellpack.autopack.ingredient.single_sphere.singlesphereingr method)": [[3, "cellpack.autopack.ingredient.single_sphere.SingleSphereIngr.collides_with_compartment"]], "collision_jitter() (cellpack.autopack.ingredient.multi_cylinder.multicylindersingr method)": [[3, "cellpack.autopack.ingredient.multi_cylinder.MultiCylindersIngr.collision_jitter"]], "collision_jitter() (cellpack.autopack.ingredient.multi_sphere.multisphereingr method)": [[3, "cellpack.autopack.ingredient.multi_sphere.MultiSphereIngr.collision_jitter"]], "collision_jitter() (cellpack.autopack.ingredient.single_cube.singlecubeingr method)": [[3, "cellpack.autopack.ingredient.single_cube.SingleCubeIngr.collision_jitter"]], "collision_jitter() (cellpack.autopack.ingredient.single_cylinder.singlecylinderingr method)": [[3, "cellpack.autopack.ingredient.single_cylinder.SingleCylinderIngr.collision_jitter"]], "collision_jitter() (cellpack.autopack.ingredient.single_sphere.singlesphereingr method)": [[3, "cellpack.autopack.ingredient.single_sphere.SingleSphereIngr.collision_jitter"]], "correctbb() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.correctBB"]], "create_circular_mask() (cellpack.autopack.ingredient.single_sphere.singlesphereingr static method)": [[3, "cellpack.autopack.ingredient.single_sphere.SingleSphereIngr.create_circular_mask"]], "create_voxelization() (cellpack.autopack.ingredient.single_sphere.singlesphereingr method)": [[3, "cellpack.autopack.ingredient.single_sphere.SingleSphereIngr.create_voxelization"]], "cube_surface_distance() (cellpack.autopack.ingredient.single_cube.singlecubeingr method)": [[3, "cellpack.autopack.ingredient.single_cube.SingleCubeIngr.cube_surface_distance"]], "deleteblist() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.deleteblist"]], "far_enough_from_surfaces() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.far_enough_from_surfaces"]], "getaxisrotation() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.getAxisRotation"]], "getbiasedrotation() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.getBiasedRotation"]], "getbigbb() (cellpack.autopack.ingredient.multi_cylinder.multicylindersingr method)": [[3, "cellpack.autopack.ingredient.multi_cylinder.MultiCylindersIngr.getBigBB"]], "getbigbb() (cellpack.autopack.ingredient.single_cylinder.singlecylinderingr method)": [[3, "cellpack.autopack.ingredient.single_cylinder.SingleCylinderIngr.getBigBB"]], "getdata() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.getData"]], "getdihedral() (in module cellpack.autopack.ingredient.utils)": [[3, "cellpack.autopack.ingredient.utils.getDihedral"]], "getencapsulatingradius() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.getEncapsulatingRadius"]], "getfirstpoint() (cellpack.autopack.ingredient.grow.growingredient method)": [[3, "cellpack.autopack.ingredient.grow.GrowIngredient.getFirstPoint"]], "getingredientsinbox() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.getIngredientsInBox"]], "getinterpolatedsphere() (cellpack.autopack.ingredient.grow.growingredient method)": [[3, "cellpack.autopack.ingredient.grow.GrowIngredient.getInterpolatedSphere"]], "getjtransrot() (cellpack.autopack.ingredient.grow.growingredient method)": [[3, "cellpack.autopack.ingredient.grow.GrowIngredient.getJtransRot"]], "getjtransrot_r() (cellpack.autopack.ingredient.grow.growingredient method)": [[3, "cellpack.autopack.ingredient.grow.GrowIngredient.getJtransRot_r"]], "getlistcompfrommask() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.getListCompFromMask"]], "getmaxjitter() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.getMaxJitter"]], "getmesh() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.getMesh"]], "getnextpoint() (cellpack.autopack.ingredient.grow.growingredient method)": [[3, "cellpack.autopack.ingredient.grow.GrowIngredient.getNextPoint"]], "getnextptindcyl() (cellpack.autopack.ingredient.grow.growingredient method)": [[3, "cellpack.autopack.ingredient.grow.GrowIngredient.getNextPtIndCyl"]], "getnormedvector() (in module cellpack.autopack.ingredient.utils)": [[3, "cellpack.autopack.ingredient.utils.getNormedVector"]], "getnormedvectorones() (in module cellpack.autopack.ingredient.utils)": [[3, "cellpack.autopack.ingredient.utils.getNormedVectorOnes"]], "getnormedvectoru() (in module cellpack.autopack.ingredient.utils)": [[3, "cellpack.autopack.ingredient.utils.getNormedVectorU"]], "getsubweighted() (cellpack.autopack.ingredient.agent.agent method)": [[3, "cellpack.autopack.ingredient.agent.Agent.getSubWeighted"]], "getv3() (cellpack.autopack.ingredient.grow.growingredient method)": [[3, "cellpack.autopack.ingredient.grow.GrowIngredient.getV3"]], "get_all_positions_to_check() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.get_all_positions_to_check"]], "get_alternate_position() (cellpack.autopack.ingredient.grow.growingredient method)": [[3, "cellpack.autopack.ingredient.grow.GrowIngredient.get_alternate_position"]], "get_alternate_position_p() (cellpack.autopack.ingredient.grow.growingredient method)": [[3, "cellpack.autopack.ingredient.grow.GrowIngredient.get_alternate_position_p"]], "get_compartment() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.get_compartment"]], "get_cuttoff_value() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.get_cuttoff_value"]], "get_cuttoff_value() (cellpack.autopack.ingredient.multi_cylinder.multicylindersingr method)": [[3, "cellpack.autopack.ingredient.multi_cylinder.MultiCylindersIngr.get_cuttoff_value"]], "get_cuttoff_value() (cellpack.autopack.ingredient.single_cylinder.singlecylinderingr method)": [[3, "cellpack.autopack.ingredient.single_cylinder.SingleCylinderIngr.get_cuttoff_value"]], "get_list_of_free_indices() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.get_list_of_free_indices"]], "get_new_distance_values() (cellpack.autopack.ingredient.grow.growingredient method)": [[3, "cellpack.autopack.ingredient.grow.GrowIngredient.get_new_distance_values"]], "get_new_distance_values() (cellpack.autopack.ingredient.multi_sphere.multisphereingr method)": [[3, "cellpack.autopack.ingredient.multi_sphere.MultiSphereIngr.get_new_distance_values"]], "get_new_distance_values() (cellpack.autopack.ingredient.single_cube.singlecubeingr method)": [[3, "cellpack.autopack.ingredient.single_cube.SingleCubeIngr.get_new_distance_values"]], "get_new_distance_values() (cellpack.autopack.ingredient.single_sphere.singlesphereingr method)": [[3, "cellpack.autopack.ingredient.single_sphere.SingleSphereIngr.get_new_distance_values"]], "get_new_distances_and_inside_points() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.get_new_distances_and_inside_points"]], "get_new_jitter_location_and_rotation() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.get_new_jitter_location_and_rotation"]], "get_new_pos() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.get_new_pos"]], "get_partners() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.get_partners"]], "get_radius() (cellpack.autopack.ingredient.multi_sphere.multisphereingr method)": [[3, "cellpack.autopack.ingredient.multi_sphere.MultiSphereIngr.get_radius"]], "get_radius() (cellpack.autopack.ingredient.single_sphere.singlesphereingr method)": [[3, 