Merge pull request #1 from insilichem/dev_output

Release 1.0.1

MANIFEST.in

@@ -7,5 +7,5 @@ recursive-include docs *
 recursive-include examples *
 recursive-include resources *
 recursive-include tests *include versioneer.py
-include gaudi/_version.py
+include gpath/_version.py
 include versioneer.py

README.rst

@@ -70,6 +70,19 @@ Features
 - Vina scoring function
 - Smoothness of the ligand movements
 
+.. image:: docs/data/new.jpeg
+    :align: left
+    :height: 30px
+    :alt: NEW!    
+Version 1.0.1 25th July 2019
+----------------------------
+
+- New ``summary.csv`` file in the output with score data of all the solutions.
+- New format for the ``.pdb`` files of the output that can be imported as a MD movie in UCSF Chimera.
+- New ``trajectory.pdb`` file in the output. For each solution, shows the trajectory of the ligand, taking its center as a reference.
+- Command to lauch the program is now ``gpath run`` instead of ``gaudi run`` to ensure compatibility with GaudiMM.
+- Similarity between solutions is calculated now at each generation, to avoid some cases where repeated or very similar solutions appeared, especially when using only clashes evaluation.
+
 Documentation and support
 -------------------------
 
@@ -89,6 +102,17 @@ GPathFinder and GaudiMM are licensed under the Apache License, Version 2.0. Chec
 History of versions
 -------------------
 
+- **v1.0.1:** 25th July 2019
+New ``summary.csv`` file in the output with score data of all the solutions.
+
+New format for the ``.pdb`` files of the output that can be imported as a MD movie in UCSF Chimera.
+
+New ``trajectory.pdb`` file in the output. For each solution, shows the trajectory of the ligand, taking its center as a reference.
+
+Command to lauch the program is now ``gpath run`` instead of `gaudi run` to ensure compatibility with GaudiMM.
+
+Bug fix: similarity between solutions is calculated now at each generation, to avoid some cases where repeated or very similar solutions appeared, especially when using only clashes evaluation.
+
 - **v1.0.0:** Release version. Used in the benchmark and cases study of the article.
 
 OS Compatibility

conda-recipe/meta.yaml

@@ -3,13 +3,13 @@
 
 package:
   name: gpathfinder
-  version: 1.0.0
+  version: 1.0.1
 
 about:
-  home: https://github.com/insilichem/gaudi/tree/gpathfinder
+  home: https://github.com/insilichem/gpathfinder
   license: Apache
   license_file: LICENSE
-  summary: identification of ligand binding pathways by a multi-objective gentic algorithm
+  summary: identification of ligand binding pathways by a multi-objective genetic algorithm
 
 source:
   path: ../
@@ -45,10 +45,10 @@ requirements:
 
 test:
   imports:
-    - gaudi
+    - gpath
   commands:
-    - gaudi -h
-    - gaudi run -h
+    - gpath -h
+    - gpath run -h
     - cd tests && python run_test.py -v --benchmark-disable; cd ..
   source_files:
     - tests

docs/input.rst

@@ -36,7 +36,7 @@ If you are considering to minimize the sample structures generated by Normal Mod
 `.yaml` configuration file
 ==========================
 
-GaudiMM uses a YAML-formatted input file for setting up the calculation. YAML is a human-readable serialization format, already implemented in a broad range of languages. Input files must contain these five sections:
+GPathFinder uses a YAML-formatted input file for setting up the calculation. YAML is a human-readable serialization format, already implemented in a broad range of languages. Input files must contain these five sections:
 
 - **output**. Project options. Configure it to your liking
 - **ga**. Genetic algorithm configuration. Normally, you don't have to touch this, except maybe the number of generations and population size.

docs/installation.rst

@@ -63,9 +63,14 @@ or
 
 5 - Run it!
 
+.. image:: data/new.jpeg
+    :align: left
+    :height: 30px
+    :alt: NEW!
+
 ::
 
-  gaudi
+  gpath
 
 
 Check everything is OK
@@ -75,22 +80,22 @@ If everything went OK, you will get the usage screen:
 
 .. code-block:: console
 
-    Usage: gaudi [OPTIONS] COMMAND [ARGS]...
+    Usage: gpath [OPTIONS] COMMAND [ARGS]...
 
-      GaudiMM: Genetic Algorithms with Unrestricted Descriptors for Intuitive
-      Molecular Modeling
+      GPathFinder: Indentification of ligand pathways by a multi-objective
+      genetic algorithm
 
-      (C) 2017, InsiliChem
-      https://github.com/insilichem/gaudi
+      (C) 2019, InsiliChem
+      https://github.com/insilichem/gpathfinder
 
     Options:
       --version   Show the version and exit.
       -h, --help  Show this message and exit.
 
     Commands:
-      prepare  Create or edit a GAUDI input file.
-      run      Launch a GAUDI input file.
-      view     Analyze the results in a GAUDI output file.
+      prepare  Create or edit a GPATH input file.
+      run      Launch a GPATH input file.
+      view     Analyze the results in a GPATH output file.
 
