Merge pull request #99 from martimunicoy/devel

peleffy 1.1.0 release

.github/workflows/master.yml

@@ -20,7 +20,7 @@ jobs:
         activate-environment: standard
         environment-file: devtools/envs/standard.yaml
         auto-activate-base: false
-  
+
     - name: Install dependencies
       shell: bash -l {0}
       run: |

.github/workflows/test.yml

@@ -28,7 +28,7 @@ jobs:
         activate-environment: standard
         environment-file: devtools/envs/standard.yaml
         auto-activate-base: false
-        
+
     - name: Environment Information
       shell: bash -l {0}
       run: |

README.md

@@ -4,9 +4,68 @@
 | **Installation** | [![Conda](https://img.shields.io/conda/v/martimunicoy/peleffy.svg)](https://anaconda.org/martimunicoy/peleffy) [![PyPI](https://img.shields.io/pypi/v/peleffy)](https://pypi.org/project/peleffy/) |
 
 # PELE Force Field Yielder
+
+<p align="left">
+  <img src="docs/figures/logo.png" width="350" title="peleffy logo", alt="peleffy logo">
+</p>
+
 The `peleffy` (PELE Force Field Yielder) is a Python package that builds [PELE](https://pele.bsc.es/pele.wt)-compatible force field templates. The current supported force fields are:
 - Any force field from the [Open Force Field toolkit](https://github.com/openforcefield/openforcefield).
 - OPLS2005.
+- A combination of them.
 
 ## Documentation
 The documentation for the `peleffy` package is available at [GitHub Pages](https://martimunicoy.github.io/peleffy).
+
+## Main features
+
+### Small molecules parameterization
+It can take a molecular structure from a PDB file or a SMILES tag and parameterize it with any of the supported force fields. The resulting parameters are stored in a dictionary-like object that can be easily manipulated.
+
+```python
+from peleffy.topology import Molecule
+from peleffy.forcefield import OpenForceField
+
+molecule = Molecule('path_to_pdb_file.pdb')
+openff = OpenForceField('openff_unconstrained-1.3.0.offxml')
+
+parameters = openff.parameterize(molecule)
+```
+
+### Template generation
+A peleffy's molecular representation can be employed, along with its parameters, to build a Topology file. A Topology file is a wrapper of topological elements that can be written as an Impact template file, compatible with PELE.
+
+```python
+from peleffy.topology import Topology
+from peleffy.template import Impact
+
+topology = Topology(molecule, parameters)
+
+impact_template = Impact(topology)
+impact_template.to_file('ligand_parameters.txt')
+```
+
+A template with the OBC parameters for the implicit solvent of PELE can also be generated.
+```python
+from peleffy.solvent import OBC2
+
+obc2_solvent = OBC2(topology)
+obc2_solvent.to_file('ligand_obc.txt')
+```
+
+It can also generate the rotamer library file for the side chain exploration of PELE.
+```python
+from peleffy.topology import RotamerLibrary
+
+rotamer_library = RotamerLibrary(molecule)
+rotamer_library.to_file('ligand_rotamers.txt')
+```
+
+### User-friendly CLI
+All the commands above can be run with a single CLI directive.
+```bash
+python -m peleffy.main path_to_pdb_file.pdb -f 'openff_unconstrained-1.3.0.offxml' --with_solvent
+```
+
+## Contributors
+For a full list of contributors, see the [GitHub Contributors page](https://github.com/martimunicoy/peleffy/graphs/contributors).

devtools/conda/meta.yaml

@@ -26,7 +26,7 @@ requirements:
     - networkx
     - rdkit
     - ambertools
-    - openforcefield==0.7.1
+    - openforcefield==0.8.0
 
 about:
   home: https://github.com/martimunicoy/peleffy

devtools/envs/standard.yaml

@@ -13,4 +13,4 @@ dependencies:
   - coverage < 5.0
   - ambertools
   - rdkit
-  - openforcefield ==0.7.1
+  - openforcefield ==0.8.0

docs/forcefield.rst

@@ -4,7 +4,7 @@ Forcefield methods
 ==============
 
 This module defines the different force fields that are available
-to parameterize molecules for PELE.
+in `peleffy` to parameterize molecules for PELE.
 