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"module-cellpack.autopack.interface_objects.default_values"]], "cellpack.autopack.interface_objects.gradient_data": [[4, "module-cellpack.autopack.interface_objects.gradient_data"]], "cellpack.autopack.interface_objects.ingredient_types": [[4, "module-cellpack.autopack.interface_objects.ingredient_types"]], "cellpack.autopack.interface_objects.meta_enum": [[4, "module-cellpack.autopack.interface_objects.meta_enum"]], "cellpack.autopack.interface_objects.packed_objects": [[4, "module-cellpack.autopack.interface_objects.packed_objects"]], "cellpack.autopack.interface_objects.partners": [[4, "module-cellpack.autopack.interface_objects.partners"]], "cellpack.autopack.interface_objects.representations": [[4, "module-cellpack.autopack.interface_objects.representations"]], "center (cellpack.autopack.interface_objects.gradient_data.modeoptions attribute)": [[4, "cellpack.autopack.interface_objects.gradient_data.ModeOptions.center"]], "decay_length 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"selectvertices() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.selectVertices"]], "setcurrentselection() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.setCurrentSelection"]], "setframe() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.setFrame"]], "setkeyframe() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.setKeyFrame"]], "setlayers() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.setLayers"]], "setmeshedge() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.setMeshEdge"]], "setmeshedges() (cellpack.autopack.upy.hosthelper.helper method)": [[6, "cellpack.autopack.upy.hostHelper.Helper.setMeshEdges"]], "setmeshface() (cellpack.autopack.upy.hosthelper.helper method)": [[6, 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"cellpack.autopack.upy", "cellpack.autopack.upy.simularium", "cellpack.autopack.writers", "cellpack.bin", "contributing", "index", "installation", "modules", "recipe-schema"], "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"], "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!", 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"cellpack.autopack.Environment.Environment.compartment_id_for_nearest_grid_point"]], "compile_db_recipe_data() (cellpack.autopack.dbrecipehandler.dbrecipeloader static method)": [[2, "cellpack.autopack.DBRecipeHandler.DBRecipeLoader.compile_db_recipe_data"]], "completemapping() (cellpack.autopack.trajectory.trajectory method)": [[2, "cellpack.autopack.trajectory.Trajectory.completeMapping"]], "computeexteriorvolume() (cellpack.autopack.basegrid.basegrid method)": [[2, "cellpack.autopack.BaseGrid.BaseGrid.computeExteriorVolume"]], "computegridnumberofpoint() (cellpack.autopack.basegrid.basegrid method)": [[2, "cellpack.autopack.BaseGrid.BaseGrid.computeGridNumberOfPoint"]], "computevolume() (cellpack.autopack.basegrid.basegrid method)": [[2, "cellpack.autopack.BaseGrid.BaseGrid.computeVolume"]], "compute_volume_and_set_count() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.compute_volume_and_set_count"]], "contains_point() (cellpack.autopack.meshstore.meshstore method)": [[2, "cellpack.autopack.MeshStore.MeshStore.contains_point"]], "contains_points_mesh() (cellpack.autopack.meshstore.meshstore method)": [[2, "cellpack.autopack.MeshStore.MeshStore.contains_points_mesh"]], "convertpickletotext() (cellpack.autopack.environment.environment class method)": [[2, "cellpack.autopack.Environment.Environment.convertPickleToText"]], "convert_db_shortname_to_url() (in module cellpack.autopack)": [[2, "cellpack.autopack.convert_db_shortname_to_url"]], "convert_positions_in_representation() (cellpack.autopack.dbrecipehandler.objectdoc static method)": [[2, "cellpack.autopack.DBRecipeHandler.ObjectDoc.convert_positions_in_representation"]], "convert_representation() (cellpack.autopack.dbrecipehandler.objectdoc static method)": [[2, "cellpack.autopack.DBRecipeHandler.ObjectDoc.convert_representation"]], "correlation() (cellpack.autopack.analysis.analysis method)": [[2, 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method)": [[2, "cellpack.autopack.FirebaseHandler.FirebaseHandler.create_path"]], "create_presigned_url() (cellpack.autopack.awshandler.awshandler method)": [[2, "cellpack.autopack.AWSHandler.AWSHandler.create_presigned_url"]], "create_rbnode() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.create_rbnode"]], "create_report() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.create_report"]], "create_sphere() (cellpack.autopack.meshstore.meshstore method)": [[2, "cellpack.autopack.MeshStore.MeshStore.create_sphere"]], "create_sphere_data() (cellpack.autopack.meshstore.meshstore method)": [[2, "cellpack.autopack.MeshStore.MeshStore.create_sphere_data"]], "create_timestamp() (cellpack.autopack.firebasehandler.firebasehandler static method)": [[2, "cellpack.autopack.FirebaseHandler.FirebaseHandler.create_timestamp"]], "create_voxelization() (cellpack.autopack.compartment.compartment method)": [[2, 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"cellpack.autopack.Graphics.AutopackViewer.displayCompartment"]], "displaycompartmentpoints() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.displayCompartmentPoints"]], "displaycompartments() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.displayCompartments"]], "displaycompartmentsingredients() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.displayCompartmentsIngredients"]], "displaycompartmentspoints() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.displayCompartmentsPoints"]], "displaycytoplasmingredients() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.displayCytoplasmIngredients"]], "displaydistance() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.displayDistance"]], "displaydistance() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.displayDistance"]], "displaydistancecube() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.displayDistanceCube"]], "displaydistanceplane() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.displayDistancePlane"]], "displayenv() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.displayEnv"]], "displayfill() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.displayFill"]], "displayfillbox() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.displayFillBox"]], "displayfreepoints() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.displayFreePoints"]], "displayfreepointsasps() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.displayFreePointsAsPS"]], "displaygradient() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.displayGradient"]], "displayingrcylinders() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.displayIngrCylinders"]], "displayingrgrow() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.displayIngrGrow"]], "displayingrgrows() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.displayIngrGrows"]], "displayingrmesh() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.displayIngrMesh"]], "displayingrresults() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.displayIngrResults"]], "displayingrspheres() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.displayIngrSpheres"]], "displayingredients() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.displayIngredients"]], "displayinstancesingredient() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.displayInstancesIngredient"]], "displayleafoctree() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.displayLeafOctree"]], "displayoctree() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.displayOctree"]], "displayoctreeleaf() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.displayOctreeLeaf"]], "displayonenodeoctree() (cellpack.autopack.graphics.autopackviewer method)": [[2, 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method)": [[2, "cellpack.autopack.FirebaseHandler.FirebaseHandler.doc_id"]], "doc_to_dict() (cellpack.autopack.firebasehandler.firebasehandler