Merge pull request #161 from martimunicoy/devel

peleffy 1.4.0 release
martimunicoy · Dec 15, 2021 · e9e802d · e9e802d
2 parents e91a3a1 + bbdb38d
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diff --git a/.gitignore b/.gitignore
@@ -128,3 +128,6 @@ dmypy.json
 
 # Pyre type checker
 .pyre/
+
+# MacOS
+.DS_Store
diff --git a/devtools/conda/meta.yaml b/devtools/conda/meta.yaml
@@ -24,7 +24,7 @@ requirements:
     - networkx
     - rdkit
     - ambertools
-    - openff-toolkit==0.10.0
+    - openff-toolkit==0.10.1
 
 about:
   home: https://github.com/martimunicoy/peleffy

diff --git a/devtools/envs/standard.yaml b/devtools/envs/standard.yaml
@@ -13,4 +13,4 @@ dependencies:
   - ipython
   - ambertools
   - rdkit
-  - openff-toolkit==0.10.0
+  - openff-toolkit==0.10.1
diff --git a/docs/releasehistory.rst b/docs/releasehistory.rst
@@ -8,6 +8,29 @@ Releases follow the ``major.minor.micro`` scheme recommended by `PEP440 <https:/
 * ``micro`` increments represent bugfix releases or improvements in documentation
 
 
+1.4.0 - Alchemistry and AMBER support
+---------------------------------------------------------
+
+This is a minor release of peleffy that adds a new module to generate alchemical templates. It also adds support for AMBER's implementation in PELE.
+
+New features
+""""""""""""
+- `PR #154 <https://github.com/martimunicoy/peleffy/pull/154>`_: Introduces Alchemizer module to generate hybrid topologies
+- `PR #155 <https://github.com/martimunicoy/peleffy/pull/155>`_: Adds support for PELE's AMBER with a new Impact template
+- `PR #162 <https://github.com/martimunicoy/peleffy/pull/162>`_: Upgrade to openff-toolkit 0.10.1
+
+Bugfixes
+""""""""
+- `PR #158 <https://github.com/martimunicoy/peleffy/pull/158>`_: Fix minor bug when using the --chain flag and introduces checks for the input PDB in the peleffy.main module
+- `PR #159 <https://github.com/martimunicoy/peleffy/pull/159>`_: Fix issues with long atom numbers and heteromolecules extraction
+
+Tests added
+"""""""""""
+- `PR #154 <https://github.com/martimunicoy/peleffy/pull/154>`_: Adds a collection of tests for Alchemizer module
+- `PR #155 <https://github.com/martimunicoy/peleffy/pull/155>`_: Extends the tests for utils module and introduces new tests for the new AMBER-compatible Impact template
+- `PR #158 <https://github.com/martimunicoy/peleffy/pull/158>`_: Extends the tests for the new checks in the peleffy.main module
+
+
 1.3.4 - OpenFF-2.0 Support
 ---------------------------------------------------------
 

diff --git a/docs/usage.rst b/docs/usage.rst
@@ -245,3 +245,15 @@ It always includes terminal rotamers, even if they belong to a terminal methyl g
   .. code-block:: bash
 
         $ python -m peleffy.main path/to/my_ligand.pdb --include_terminal_rotamers
+
+AMBER-compatible template
+-------------------------
+It generates an Impact template that will be compatible with PELE's AMBER force field implementation. The default template is compatible with OPLS's implementation.
+
+- Flag: ``--for_amber``
+- Default: ``False``, compatible with OPLS
+- Example: the code below will generate an Impact template compatible with PELE'S AMBER
+
+  .. code-block:: bash
+
+        $ python -m peleffy.main path/to/my_ligand.pdb --for_amber
diff --git a/examples/OFF_parameterization/AMBER-compatible_templates.ipynb b/examples/OFF_parameterization/AMBER-compatible_templates.ipynb
@@ -0,0 +1,187 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "13879cec",
+   "metadata": {},
+   "source": [
+    "# Generation of an AMBER-compatible templates\n",
+    "This notebook shows how to use the API of `peleffy` to generate an Impact template that supports the AMBER force field implementation we have in PELE."
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "d22b7fdb",
+   "metadata": {},
+   "source": [
+    "### Load `peleffy`'s molecule representation with a PDB file of anthracene"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "id": "b380cbf2",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from peleffy.topology import Molecule"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "id": "9438c0b7",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      " - Initializing molecule from a SMILES tag\n",
+      "   - Loading molecule from RDKit\n",
+      "   - Setting molecule name to 'c1ccc2cc3ccccc3cc2c1'\n",
+      "   - Representing molecule with the Open Force Field Toolkit\n",
+      " - Generating rotamer library\n",
+      "   - Core set to the center of the molecule\n"
+     ]
+    },
+    {
+     "data": {
+      "image/svg+xml": [
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+       "</svg>"
+      ],
+      "text/plain": [
+       "<IPython.core.display.SVG object>"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    }
+   ],
+   "source": [
+    "anthracene = Molecule(smiles='c1ccc2cc3ccccc3cc2c1', hydrogens_are_explicit=False)\n",
+    "display(anthracene)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "c154396b",
+   "metadata": {},
+   "source": [
+    "### Parameterize with `Open Force Field Toolkit` and generate the Impact template\n",
+    "Please, note that to save the Impact template in the required format for PELE's AMBER, we need to set `for_amber` to `True` when initializing the `Impact` class."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "id": "a817c5b9",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from peleffy.forcefield import OpenForceField\n",
+    "from peleffy.topology import Topology\n",
+    "from peleffy.template import Impact"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "id": "71042711",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "openff = OpenForceField('openff_unconstrained-2.0.0.offxml')\n",
+    "parameters = openff.parameterize(anthracene)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "id": "d228e024",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "topology = Topology(anthracene, parameters)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 6,
+   "id": "7d3888da",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "impact = Impact(topology, for_amber=True)\n",
+    "impact.to_file('antz')"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.7.10"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}