 .. currentmodule:: peleffy.forcefield
 
@@ -19,3 +19,22 @@ Primary objects
     OpenForceField
     OPLS2005ForceField
     OpenFFOPLS2005ForceField
+    selectors.ForceFieldSelector
+
+Secondary objects
+-----------------
+
+.. autosummary::
+    :nosignatures:
+    :toctree: api/autogenerated
+    :template: class.rst
+
+    calculators.Am1bccCalculator
+    calculators.GasteigerCalculator
+    calculators.OPLSChargeCalculator
+    calculators.DummyChargeCalculator
+    selectors.ChargeCalculatorSelector
+    parameters.BaseParameterWrapper
+    parameters.OpenForceFieldParameterWrapper
+    parameters.OPLS2005ParameterWrapper
+    parameters.OpenFFOPLS2005ParameterWrapper

docs/index.rst

@@ -4,8 +4,25 @@ PELE Force Field Yielder
 The `peleffy` (PELE Force Field Yielder) is a Python package that builds
 PELE-compatible force field templates. The current supported force fields
 are:
-- Any force field from the [Open Force Field toolkit](https://github.com/openforcefield/openforcefield).
-- OPLS2005.
+
+* The following force field from the `Open Force Field toolkit <https://github.com/openforcefield/openforcefield>`_:
+
+  * openff_unconstrained-1.2.1.offxml
+
+  * openff_unconstrained-1.2.0.offxml
+
+  * openff_unconstrained-1.1.1.offxml
+
+  * openff_unconstrained-1.1.0.offxml
+
+  * openff_unconstrained-1.0.1.offxml
+
+  * openff_unconstrained-1.0.0.offxml
+
+* OPLS2005
+
+It also generates other files required by PELE such as rotamer libraries or
+solvent templates.
 
 
 User guide
@@ -27,7 +44,6 @@ API documentation
   :maxdepth: 1
 
   topology
+  forcefield
   template
   solvent
-  charge
-  forcefield

docs/releasehistory.rst

@@ -8,6 +8,46 @@ Releases follow the ``major.minor.micro`` scheme recommended by `PEP440 <https:/
 * ``micro`` increments represent bugfix releases or improvements in documentation
 
 
+1.1.0 - Improvements in parameterization API, OBC template for OPLS2005 and Molecule initializators 
+---------------------------------------------------------------------------------------------------
+
+This minor release introduces improvements to the parameterization API of peleffy. It also integrates the parameterization of OBC radii and scale factors required by the OPLS2005 implementation of PELE. It also improves the initialization of the Molecule class with a PDB checking and fixer and taking RDKit and OpenFF molecular representations as input. It also adds support for the new openff-1.3.0. Besides, it fixes a serious bug in the atom ordering of the Impact template that affected PELE's side chain prediction algorithm.
+
+New features
+""""""""""""
+- `PR #86 <https://github.com/martimunicoy/peleffy/pull/86>`_: New method to check the input PDB prior building the molecule.
+- `PR #88 <https://github.com/martimunicoy/peleffy/pull/88>`_: New method to retrieve atom degrees with RDKit.
+- `PR #90 <https://github.com/martimunicoy/peleffy/pull/90>`_: Add support for openff-1.3.0.
+- `PR #92 <https://github.com/martimunicoy/peleffy/pull/92>`_: New parameter to skip the stereochemistry assignment (and the checking from the OpenFF toolkit).
+- `PR #94 <https://github.com/martimunicoy/peleffy/pull/94>`_: New method for the OPLS OBC parameters.
+- `PR #100 <https://github.com/martimunicoy/peleffy/pull/100>`_: New writer for the OPLS OBC parameters.
+- `PR #106 <https://github.com/martimunicoy/peleffy/pull/106>`_: New method to initialize a Molecule object directly from an RDKit and OpenFF molecular representations.
+- `PR #112 <https://github.com/martimunicoy/peleffy/pull/112>`_: New method to fix an input PDB file with no atomic element identifiers.
+
+Bugfixes
+""""""""
+- `PR #107 <https://github.com/martimunicoy/peleffy/pull/107>`_: A bad ordering of the atoms in the Impact template generated by peleffy is now fixed.
+- `PR #115 <https://github.com/martimunicoy/peleffy/pull/115>`_: The rotamer library writer now writes molecule's tag not its name, as expected.
+
+API-breaking changes
+""""""""""""""""""""
+- `PR #94 <https://github.com/martimunicoy/peleffy/pull/94>`_: Methods to write to a file are given a unique standard name, to_file(), to simplify the API.
+- `PR #97 <https://github.com/martimunicoy/peleffy/pull/97>`_: The parameterization API changes and a new Topology class is used as a container for all the topological elements.
+- `PR #103 <https://github.com/martimunicoy/peleffy/pull/103>`_: The OpenFF output of PELE changes from DataLocal/Templates/OFF/Parsley/HeteroAtoms/ to DataLocal/Templates/OpenFF/Parsley/.
+
+Tests added
+"""""""""""
+- `PR #88 <https://github.com/martimunicoy/peleffy/pull/88>`_: Adds tests to validate the atom degrees getter.
+- `PR #86 <https://github.com/martimunicoy/peleffy/pull/86>`_: Adds tests to validate the PDB check up.
+- `PR #90 <https://github.com/martimunicoy/peleffy/pull/90>`_: General validation of supported force fields.
+- `PR #92 <https://github.com/martimunicoy/peleffy/pull/92>`_: New test to check the behaviour of the allow_undefined_stereo parameter.
+- `PR #94 <https://github.com/martimunicoy/peleffy/pull/94>`_: Adds tests to validate the OPLS OBC parameters generator.
+- `PR #97 <https://github.com/martimunicoy/peleffy/pull/97>`_: Includes tests for the new Topology container class.
+- `PR #100 <https://github.com/martimunicoy/peleffy/pull/100>`_: Adds tests to validate the solvent template writers.
+- `PR #106 <https://github.com/martimunicoy/peleffy/pull/106>`_: Adds tests to check the RDKit and OpenFF molecular initializers.
+- `PR #112 <https://github.com/martimunicoy/peleffy/pull/112>`_: Adds one test to check the new PDB fixer method.
+
+
 1.0.0 - Full compatibility for OPLS2005 and OpenFF dihedrals and rotamer library improvements
 ---------------------------------------------------------------------------------------------
 