 OS Compatibility
 ================

docs/output.rst

@@ -31,7 +31,12 @@ The results of the calculation will be saved inside a folder on the path indicat
 
 - **A `.gaudi-log` file**: contains the log information of the calculation, with data about the time employed in the execution, the evolution of the scores along the calculation and possible errors/warnings.
 - **A `.yaml` file**: contains a replica of the `.yaml` input file employed in the calculation.
-- **A `.gaudi-output` file**: contains a summary of the obtained results, with data about their scores and name of the file that actually has the pathway.
+- **A `.gpath-output` file**: contains a summary of the obtained results, with data about their scores and name of the file that actually has the pathway. Can be used to get an overview of the quality of the solutions.
+.. image:: data/new.jpeg
+    :align: left
+    :height: 30px
+    :alt: NEW!
+- **A `summary.csv` file**: contains a summary of the scoring of all obtained results, detailed by frame. Also contains the coordinates of every solution (considering the center of mass of the ligand at every frame of the pathway). Can be used to see at a frame detail the quality of a concrete solution and differences between solutions.
 - **A set of `.zip` files**: contain the different pathways obtained from the calculation. The number of solutions will be equal to the population size if ``output.pareto`` was set to `False` or equal to the size of the pareto frontier (i.e. dominant solutions) otherwise.
 
 **Optional files**
@@ -49,3 +54,9 @@ Each `.zip` file contains all the necessary information to reproduce at atomic l
 - **Another `.zip` file** which contains a set of `.pdb` files with all the frames of the pathway (each one has a conformation of the ligand and receptor molecules). You can open these `.pdb` files in any visualization tool like a MD-movie and work with them and analyze each frame. An example of a pathway that represents a GPathFinder solution can be found `here <https://raw.githubusercontent.com/insilichem/gpathfinder/master/examples/output_files/example_pathway.zip>`_. 
 
 Moreover, an `allele.txt` and a `scores.txt` files are present with all the necessary information to reconstruct the pathway from the original structures and the score information for every frame. These additional files can be used by your own scripts to analyze the results in further detail.
+
+.. image:: data/new.jpeg
+    :align: left
+    :height: 30px
+    :alt: NEW!
+Finally, a `trajectory.pdb` file which contains the route that follows the ligand, as a set of points that represent the center of the ligand at each step of the trajectory. This can be used to easily compare the trajectory of different solutions obtained from GPathFinder calculations.

docs/parameters.rst

@@ -25,8 +25,8 @@
 List of parameters
 ==================
 
-Parameters for version 1.0.0
-============================
+Parameters for versions 1.0.x 
+=============================
 
 **Genetic Algorithm parameters**
 

docs/reproducibility.rst

@@ -30,6 +30,6 @@ One of the key aspects of every research project is its reproducibility. Sometim
 When reporting results obtained by a GPathFinder calculation, you should provide the following information:
 
 - The full `.yaml` file, for example, in the supporting information.
-- The version of the program you have used (for example, v.1.0.0). This will allow to deduce the values for the parameters that are not explicitly reported in the `.yaml` file.
+- The version of the program you have used (for example, v.1.0.1). This will allow to deduce the values for the parameters that are not explicitly reported in the `.yaml` file.
 
 The information of the default parameters for each version is provided in :ref:`parameters` section.

docs/tutorial-first.rst

@@ -116,7 +116,7 @@ Finally, you have to save your `.yaml` inside your calculation folder, for examp
 3. Running the calculation
 ==========================
 
-- **Necessary files for this section**: ligand.mol2/ligand_with_H.mol2, receptor.mol2/receptor_with_H.mol2, input_clashes.yaml/input_clashesvina.yaml
+- **Necessary files for this section**: ligand.mol2/ligand_with_H.mol2, receptor.mol2/receptor_with_H.mol2, input_clashes.yaml/input_clashes_vina.yaml
 - **Output files from this section**: folder with GPathFinder results
 
 Running your calculation is as easy as open a **terminal**, activate your **conda environment** with:
@@ -135,13 +135,13 @@ Go to your calculation folder, where `input_clashes.yaml` or `input_clashes_vina
 
 ::
 
-   gaudi run input_clashes.yaml
+   gpath run input_clashes.yaml
 
 or
 
 ::
 
-   gaudi run input_clashes_vina.yaml
+   gpath run input_clashes_vina.yaml
 
 4. Visualizing results
 ======================

docs/usage.rst

@@ -37,9 +37,14 @@ or
 
 Running GAUDI jobs is quite easy with :mod:`gaudi.cli.gaudi_run`. Put in your terminal:
 
+.. image:: data/new.jpeg
+    :align: left
+    :height: 30px
+    :alt: NEW!
+
 ::
 
-    gaudi run /path/to/input_file.yaml
+    gpath run /path/to/input_file.yaml
 
 You will need at least three input files. A `.yaml` file with the configuration of the job and two `.mol2` files for the ligand and the receptor molecules. To learn how to create input files, go to :ref:`input`. You can also check the tutorials :ref:`tutorial-input` and :ref:`tutorial-mol2`.
 