static method)": [[2, "cellpack.autopack.FirebaseHandler.FirebaseHandler.doc_to_dict"]], "doloop() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.doloop"]], "dot() (in module cellpack.autopack.ray)": [[2, "cellpack.autopack.ray.dot"]], "download_file() (in module cellpack.autopack)": [[2, "cellpack.autopack.download_file"]], "droponeingr() (cellpack.autopack.environment.environment class method)": [[2, "cellpack.autopack.Environment.Environment.dropOneIngr"]], "droponeingrjson() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.dropOneIngrJson"]], "dspmesh() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.dspMesh"]], "dspsph() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.dspSph"]], "expand_object_using_key() (in module cellpack.autopack.utils)": [[2, "cellpack.autopack.utils.expand_object_using_key"]], "exportasindexedmeshs() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.exportAsIndexedMeshs"]], "exportingredient() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.exportIngredient"]], "exportrecipeingredients() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.exportRecipeIngredients"]], "exporttobd_box() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.exportToBD_BOX"]], "exporttoreaddy() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.exportToReaDDy"]], "exporttotem() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.exportToTEM"]], "exporttotem_sim() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.exportToTEM_SIM"]], "extendgridarrays() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.extendGridArrays"]], "extend_bounding_box_for_compartments() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.extend_bounding_box_for_compartments"]], "extractmeshcomponent() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.extractMeshComponent"]], "f_dot_product() (in module cellpack.autopack.ray)": [[2, "cellpack.autopack.ray.f_dot_product"]], "f_ray_intersect_polyhedron() (in module cellpack.autopack.ray)": [[2, "cellpack.autopack.ray.f_ray_intersect_polyhedron"]], "filter_surface_pts_to_fill_box() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.filter_surface_pts_to_fill_box"]], "findbranch() (cellpack.autopack.octree.octree method)": [[2, "cellpack.autopack.octree.Octree.findBranch"]], "findpointscenter() (in module cellpack.autopack.ray)": [[2, "cellpack.autopack.ray.findPointsCenter"]], "findposition() (cellpack.autopack.octree.octree method)": [[2, "cellpack.autopack.octree.Octree.findPosition"]], "find_nearest() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.find_nearest"]], "finishwithwater() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.finishWithWater"]], "fixonepath() (in module cellpack.autopack)": [[2, "cellpack.autopack.fixOnePath"]], "fixpath() (in module cellpack.autopack)": [[2, "cellpack.autopack.fixPath"]], "flush() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.flush"]], "format_color() (cellpack.autopack.plotly_result.plotlyanalysis static method)": [[2, "cellpack.autopack.plotly_result.PlotlyAnalysis.format_color"]], "gatherresult() (in module cellpack.autopack.ioutils)": [[2, "cellpack.autopack.IOutils.gatherResult"]], "generalapply() (cellpack.autopack.trajectory.trajectory method)": [[2, "cellpack.autopack.trajectory.Trajectory.generalApply"]], "get() (cellpack.autopack.randomrot.randomrot method)": [[2, "cellpack.autopack.randomRot.RandomRot.get"]], "getactiveing() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.getActiveIng"]], "getallposrot() (in module cellpack.autopack.ioutils)": [[2, "cellpack.autopack.IOutils.getAllPosRot"]], "getareashell() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.getAreaShell"]], "getbinaryweighted() (cellpack.autopack.gradient.gradient method)": [[2, "cellpack.autopack.Gradient.Gradient.getBinaryWeighted"]], "getboundary() (cellpack.autopack.geometrytools.geometrytools method)": [[2, "cellpack.autopack.GeometryTools.GeometryTools.getBoundary"]], "getboundingbox() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.getBoundingBox"]], "getcenter() (cellpack.autopack.basegrid.basegrid method)": [[2, "cellpack.autopack.BaseGrid.BaseGrid.getCenter"]], "getcenter() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.getCenter"]], "getclosestdistance() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.getClosestDistance"]], "getclosestfreegridpoint() (cellpack.autopack.basegrid.basegrid method)": [[2, "cellpack.autopack.BaseGrid.BaseGrid.getClosestFreeGridPoint"]], "getclosestgridpoint() (cellpack.autopack.basegrid.basegrid method)": [[2, "cellpack.autopack.BaseGrid.BaseGrid.getClosestGridPoint"]], "getdiagonal() (cellpack.autopack.basegrid.basegrid method)": [[2, "cellpack.autopack.BaseGrid.BaseGrid.getDiagonal"]], "getdistancefrom() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.getDistanceFrom"]], "getfacenormals() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.getFaceNormals"]], "getfacesnfromv() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.getFacesNfromV"]], "getforwweight() (cellpack.autopack.gradient.gradient method)": [[2, "cellpack.autopack.Gradient.Gradient.getForwWeight"]], "gethaltonunique() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.getHaltonUnique"]], "getijk() (cellpack.autopack.basegrid.basegrid method)": [[2, "cellpack.autopack.BaseGrid.BaseGrid.getIJK"]], "getijk() (cellpack.autopack.grid.grid method)": [[2, "cellpack.autopack.Grid.Grid.getIJK"]], "getindex() (cellpack.autopack.binvox_rw.voxels method)": [[2, "cellpack.autopack.binvox_rw.Voxels.getIndex"]], "getindexdata() (cellpack.autopack.binvox_rw.voxels method)": [[2, "cellpack.autopack.binvox_rw.Voxels.getIndexData"]], "getingrfromnameinrecipe() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.getIngrFromNameInRecipe"]], "getingredientinstancepos() (cellpack.autopack.trajectory.trajectory method)": [[2, "cellpack.autopack.trajectory.Trajectory.getIngredientInstancePos"]], "getinterpolatednormal() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.getInterpolatedNormal"]], "getlinearweighted() (cellpack.autopack.gradient.gradient method)": [[2, "cellpack.autopack.Gradient.Gradient.getLinearWeighted"]], "getmaxweight() (cellpack.autopack.gradient.gradient method)": [[2, "cellpack.autopack.Gradient.Gradient.getMaxWeight"]], "getmesh() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.getMesh"]], "getminmaxproteinsize() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.getMinMaxProteinSize"]], "getminmaxproteinsize() (cellpack.autopack.recipe.recipe method)": [[2, "cellpack.autopack.Recipe.Recipe.getMinMaxProteinSize"]], "getminweight() (cellpack.autopack.gradient.gradient method)": [[2, "cellpack.autopack.Gradient.Gradient.getMinWeight"]], "getnbgridpoints() (cellpack.autopack.basegrid.haltongrid method)": [[2, "cellpack.autopack.BaseGrid.HaltonGrid.getNBgridPoints"]], "getold() (cellpack.autopack.randomrot.randomrot method)": [[2, "cellpack.autopack.randomRot.RandomRot.getOld"]], "getoneingr() (cellpack.autopack.environment.environment class method)": [[2, "cellpack.autopack.Environment.Environment.getOneIngr"]], "getoneingrjson() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.getOneIngrJson"]], "getpointfrom3d() (cellpack.autopack.basegrid.basegrid method)": [[2, "cellpack.autopack.BaseGrid.BaseGrid.getPointFrom3D"]], "getpointfrom3d() (cellpack.autopack.basegrid.haltongrid method)": [[2, "cellpack.autopack.BaseGrid.HaltonGrid.getPointFrom3D"]], "getpointtodrop() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.getPointToDrop"]], "getpointsincube() (cellpack.autopack.basegrid.basegrid