Merge pull request #127 from martimunicoy/devel

1.2.0 Release
martimunicoy · Feb 1, 2021 · a81633a · a81633a
2 parents 2216baa + e118be1
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diff --git a/devtools/conda/meta.yaml b/devtools/conda/meta.yaml
@@ -26,7 +26,7 @@ requirements:
     - networkx
     - rdkit
     - ambertools
-    - openforcefield==0.8.0
+    - openforcefield==0.8.3
 
 about:
   home: https://github.com/martimunicoy/peleffy

diff --git a/devtools/envs/standard.yaml b/devtools/envs/standard.yaml
@@ -13,4 +13,4 @@ dependencies:
   - coverage < 5.0
   - ambertools
   - rdkit
-  - openforcefield ==0.8.0
+  - openforcefield ==0.8.3
diff --git a/docs/index.rst b/docs/index.rst
@@ -7,6 +7,8 @@ are:
 
 * The following force field from the `Open Force Field toolkit <https://github.com/openforcefield/openforcefield>`_:
 
+  * openff_unconstrained-1.3.0.offxml
+
   * openff_unconstrained-1.2.1.offxml
 
   * openff_unconstrained-1.2.0.offxml

diff --git a/docs/releasehistory.rst b/docs/releasehistory.rst
@@ -7,8 +7,32 @@ 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 - New tools for parameters and templates
+----------------------------------------------
 
-1.1.0 - Improvements in parameterization API, OBC template for OPLS2005 and Molecule initializators 
+This is a minor release of peleffy that includes new useful tools to handle parameters and their templates more easily. It also supports the newest version of the OpenForceField toolkit, which is 0.8.3.
+
+New features
+""""""""""""
+- `PR #117 <https://github.com/martimunicoy/peleffy/pull/117>`_: New method to assign external partial charges.
+- `PR #118 <https://github.com/martimunicoy/peleffy/pull/118>`_: New method to load parameters from an Impact Template.
+- `PR #119 <https://github.com/martimunicoy/peleffy/pull/119>`_: Adds explanatory error message when using an invalid Impact Template in the from_impact_template method.
+- `PR #119 <https://github.com/martimunicoy/peleffy/pull/119>`_: Supports Openforcefield-0.8.3 .
+- `PR #126 <https://github.com/martimunicoy/peleffy/pull/126>`_: Allows the Solvent class to be compatible with multiple topologies. 
+
+Bugfixes
+""""""""
+- `PR #125 <https://github.com/martimunicoy/peleffy/pull/125>`_: A bad index slicing in the molecule.Molecule._pdb_checkup() is now fixed. 
+
+Tests added
+"""""""""""
+- `PR #117 <https://github.com/martimunicoy/peleffy/pull/117>`_: Adds tests to validate the MAE parse for external partial charges.
+- `PR #118 <https://github.com/martimunicoy/peleffy/pull/118>`_: Adds tests to validate the new method to load parameters from an Impact Template.
+- `PR #119 <https://github.com/martimunicoy/peleffy/pull/119>`_: Adds tests for the new error message when using an invalid Impact Template in the from_impact_template method.
+- `PR #126 <https://github.com/martimunicoy/peleffy/pull/126>`_: Adds tests for the new compatibility of the Solvent class with multiple topologies. 
+
+
+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
diff --git a/examples/molecular_representations/benzamidine_representation.ipynb b/examples/molecular_representations/benzamidine_representation.ipynb
@@ -0,0 +1,145 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Benzamidine representation\n",
+    "This notebook checks that the molecular representation of benzamidine (problematic compound according to one RDKit's [issue](https://github.com/rdkit/rdkit/issues/1031)) is of correct type."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from peleffy.topology import Molecule\n",
+    "from peleffy.utils import get_data_file_path"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      " - Initializing molecule from PDB\n",
+      "   - Loading molecule from RDKit\n",
+      "   - Assigning stereochemistry from 3D coordinates\n",
+      "   - Setting molecule name to 'benzamidine'\n",
+      "   - Setting molecule tag to 'BEN'\n",
+      "   - Representing molecule with the Open Force Field Toolkit\n"
+     ]
+    },
+    {
+     "data": {
+      "application/vnd.jupyter.widget-view+json": {
+       "model_id": "f962e6415594449fbfad0b728d1b3cb8",
+       "version_major": 2,
+       "version_minor": 0
+      },
+      "text/plain": []
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    },
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      " - Generating rotamer library\n",
+      "   - Core set to the center of the molecule\n"
+     ]
+    },
+    {
+     "data": {
+      "image/svg+xml": [
+       "<svg baseProfile=\"full\" height=\"500px\" version=\"1.1\" viewBox=\"0 0 500 500\" width=\"500px\" xml:space=\"preserve\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:rdkit=\"http://www.rdkit.org/xml\" xmlns:xlink=\"http://www.w3.org/1999/xlink\">\n",
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+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    }
+   ],
+   "source": [
+    "m = Molecule(get_data_file_path('ligands/benzamidine.pdb'))\n",
+    "display(m)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "As long as the input PDB file has the connectivity properly assigned, the molecular representation obtained by RDKit in peleffy is valid."
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
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+ "nbformat_minor": 4
+}