environment.yml

@@ -1,4 +1,4 @@
-name: gaudi
+name: gpath
 channels:
 - insilichem
 - omnia

examples/input_files/analyze_clashes.yaml

@@ -6,19 +6,19 @@ ga:         # Section to configure the Genetic Algorithm parameters
     generations: 500
     population: 12
 genes:      # Section to configure the genes
--   module: gaudi.genes.molecule
+-   module: gpath.genes.molecule
     name: Ligand
     path: ./mol_files/ligand_without_H.mol2 #optionally could be the ligand with H
--   module: gaudi.genes.molecule
+-   module: gpath.genes.molecule
     name: Protein
     path: ./mol_files/protein_without_H.mol2 #optionally could be the ligand with H 
--   module: gaudi.genes.path_torsion
+-   module: gpath.genes.path_torsion
     name: T
     target: Ligand
     anchor: Ligand/1 # This anchor atom has to be set in function of the concrete ligand (see tutorial section for more information)
--   module: gaudi.genes.path_rotamers
+-   module: gpath.genes.path_rotamers
     name: R
--   module: gaudi.genes.path_normalmodes
+-   module: gpath.genes.path_normalmodes
     name: NM
     target: Protein
     modes: [0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19]
@@ -27,7 +27,7 @@ genes:      # Section to configure the genes
     n_samples: 100
     write_modes: True
     write_samples: True
--   module: gaudi.genes.path
+-   module: gpath.genes.path
     name: Pathway
     ligand: Ligand
     protein: Protein
@@ -38,7 +38,7 @@ genes:      # Section to configure the genes
     origin: [X.xxx, Y.yyy, Z.zzz]  #Coordinates of the initial point of the pathway object of study (referred to protein .mol2 file system of coordinates)
     destination: [X.xxx, Y.yyy, Z.zzz]  #Coordinates of the final point of the pathway object of study (referred to protein .mol2 file system of coordinates)
 objectives:     # Section to configure the evaluation of the pathways
--   module: gaudi.objectives.path_scoring
+-   module: gpath.objectives.path_scoring
     name: Clashes
     probe: Pathway
     which: clashes
@@ -52,6 +52,8 @@ output:
 similarity:
     args:
     - Pathway
-    - 0.05
+    - 1.0
     kwargs: {}
-    module: gaudi.path_similarity.pathways_rmsd
+    module: gpath.path_similarity.pathways_rmsd
+
+# Input file to be used with GPathFinder v.1.0.1

examples/input_files/analyze_clashes_vina.yaml

@@ -6,19 +6,19 @@ ga:         # Section to configure the Genetic Algorithm parameters
     generations: 750
     population: 12
 genes:      # Section to configure the genes
--   module: gaudi.genes.molecule
+-   module: gpath.genes.molecule
     name: Ligand
     path: ./mol_files/ligand_with_H.mol2
--   module: gaudi.genes.molecule
+-   module: gpath.genes.molecule
     name: Protein
     path: ./mol_files/protein_with_H.mol2 
--   module: gaudi.genes.path_torsion
+-   module: gpath.genes.path_torsion
     name: T
     target: Ligand
     anchor: Ligand/1 # This anchor atom has to be set in function of the concrete ligand (see tutorial section for more information)
--   module: gaudi.genes.path_rotamers
+-   module: gpath.genes.path_rotamers
     name: R
--   module: gaudi.genes.path_normalmodes
+-   module: gpath.genes.path_normalmodes
     name: NM
     target: Protein
     modes: [0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19]
@@ -27,7 +27,7 @@ genes:      # Section to configure the genes
     n_samples: 100
     write_modes: True
     write_samples: True
--   module: gaudi.genes.path
+-   module: gpath.genes.path
     name: Pathway
     ligand: Ligand
     protein: Protein
@@ -38,13 +38,13 @@ genes:      # Section to configure the genes
     origin: [X.xxx, Y.yyy, Z.zzz]  #Coordinates of the initial point of the pathway object of study (referred to protein .mol2 file system of coordinates)
     destination: [X.xxx, Y.yyy, Z.zzz]  #Coordinates of the final point of the pathway object of study (referred to protein .mol2 file system of coordinates)
 objectives:     # Section to configure the evaluation of the pathways
--   module: gaudi.objectives.path_scoring
+-   module: gpath.objectives.path_scoring
     name: Clashes
     probe: Pathway
     which: clashes
     method: average
     weight: -1.0
--   module: gaudi.objectives.path_scoring
+-   module: gpath.objectives.path_scoring
     name: Vina
     probe: Pathway
     which: vina
@@ -58,6 +58,8 @@ output:
 similarity:
     args:
     - Pathway
-    - 0.05
+    - 1.0
     kwargs: {}
-    module: gaudi.path_similarity.pathways_rmsd
+    module: gpath.path_similarity.pathways_rmsd
+
+# Input file to be used with GPathFinder v.1.0.1