method)": [[2, "cellpack.autopack.BaseGrid.BaseGrid.getPointsInCube"]], "getpointsincubefillbb() (cellpack.autopack.basegrid.basegrid method)": [[2, "cellpack.autopack.BaseGrid.BaseGrid.getPointsInCubeFillBB"]], "getpointsinsphere() (cellpack.autopack.basegrid.basegrid method)": [[2, "cellpack.autopack.BaseGrid.BaseGrid.getPointsInSphere"]], "getposat() (cellpack.autopack.trajectory.dcdtrajectory method)": [[2, "cellpack.autopack.trajectory.dcdTrajectory.getPosAt"]], "getposat() (cellpack.autopack.trajectory.molbtrajectory method)": [[2, "cellpack.autopack.trajectory.molbTrajectory.getPosAt"]], "getposat() (cellpack.autopack.trajectory.xyztrajectory method)": [[2, "cellpack.autopack.trajectory.xyzTrajectory.getPosAt"]], "getposline() (cellpack.autopack.trajectory.xyztrajectory method)": [[2, "cellpack.autopack.trajectory.xyzTrajectory.getPosLine"]], "getpositionperidocity() (cellpack.autopack.basegrid.basegrid method)": [[2, "cellpack.autopack.BaseGrid.BaseGrid.getPositionPeridocity"]], "getpositionsfromobject() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.getPositionsFromObject"]], "getpositionsfromresfile() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.getPositionsFromResFile"]], "getradius() (cellpack.autopack.basegrid.basegrid method)": [[2, "cellpack.autopack.BaseGrid.BaseGrid.getRadius"]], "getradius() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.getRadius"]], "getrndweighted() (cellpack.autopack.gradient.gradient method)": [[2, "cellpack.autopack.Gradient.Gradient.getRndWeighted"]], "getrottransrb() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.getRotTransRB"]], "getscale() (cellpack.autopack.basegrid.haltongrid method)": [[2, "cellpack.autopack.BaseGrid.HaltonGrid.getScale"]], "getsizexyz() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.getSizeXYZ"]], "getsortedactiveingredients() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.getSortedActiveIngredients"]], "getstringvalueoptions() (in module cellpack.autopack.ioutils)": [[2, "cellpack.autopack.IOutils.getStringValueOptions"]], "getsubweighted() (cellpack.autopack.gradient.gradient method)": [[2, "cellpack.autopack.Gradient.Gradient.getSubWeighted"]], "getsurfaceinnerpoints() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.getSurfaceInnerPoints"]], "getsurfaceinnerpoints_kevin() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.getSurfaceInnerPoints_kevin"]], "getsurfaceinnerpoints_sdf() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.getSurfaceInnerPoints_sdf"]], "getsurfaceinnerpoints_sdf_interpolate() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.getSurfaceInnerPoints_sdf_interpolate"]], "getsurfacepoint() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.getSurfacePoint"]], "gettotalnbobject() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.getTotalNbObject"]], "getvnfromf() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.getVNfromF"]], "getvertexnormals() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.getVertexNormals"]], "getvolumeshell() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.getVolumeShell"]], "get_all_distances() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.get_all_distances"]], "get_attributes_to_update() (cellpack.autopack.environment.environment static method)": [[2, "cellpack.autopack.Environment.Environment.get_attributes_to_update"]], "get_aws_object_key() (cellpack.autopack.awshandler.awshandler method)": [[2, "cellpack.autopack.AWSHandler.AWSHandler.get_aws_object_key"]], "get_bbox() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.get_bbox"]], "get_bounding_box_limits() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.get_bounding_box_limits"]], "get_cache_location() (in module cellpack.autopack)": [[2, "cellpack.autopack.get_cache_location"]], "get_center() (cellpack.autopack.gradient.gradient method)": [[2, "cellpack.autopack.Gradient.Gradient.get_center"]], "get_centroid() (cellpack.autopack.meshstore.meshstore method)": [[2, "cellpack.autopack.MeshStore.MeshStore.get_centroid"]], "get_closest_ingredients() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.get_closest_ingredients"]], "get_collada_material() (cellpack.autopack.meshstore.meshstore static method)": [[2, "cellpack.autopack.MeshStore.MeshStore.get_collada_material"]], "get_collection_id_from_path() (cellpack.autopack.firebasehandler.firebasehandler static method)": [[2, "cellpack.autopack.FirebaseHandler.FirebaseHandler.get_collection_id_from_path"]], "get_compartment_object_by_name() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.get_compartment_object_by_name"]], "get_dev_creds() (cellpack.autopack.firebasehandler.firebasehandler static method)": [[2, "cellpack.autopack.FirebaseHandler.FirebaseHandler.get_dev_creds"]], "get_dict_from_glob() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.get_dict_from_glob"]], "get_distance() (in module cellpack.autopack.utils)": [[2, "cellpack.autopack.utils.get_distance"]], "get_distances() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.get_distances"]], "get_distances_and_angles() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.get_distances_and_angles"]], "get_distances_from_point() (in module cellpack.autopack.utils)": [[2, "cellpack.autopack.utils.get_distances_from_point"]], "get_doc_by_id() (cellpack.autopack.firebasehandler.firebasehandler method)": [[2, "cellpack.autopack.FirebaseHandler.FirebaseHandler.get_doc_by_id"]], "get_doc_by_name() (cellpack.autopack.firebasehandler.firebasehandler method)": [[2, "cellpack.autopack.FirebaseHandler.FirebaseHandler.get_doc_by_name"]], "get_doc_by_ref() (cellpack.autopack.firebasehandler.firebasehandler method)": [[2, "cellpack.autopack.FirebaseHandler.FirebaseHandler.get_doc_by_ref"]], "get_dpad() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.get_dpad"]], "get_gauss_weights() (cellpack.autopack.gradient.gradient method)": [[2, "cellpack.autopack.Gradient.Gradient.get_gauss_weights"]], "get_ingredient_angles() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.get_ingredient_angles"]], "get_ingredient_by_name() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.get_ingredient_by_name"]], "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"]], "get_ingredient_radii() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.get_ingredient_radii"]], "get_ingredients_in_tree() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.get_ingredients_in_tree"]], "get_list_of_dims() (cellpack.autopack.analysis.analysis static method)": [[2, "cellpack.autopack.Analysis.Analysis.get_list_of_dims"]], "get_local_file_location() (in module cellpack.autopack)": [[2, "cellpack.autopack.get_local_file_location"]], "get_max_value_from_distribution() (in module cellpack.autopack.utils)": [[2, "cellpack.autopack.utils.get_max_value_from_distribution"]], "get_mesh() (cellpack.autopack.meshstore.meshstore method)": [[2, "cellpack.autopack.MeshStore.MeshStore.get_mesh"]], "get_mesh_filepath_and_extension() (cellpack.autopack.meshstore.meshstore static method)": [[2, "cellpack.autopack.MeshStore.MeshStore.get_mesh_filepath_and_extension"]], "get_midpoint() (cellpack.autopack.meshstore.meshstore static method)": [[2, "cellpack.autopack.MeshStore.MeshStore.get_midpoint"]], "get_min_value_from_distribution() (in module cellpack.autopack.utils)": [[2, "cellpack.autopack.utils.get_min_value_from_distribution"]], "get_minimum_expected_distance_from_recipe() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.get_minimum_expected_distance_from_recipe"]], "get_normal() (cellpack.autopack.meshstore.meshstore