docs/solvent.rst

@@ -16,5 +16,16 @@ Primary objects
     :toctree: api/autogenerated
     :template: class.rst
 
-    OBC1
     OBC2
+    OPLSOBC
+
+
+Secondary objects
+-----------------
+
+.. autosummary::
+    :nosignatures:
+    :toctree: api/autogenerated
+    :template: class.rst
+
+    OBC1

docs/topology.rst

@@ -18,6 +18,7 @@ Primary objects
     :template: class.rst
 
     Molecule
+    Topology
 
 
 Secondary objects
@@ -34,10 +35,10 @@ Secondary objects
     Dihedral
     Proper
     Improper
-    molecule.DummyAtom
-    topology.OFFDihedral
-    topology.OFFProper
-    topology.OFFImproper
+    elements.DummyAtom
+    elements.OFFDihedral
+    elements.OFFProper
+    elements.OFFImproper
     ZMatrix
     rotamer.Rotamer
     rotamer.RotamerLibrary

docs/usage.rst

@@ -33,27 +33,41 @@ The more straightforward way to install `peleffy` along with the required depend
 .. code-block::
 
      ------------------------------------------------------------
-     Open Force Field parameterizer for PELE v0.3.0
+     Open Force Field parameterizer for PELE 1.1.0
      ------------------------------------------------------------
       - General:
-        - Input PDB: my_ligand.pdb
+        - Input PDB: my_ligand
         - Output path: None
         - Write solvent parameters: False
         - DataLocal-like output: False
       - Parameterization:
-        - Force field: openff_unconstrained-1.2.0.offxml
-        - Charges method: am1bcc
-        - Use OPLS nonbonding parameters: False
-        - Use OPLS bonds and angles: False
+        - Force field: openff_unconstrained-1.3.0.offxml
+        - Charge method: am1bcc
       - Rotamer library:
         - Resolution: 30
         - Exclude terminal rotamers: True
      ------------------------------------------------------------
-      - Loading molecule from RDKit
+      - Initializing molecule from PDB
+        - Loading molecule from RDKit
+        - Assigning stereochemistry from 3D coordinates
+        - Setting molecule name to 'ligand'
+        - Setting molecule tag to 'LIG'
+        - Representing molecule with the Open Force Field Toolkit
       - Generating rotamer library
-      - Loading forcefield
-      - Computing partial charges with am1bcc
-      - All files were generated successfully
+        - Core set to the center of the molecule
+      - Loading 'openff_unconstrained-1.3.0.offxml'
+      - Parameterizing molecule
+      - Parameters were built successfully:
+        - 12 atoms
+        - 12 bonds
+        - 18 torsions
+        - 24 propers
+        - 6 impropers
+      - Generating solvent parameters
+      - All files were generated successfully:
+        - /Users/martimunicoy/repos/BSC/peleffy/LIG.rot.assign
+        - /Users/martimunicoy/repos/BSC/peleffy/ligz
+        - /Users/martimunicoy/repos/BSC/peleffy/ligandParams.txt
      ------------------------------------------------------------
 
 Command-line arguments