Merge pull request #117 from martimunicoy/mae_charges

Assignment of external partial charges
martimunicoy · Dec 21, 2020 · 549a6c3 · 549a6c3
2 parents 410c7c4 + d9c72be
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diff --git a/docs/releasehistory.rst b/docs/releasehistory.rst
@@ -7,8 +7,19 @@ Releases follow the ``major.minor.micro`` scheme recommended by `PEP440 <https:/
 * ``minor`` increments add features but do not break API compatibility
 * ``micro`` increments represent bugfix releases or improvements in documentation
 
+1.2.0 - Current development
+---------------------------
 
-1.1.0 - Improvements in parameterization API, OBC template for OPLS2005 and Molecule initializators 
+New features
+""""""""""""
+- `PR #117 <https://github.com/martimunicoy/peleffy/pull/117>`_: New method to assign external partial charges.
+
+Tests added
+"""""""""""
+- `PR #117 <https://github.com/martimunicoy/peleffy/pull/117>`_: Adds tests to validate the MAE parse for external partial charges.
+
+
+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.

diff --git a/docs/usage.rst b/docs/usage.rst
@@ -206,6 +206,19 @@ It sets the method to compute the partial charges.
 
         $ python -m peleffy.main path/to/my_ligand.pdb -c gasteiger
 
+Charge from file
+----------------
+It sets the method to load external partial charges.
+
+- Flag: ``--charges_from_file PATH``
+- Type: ``string``
+- Default: ``None``
+- Example: the code below will load the partial charges from a MAE file
+
+  .. code-block:: bash
+
+        $ python -m peleffy.main path/to/my_ligand.pdb --charges_from_file path/to/my_ligand.mae
+
 Include terminal rotamers
 -------------------------
 It always includes terminal rotamers, even if they belong to a terminal methyl group whose rotation is trivial in PELE.

diff --git a/examples/OFF_parameterization/parameterize.ipynb b/examples/OFF_parameterization/parameterize.ipynb