method)": [[2, "cellpack.autopack.MeshStore.MeshStore.get_normal"]], "get_normal_for_point() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.get_normal_for_point"]], "get_normalized_values() (cellpack.autopack.gradient.gradient method)": [[2, "cellpack.autopack.Gradient.Gradient.get_normalized_values"]], "get_nsphere() (cellpack.autopack.meshstore.meshstore method)": [[2, "cellpack.autopack.MeshStore.MeshStore.get_nsphere"]], "get_number_of_ingredients_packed() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.get_number_of_ingredients_packed"]], "get_obj_dict() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.get_obj_dict"]], "get_object() (cellpack.autopack.meshstore.meshstore method)": [[2, "cellpack.autopack.MeshStore.MeshStore.get_object"]], "get_packed_minimum_distance() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.get_packed_minimum_distance"]], "get_paired_key() (in module cellpack.autopack.utils)": [[2, "cellpack.autopack.utils.get_paired_key"]], "get_parametrized_representation() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.get_parametrized_representation"]], "get_partner_pair_dict() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.get_partner_pair_dict"]], "get_path_from_ref() (cellpack.autopack.firebasehandler.firebasehandler static method)": [[2, "cellpack.autopack.FirebaseHandler.FirebaseHandler.get_path_from_ref"]], "get_rb_model() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.get_rb_model"]], "get_rectangle_cercle_area() (cellpack.autopack.geometrytools.geometrytools method)": [[2, "cellpack.autopack.GeometryTools.GeometryTools.get_rectangle_cercle_area"]], "get_reference_data() (cellpack.autopack.dbrecipehandler.compositiondoc static method)": [[2, "cellpack.autopack.DBRecipeHandler.CompositionDoc.get_reference_data"]], "get_reference_in_obj() (cellpack.autopack.dbrecipehandler.compositiondoc static method)": [[2, "cellpack.autopack.DBRecipeHandler.CompositionDoc.get_reference_in_obj"]], "get_scaled_distances_between_surfaces() (cellpack.autopack.meshstore.meshstore method)": [[2, "cellpack.autopack.MeshStore.MeshStore.get_scaled_distances_between_surfaces"]], "get_seed_list() (in module cellpack.autopack.utils)": [[2, "cellpack.autopack.utils.get_seed_list"]], "get_size_of_bounding_box() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.get_size_of_bounding_box"]], "get_smallest_radius() (cellpack.autopack.meshstore.meshstore method)": [[2, "cellpack.autopack.MeshStore.MeshStore.get_smallest_radius"]], "get_staging_creds() (cellpack.autopack.firebasehandler.firebasehandler static method)": [[2, "cellpack.autopack.FirebaseHandler.FirebaseHandler.get_staging_creds"]], "get_username() (cellpack.autopack.firebasehandler.firebasehandler static method)": [[2, "cellpack.autopack.FirebaseHandler.FirebaseHandler.get_username"]], "get_value() (cellpack.autopack.firebasehandler.firebasehandler method)": [[2, "cellpack.autopack.FirebaseHandler.FirebaseHandler.get_value"]], "get_value_from_distribution() (in module cellpack.autopack.utils)": [[2, "cellpack.autopack.utils.get_value_from_distribution"]], "get_xyz_dict_from_all_pos_dict() (cellpack.autopack.analysis.analysis static method)": [[2, "cellpack.autopack.Analysis.Analysis.get_xyz_dict_from_all_pos_dict"]], "grab() (cellpack.autopack.ioutils.grabresult method)": [[2, "cellpack.autopack.IOutils.GrabResult.grab"]], "grabresultfromjson() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.grabResultFromJSON"]], "grabresultfromtxt() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.grabResultFromTXT"]], "gradient_list_to_dict() (cellpack.autopack.dbrecipehandler.compositiondoc static method)": [[2, "cellpack.autopack.DBRecipeHandler.CompositionDoc.gradient_list_to_dict"]], "gridpoint (class in cellpack.autopack.basegrid)": [[2, "cellpack.autopack.BaseGrid.gridPoint"]], "halton() (in module cellpack.autopack.ldsequence)": [[2, "cellpack.autopack.ldSequence.halton"]], "halton2() (in module cellpack.autopack.ldsequence)": [[2, "cellpack.autopack.ldSequence.halton2"]], "halton3() (in module cellpack.autopack.ldsequence)": [[2, "cellpack.autopack.ldSequence.halton3"]], "halton_sequence() (in module cellpack.autopack.ldsequence)": [[2, "cellpack.autopack.ldSequence.halton_sequence"]], "haltonterm() (in module cellpack.autopack.ldsequence)": [[2, "cellpack.autopack.ldSequence.haltonterm"]], "hideingrprimitive() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.hideIngrPrimitive"]], "histogram() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.histogram"]], "ijktoindex() (cellpack.autopack.binvox_rw.voxels method)": [[2, "cellpack.autopack.binvox_rw.Voxels.ijkToIndex"]], "ijktoxyz() (cellpack.autopack.binvox_rw.voxels method)": [[2, "cellpack.autopack.binvox_rw.Voxels.ijkToxyz"]], "inbox() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.inBox"]], "ingrid() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.inGrid"]], "inc() (cellpack.autopack.ldsequence.chaltonsequence3 method)": [[2, "cellpack.autopack.ldSequence.cHaltonSequence3.inc"]], "includeingrrecipe() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.includeIngrRecipe"]], "includeingrrecipes() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.includeIngrRecipes"]], "includeingredientrecipe() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.includeIngredientRecipe"]], "ingrjsonnode() (cellpack.autopack.ioutils.ioingredienttool method)": [[2, "cellpack.autopack.IOutils.IOingredientTool.ingrJsonNode"]], "ingrpythonnode() (cellpack.autopack.ioutils.ioingredienttool method)": [[2, "cellpack.autopack.IOutils.IOingredientTool.ingrPythonNode"]], "ingredient_compare0() (in module cellpack.autopack.utils)": [[2, "cellpack.autopack.utils.ingredient_compare0"]], "ingredient_compare1() (in module cellpack.autopack.utils)": [[2, "cellpack.autopack.utils.ingredient_compare1"]], "ingredient_compare2() (in module cellpack.autopack.utils)": [[2, "cellpack.autopack.utils.ingredient_compare2"]], "initialize_shape() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.initialize_shape"]], "insertnode() (cellpack.autopack.octree.octree method)": [[2, "cellpack.autopack.octree.Octree.insertNode"]], "is_db_dict() (cellpack.autopack.dbrecipehandler.datadoc static method)": [[2, "cellpack.autopack.DBRecipeHandler.DataDoc.is_db_dict"]], "is_firebase_obj() (cellpack.autopack.firebasehandler.firebasehandler static method)": [[2, "cellpack.autopack.FirebaseHandler.FirebaseHandler.is_firebase_obj"]], "is_full_url() (in module cellpack.autopack)": [[2, "cellpack.autopack.is_full_url"]], "is_key() (cellpack.autopack.dbrecipehandler.datadoc static method)": [[2, "cellpack.autopack.DBRecipeHandler.DataDoc.is_key"]], "is_key() (cellpack.autopack.recipe.recipe static method)": [[2, "cellpack.autopack.Recipe.Recipe.is_key"]], "is_nested_list() (cellpack.autopack.dbrecipehandler.datadoc static method)": [[2, "cellpack.autopack.DBRecipeHandler.DataDoc.is_nested_list"]], "is_obj() (cellpack.autopack.dbrecipehandler.datadoc static method)": [[2, "cellpack.autopack.DBRecipeHandler.DataDoc.is_obj"]], "is_point_inside_bb() (cellpack.autopack.basegrid.basegrid method)": [[2, "cellpack.autopack.BaseGrid.BaseGrid.is_point_inside_bb"]], "is_point_inside_mesh() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.is_point_inside_mesh"]], "is_reference() (cellpack.autopack.firebasehandler.firebasehandler static method)": [[2, "cellpack.autopack.FirebaseHandler.FirebaseHandler.is_reference"]], "is_remote_path() (in module cellpack.autopack)": [[2, "cellpack.autopack.is_remote_path"]], "is_two_d() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.is_two_d"]], "is_url_valid() (cellpack.autopack.awshandler.awshandler method)": [[2, "cellpack.autopack.AWSHandler.AWSHandler.is_url_valid"]], "linktraj() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.linkTraj"]], "loadfreepoint() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.loadFreePoint"]], "loadjson() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.loadJSON"]], "loadresult() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.loadResult"]], "load_json() (in module cellpack.autopack.ioutils)": [[2, "cellpack.autopack.IOutils.load_Json"]], "load_jsonstring() (in module cellpack.autopack.ioutils)": [[2, "cellpack.autopack.IOutils.load_JsonString"]], "load_mixedasjson() (in module cellpack.autopack.ioutils)": [[2, "cellpack.autopack.IOutils.load_MixedasJson"]], "load_asjson() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.load_asJson"]], "load_astxt() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.load_asTxt"]], "load_file() (in module cellpack.autopack)": [[2, "cellpack.autopack.load_file"]], "load_object_from_pickle() (in module cellpack.autopack.utils)": [[2, "cellpack.autopack.utils.load_object_from_pickle"]], "loopthroughingr() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.loopThroughIngr"]], "makeingrmapping() (cellpack.autopack.trajectory.trajectory method)": [[2, "cellpack.autopack.trajectory.Trajectory.makeIngrMapping"]], "makeingredient() (cellpack.autopack.ioutils.ioingredienttool method)": [[2, "cellpack.autopack.IOutils.IOingredientTool.makeIngredient"]], "makeingredientfromjson() (cellpack.autopack.ioutils.ioingredienttool method)": [[2, "cellpack.autopack.IOutils.IOingredientTool.makeIngredientFromJson"]], "makemarchingcube() (in module cellpack.autopack.ray)": [[2, "cellpack.autopack.ray.makeMarchingCube"]], "make_and_show_heatmap() (cellpack.autopack.plotly_result.plotlyanalysis method)": [[2, "cellpack.autopack.plotly_result.PlotlyAnalysis.make_and_show_heatmap"]], "make_directory_if_needed() (in module cellpack.autopack)": [[2, "cellpack.autopack.make_directory_if_needed"]], "make_grid_heatmap() (cellpack.autopack.plotly_result.plotlyanalysis method)": [[2, 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"cellpack.autopack.Graphics.AutopackViewer.showIngrPrimitive"]], "simpleplot() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.simpleplot"]], "slow_box_fill() (cellpack.autopack.basegrid.basegrid method)": [[2, "cellpack.autopack.BaseGrid.BaseGrid.slow_box_fill"]], "sort() (cellpack.autopack.recipe.recipe method)": [[2, "cellpack.autopack.Recipe.Recipe.sort"]], "sortingredient() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.sortIngredient"]], "sparse_to_dense() (in module cellpack.autopack.binvox_rw)": [[2, "cellpack.autopack.binvox_rw.sparse_to_dense"]], "static_id (cellpack.autopack.serializable.scompartment attribute)": [[2, "cellpack.autopack.Serializable.sCompartment.static_id"]], "static_id (cellpack.autopack.serializable.singredient attribute)": [[2, "cellpack.autopack.Serializable.sIngredient.static_id"]], "static_id (cellpack.autopack.serializable.singredientfiber attribute)": [[2, 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"cellpack.autopack.Graphics.AutopackViewer.timeFunction"]], "tobinary() (in module cellpack.autopack.ioutils)": [[2, "cellpack.autopack.IOutils.toBinary"]], "to_json() (cellpack.autopack.serializable.scompartment method)": [[2, "cellpack.autopack.Serializable.sCompartment.to_JSON"]], "to_json() (cellpack.autopack.serializable.singredient method)": [[2, "cellpack.autopack.Serializable.sIngredient.to_JSON"]], "to_json() (cellpack.autopack.serializable.singredientfiber method)": [[2, "cellpack.autopack.Serializable.sIngredientFiber.to_JSON"]], "to_json() (cellpack.autopack.serializable.singredientgroup method)": [[2, "cellpack.autopack.Serializable.sIngredientGroup.to_JSON"]], "toggleorganelmatr() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.toggleOrganelMatr"]], "toggleorganelmesh() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.toggleOrganelMesh"]], "toggleorganelsurf() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.toggleOrganelSurf"]], "traj_type (cellpack.autopack.trajectory.trajectory attribute)": [[2, "cellpack.autopack.trajectory.Trajectory.traj_type"]], "traj_type (cellpack.autopack.trajectory.dcdtrajectory attribute)": [[2, "cellpack.autopack.trajectory.dcdTrajectory.traj_type"]], "traj_type (cellpack.autopack.trajectory.molbtrajectory attribute)": [[2, "cellpack.autopack.trajectory.molbTrajectory.traj_type"]], "traj_type (cellpack.autopack.trajectory.xyztrajectory attribute)": [[2, "cellpack.autopack.trajectory.xyzTrajectory.traj_type"]], "transformmesh() (cellpack.autopack.compartment.compartment method)": [[2, "cellpack.autopack.Compartment.Compartment.transformMesh"]], "transformpoints2d() (cellpack.autopack.plotly_result.plotlyanalysis method)": [[2, "cellpack.autopack.plotly_result.PlotlyAnalysis.transformPoints2D"]], "undspmesh() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.undspMesh"]], "undspsph() (cellpack.autopack.graphics.autopackviewer method)": [[2, "cellpack.autopack.Graphics.AutopackViewer.undspSph"]], "unlinktraj() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.unlinkTraj"]], "updatedistances() (cellpack.autopack.basegrid.basegrid static method)": [[2, "cellpack.autopack.BaseGrid.BaseGrid.updateDistances"]], "updatepath() (in module cellpack.autopack)": [[2, "cellpack.autopack.updatePath"]], "updatepathjson() (in module cellpack.autopack)": [[2, "cellpack.autopack.updatePathJSON"]], "updatepositionsradii() (in module cellpack.autopack.ioutils)": [[2, "cellpack.autopack.IOutils.updatePositionsRadii"]], "updaterecipavailablexml() (in module cellpack.autopack)": [[2, "cellpack.autopack.updateRecipAvailableXML"]], "updatereplacepath() (in module cellpack.autopack)": [[2, "cellpack.autopack.updateReplacePath"]], "update_after_place() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.update_after_place"]], "update_crosswise_distances() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.update_crosswise_distances"]], "update_distance_distribution_dictionaries() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.update_distance_distribution_dictionaries"]], "update_doc() (cellpack.autopack.firebasehandler.firebasehandler method)": [[2, "cellpack.autopack.FirebaseHandler.FirebaseHandler.update_doc"]], "update_elements_in_array() (cellpack.autopack.firebasehandler.firebasehandler static method)": [[2, "cellpack.autopack.FirebaseHandler.FirebaseHandler.update_elements_in_array"]], "update_largest_smallest_size() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.update_largest_smallest_size"]], "update_or_create() (cellpack.autopack.firebasehandler.firebasehandler method)": [[2, "cellpack.autopack.FirebaseHandler.FirebaseHandler.update_or_create"]], "update_reference() (cellpack.autopack.dbrecipehandler.compositiondoc static method)": [[2, "cellpack.autopack.DBRecipeHandler.CompositionDoc.update_reference"]], "update_reference_on_doc() (cellpack.autopack.firebasehandler.firebasehandler static method)": [[2, "cellpack.autopack.FirebaseHandler.FirebaseHandler.update_reference_on_doc"]], "update_title() (cellpack.autopack.plotly_result.plotlyanalysis method)": [[2, "cellpack.autopack.plotly_result.PlotlyAnalysis.update_title"]], "update_variable_ingredient_attributes() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.update_variable_ingredient_attributes"]], "upload_collections() (cellpack.autopack.dbrecipehandler.dbuploader method)": [[2, "cellpack.autopack.DBRecipeHandler.DBUploader.upload_collections"]], "upload_compositions() (cellpack.autopack.dbrecipehandler.dbuploader method)": [[2, "cellpack.autopack.DBRecipeHandler.DBUploader.upload_compositions"]], "upload_data() (cellpack.autopack.dbrecipehandler.dbuploader method)": [[2, "cellpack.autopack.DBRecipeHandler.DBUploader.upload_data"]], "upload_doc() (cellpack.autopack.firebasehandler.firebasehandler method)": [[2, "cellpack.autopack.FirebaseHandler.FirebaseHandler.upload_doc"]], "upload_file() (cellpack.autopack.awshandler.awshandler method)": [[2, "cellpack.autopack.AWSHandler.AWSHandler.upload_file"]], "upload_gradients() (cellpack.autopack.dbrecipehandler.dbuploader method)": [[2, "cellpack.autopack.DBRecipeHandler.DBUploader.upload_gradients"]], "upload_objects() (cellpack.autopack.dbrecipehandler.dbuploader method)": [[2, "cellpack.autopack.DBRecipeHandler.DBUploader.upload_objects"]], "upload_recipe() (cellpack.autopack.dbrecipehandler.dbuploader method)": [[2, "cellpack.autopack.DBRecipeHandler.DBUploader.upload_recipe"]], "upload_result_metadata() (cellpack.autopack.dbrecipehandler.dbuploader method)": [[2, "cellpack.autopack.DBRecipeHandler.DBUploader.upload_result_metadata"]], "upload_single_object() (cellpack.autopack.dbrecipehandler.dbuploader method)": [[2, "cellpack.autopack.DBRecipeHandler.DBUploader.upload_single_object"]], "url_exists() (in module cellpack.autopack)": [[2, "cellpack.autopack.url_exists"]], "validate_input_recipe_path() (cellpack.autopack.dbrecipehandler.dbrecipeloader method)": [[2, "cellpack.autopack.DBRecipeHandler.DBRecipeLoader.validate_input_recipe_path"]], "vcross() (in module cellpack.autopack.ray)": [[2, "cellpack.autopack.ray.vcross"]], "vdiff() (in module cellpack.autopack.ray)": [[2, "cellpack.autopack.ray.vdiff"]], "vlen() (in module cellpack.autopack.ray)": [[2, "cellpack.autopack.ray.vlen"]], "vnorm() (in module cellpack.autopack.ray)": [[2, "cellpack.autopack.ray.vnorm"]], "which_db() (cellpack.autopack.firebasehandler.firebasehandler static method)": [[2, "cellpack.autopack.FirebaseHandler.FirebaseHandler.which_db"]], "write() (cellpack.autopack.binvox_rw.voxels method)": [[2, "cellpack.autopack.binvox_rw.Voxels.write"]], "write() (in module cellpack.autopack.binvox_rw)": [[2, "cellpack.autopack.binvox_rw.write"]], "writearraystofile() (cellpack.autopack.environment.environment method)": [[2, "cellpack.autopack.Environment.Environment.writeArraysToFile"]], "writejson() (cellpack.autopack.analysis.analysis method)": [[2, "cellpack.autopack.Analysis.Analysis.writeJSON"]], "write_creds_path() (cellpack.autopack.firebasehandler.firebasehandler static method)": [[2, "cellpack.autopack.FirebaseHandler.FirebaseHandler.write_creds_path"]], "write_username_to_creds() (in module cellpack.autopack)": [[2, "cellpack.autopack.write_username_to_creds"]], "xyztoijk() (cellpack.autopack.binvox_rw.voxels method)": [[2, "cellpack.autopack.binvox_rw.Voxels.xyzToijk"]], "xyztrajectory (class in cellpack.autopack.trajectory)": [[2, "cellpack.autopack.trajectory.xyzTrajectory"]], "arguments (cellpack.autopack.ingredient.ingredient.ingredient attribute)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.ARGUMENTS"]], "arguments (cellpack.autopack.ingredient.grow.growingredient attribute)": [[3, "cellpack.autopack.ingredient.grow.GrowIngredient.ARGUMENTS"]], "actiningredient (class in cellpack.autopack.ingredient.grow)": [[3, "cellpack.autopack.ingredient.grow.ActinIngredient"]], "agent (class in cellpack.autopack.ingredient.agent)": [[3, "cellpack.autopack.ingredient.agent.Agent"]], "applymatrix() (in module cellpack.autopack.ingredient.utils)": [[3, "cellpack.autopack.ingredient.utils.ApplyMatrix"]], "decomposemesh() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.DecomposeMesh"]], "distributionoptions (class in cellpack.autopack.ingredient.ingredient)": [[3, "cellpack.autopack.ingredient.Ingredient.DistributionOptions"]], "distributiontypes (class in cellpack.autopack.ingredient.ingredient)": [[3, "cellpack.autopack.ingredient.Ingredient.DistributionTypes"]], "growingredient (class in cellpack.autopack.ingredient.grow)": [[3, "cellpack.autopack.ingredient.grow.GrowIngredient"]], "ingredient (class in cellpack.autopack.ingredient.ingredient)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient"]], "ingredientinstancedrop (class in cellpack.autopack.ingredient.ingredient)": [[3, "cellpack.autopack.ingredient.Ingredient.IngredientInstanceDrop"]], "list (cellpack.autopack.ingredient.ingredient.distributiontypes attribute)": [[3, "cellpack.autopack.ingredient.Ingredient.DistributionTypes.LIST"]], "list_values (cellpack.autopack.ingredient.ingredient.distributionoptions attribute)": [[3, "cellpack.autopack.ingredient.Ingredient.DistributionOptions.LIST_VALUES"]], "max (cellpack.autopack.ingredient.ingredient.distributionoptions attribute)": [[3, "cellpack.autopack.ingredient.Ingredient.DistributionOptions.MAX"]], "mean (cellpack.autopack.ingredient.ingredient.distributionoptions attribute)": [[3, "cellpack.autopack.ingredient.Ingredient.DistributionOptions.MEAN"]], "min (cellpack.autopack.ingredient.ingredient.distributionoptions attribute)": [[3, "cellpack.autopack.ingredient.Ingredient.DistributionOptions.MIN"]], "multicylindersingr (class in cellpack.autopack.ingredient.multi_cylinder)": [[3, "cellpack.autopack.ingredient.multi_cylinder.MultiCylindersIngr"]], "multisphereingr (class in cellpack.autopack.ingredient.multi_sphere)": [[3, "cellpack.autopack.ingredient.multi_sphere.MultiSphereIngr"]], "normal (cellpack.autopack.ingredient.ingredient.distributiontypes attribute)": [[3, "cellpack.autopack.ingredient.Ingredient.DistributionTypes.NORMAL"]], "std (cellpack.autopack.ingredient.ingredient.distributionoptions attribute)": [[3, "cellpack.autopack.ingredient.Ingredient.DistributionOptions.STD"]], "singlecubeingr (class in cellpack.autopack.ingredient.single_cube)": [[3, "cellpack.autopack.ingredient.single_cube.SingleCubeIngr"]], "singlecylinderingr (class in cellpack.autopack.ingredient.single_cylinder)": [[3, "cellpack.autopack.ingredient.single_cylinder.SingleCylinderIngr"]], "singlesphereingr (class in cellpack.autopack.ingredient.single_sphere)": [[3, "cellpack.autopack.ingredient.single_sphere.SingleSphereIngr"]], "uniform (cellpack.autopack.ingredient.ingredient.distributiontypes attribute)": [[3, "cellpack.autopack.ingredient.Ingredient.DistributionTypes.UNIFORM"]], "alignrotation() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.alignRotation"]], "apply_rotation() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.apply_rotation"]], "attempt_to_pack_at_grid_location() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.attempt_to_pack_at_grid_location"]], "buildmesh() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.buildMesh"]], "bullet_checkcollision_mp() (in module cellpack.autopack.ingredient.utils)": [[3, "cellpack.autopack.ingredient.utils.bullet_checkCollision_mp"]], "cellpack.autopack.ingredient": [[3, "module-cellpack.autopack.ingredient"]], "cellpack.autopack.ingredient.ingredient": [[3, "module-cellpack.autopack.ingredient.Ingredient"]], "cellpack.autopack.ingredient.agent": [[3, "module-cellpack.autopack.ingredient.agent"]], "cellpack.autopack.ingredient.grow": [[3, "module-cellpack.autopack.ingredient.grow"]], "cellpack.autopack.ingredient.multi_cylinder": [[3, "module-cellpack.autopack.ingredient.multi_cylinder"]], "cellpack.autopack.ingredient.multi_sphere": [[3, "module-cellpack.autopack.ingredient.multi_sphere"]], "cellpack.autopack.ingredient.single_cube": [[3, "module-cellpack.autopack.ingredient.single_cube"]], "cellpack.autopack.ingredient.single_cylinder": [[3, "module-cellpack.autopack.ingredient.single_cylinder"]], "cellpack.autopack.ingredient.single_sphere": [[3, "module-cellpack.autopack.ingredient.single_sphere"]], "cellpack.autopack.ingredient.utils": [[3, "module-cellpack.autopack.ingredient.utils"]], "checkcylcollisions() (cellpack.autopack.ingredient.multi_cylinder.multicylindersingr method)": [[3, "cellpack.autopack.ingredient.multi_cylinder.MultiCylindersIngr.checkCylCollisions"]], "checkcylcollisions() (cellpack.autopack.ingredient.single_cylinder.singlecylinderingr method)": [[3, "cellpack.autopack.ingredient.single_cylinder.SingleCylinderIngr.checkCylCollisions"]], "checkdistance() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.checkDistance"]], "checkifupdate() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.checkIfUpdate"]], "check_against_one_packed_ingr() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.check_against_one_packed_ingr"]], "close_partner_check() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.close_partner_check"]], "collides_with_compartment() (cellpack.autopack.ingredient.multi_cylinder.multicylindersingr method)": [[3, "cellpack.autopack.ingredient.multi_cylinder.MultiCylindersIngr.collides_with_compartment"]], "collides_with_compartment() (cellpack.autopack.ingredient.multi_sphere.multisphereingr method)": [[3, "cellpack.autopack.ingredient.multi_sphere.MultiSphereIngr.collides_with_compartment"]], "collides_with_compartment() (cellpack.autopack.ingredient.single_cube.singlecubeingr method)": [[3, "cellpack.autopack.ingredient.single_cube.SingleCubeIngr.collides_with_compartment"]], "collides_with_compartment() (cellpack.autopack.ingredient.single_cylinder.singlecylinderingr method)": [[3, "cellpack.autopack.ingredient.single_cylinder.SingleCylinderIngr.collides_with_compartment"]], "collides_with_compartment() (cellpack.autopack.ingredient.single_sphere.singlesphereingr method)": [[3, "cellpack.autopack.ingredient.single_sphere.SingleSphereIngr.collides_with_compartment"]], "collision_jitter() (cellpack.autopack.ingredient.multi_cylinder.multicylindersingr method)": [[3, "cellpack.autopack.ingredient.multi_cylinder.MultiCylindersIngr.collision_jitter"]], "collision_jitter() (cellpack.autopack.ingredient.multi_sphere.multisphereingr method)": [[3, "cellpack.autopack.ingredient.multi_sphere.MultiSphereIngr.collision_jitter"]], "collision_jitter() (cellpack.autopack.ingredient.single_cube.singlecubeingr method)": [[3, "cellpack.autopack.ingredient.single_cube.SingleCubeIngr.collision_jitter"]], "collision_jitter() (cellpack.autopack.ingredient.single_cylinder.singlecylinderingr method)": [[3, "cellpack.autopack.ingredient.single_cylinder.SingleCylinderIngr.collision_jitter"]], "collision_jitter() (cellpack.autopack.ingredient.single_sphere.singlesphereingr method)": [[3, "cellpack.autopack.ingredient.single_sphere.SingleSphereIngr.collision_jitter"]], "correctbb() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.correctBB"]], "create_circular_mask() (cellpack.autopack.ingredient.single_sphere.singlesphereingr static method)": [[3, "cellpack.autopack.ingredient.single_sphere.SingleSphereIngr.create_circular_mask"]], "create_voxelization() (cellpack.autopack.ingredient.single_sphere.singlesphereingr method)": [[3, "cellpack.autopack.ingredient.single_sphere.SingleSphereIngr.create_voxelization"]], "cube_surface_distance() (cellpack.autopack.ingredient.single_cube.singlecubeingr method)": [[3, "cellpack.autopack.ingredient.single_cube.SingleCubeIngr.cube_surface_distance"]], "deleteblist() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.deleteblist"]], "far_enough_from_surfaces() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.far_enough_from_surfaces"]], "getaxisrotation() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.getAxisRotation"]], "getbiasedrotation() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.getBiasedRotation"]], "getbigbb() (cellpack.autopack.ingredient.multi_cylinder.multicylindersingr method)": [[3, "cellpack.autopack.ingredient.multi_cylinder.MultiCylindersIngr.getBigBB"]], "getbigbb() (cellpack.autopack.ingredient.single_cylinder.singlecylinderingr method)": [[3, "cellpack.autopack.ingredient.single_cylinder.SingleCylinderIngr.getBigBB"]], "getdata() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.getData"]], "getdihedral() (in module cellpack.autopack.ingredient.utils)": [[3, "cellpack.autopack.ingredient.utils.getDihedral"]], "getencapsulatingradius() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.getEncapsulatingRadius"]], "getfirstpoint() (cellpack.autopack.ingredient.grow.growingredient method)": [[3, "cellpack.autopack.ingredient.grow.GrowIngredient.getFirstPoint"]], "getingredientsinbox() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.getIngredientsInBox"]], "getinterpolatedsphere() (cellpack.autopack.ingredient.grow.growingredient method)": [[3, "cellpack.autopack.ingredient.grow.GrowIngredient.getInterpolatedSphere"]], "getjtransrot() (cellpack.autopack.ingredient.grow.growingredient method)": [[3, "cellpack.autopack.ingredient.grow.GrowIngredient.getJtransRot"]], "getjtransrot_r() (cellpack.autopack.ingredient.grow.growingredient method)": [[3, "cellpack.autopack.ingredient.grow.GrowIngredient.getJtransRot_r"]], "getlistcompfrommask() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.getListCompFromMask"]], "getmaxjitter() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.getMaxJitter"]], "getmesh() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.getMesh"]], "getnextpoint() (cellpack.autopack.ingredient.grow.growingredient method)": [[3, "cellpack.autopack.ingredient.grow.GrowIngredient.getNextPoint"]], "getnextptindcyl() (cellpack.autopack.ingredient.grow.growingredient method)": [[3, "cellpack.autopack.ingredient.grow.GrowIngredient.getNextPtIndCyl"]], "getnormedvector() (in module cellpack.autopack.ingredient.utils)": [[3, "cellpack.autopack.ingredient.utils.getNormedVector"]], "getnormedvectorones() (in module cellpack.autopack.ingredient.utils)": [[3, "cellpack.autopack.ingredient.utils.getNormedVectorOnes"]], "getnormedvectoru() (in module cellpack.autopack.ingredient.utils)": [[3, "cellpack.autopack.ingredient.utils.getNormedVectorU"]], "getsubweighted() (cellpack.autopack.ingredient.agent.agent method)": [[3, "cellpack.autopack.ingredient.agent.Agent.getSubWeighted"]], "getv3() (cellpack.autopack.ingredient.grow.growingredient method)": [[3, "cellpack.autopack.ingredient.grow.GrowIngredient.getV3"]], "get_all_positions_to_check() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.get_all_positions_to_check"]], "get_alternate_position() (cellpack.autopack.ingredient.grow.growingredient method)": [[3, "cellpack.autopack.ingredient.grow.GrowIngredient.get_alternate_position"]], "get_alternate_position_p() (cellpack.autopack.ingredient.grow.growingredient method)": [[3, "cellpack.autopack.ingredient.grow.GrowIngredient.get_alternate_position_p"]], "get_compartment() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.get_compartment"]], "get_cuttoff_value() (cellpack.autopack.ingredient.ingredient.ingredient method)": [[3, "cellpack.autopack.ingredient.Ingredient.Ingredient.get_cuttoff_value"]], "get_cuttoff_value() (cellpack.autopack.ingredient.multi_cylinder.multicylindersingr method)": [[3, "cellpack.autopack.ingredient.multi_cylinder.MultiCylindersIngr.get_cuttoff_value"]], "get_cuttoff_value() (cellpack.autopack.ingredient.single_cylinder.singlecylinderingr method)": [[3, 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