Merge branch 'main' into afe-md

# Conflicts: # openfe/tests/data/openmm_afe/AHFEProtocol_json_results.gz # openfe/tests/data/openmm_md/MDProtocol_json_results.gz # openfe/tests/protocols/test_solvation_afe_tokenization.py
OpenFreeEnergy · Feb 16, 2024 · 8d17ddc · 8d17ddc
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diff --git a/.github/pull_request_template.md b/.github/pull_request_template.md
@@ -1,3 +1,18 @@
+<!--
+Thank you for pull request.
+Below are a few things we ask you kindly to self-check before getting a review. Remove checks that are not relevant.
+-->
+
+<!--
+Please note any issues this fixes using [closing keywords]( https://help.github.com/articles/closing-issues-using-keywords/ ):
+-->
+
+<!--
+see https://regro.github.io/rever-docs/news.html for details on how to add news entry (you do not need to run the rever command)
+-->
+
+Checklist
+* [ ] Added a ``news`` entry
 
 ## Developers certificate of origin
 - [ ] I certify that this contribution is covered by the MIT License [here](https://github.com/OpenFreeEnergy/openfe/blob/main/LICENSE) and the **Developer Certificate of Origin** at <https://developercertificate.org/>.
diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
@@ -25,7 +25,7 @@ defaults:
 jobs:
   tests:
     runs-on: ${{ matrix.os }}-latest
-    name: "💻-${{matrix.os }} 🐍-${{ matrix.python-version }} 🗃️${{ matrix.pydantic-version }}"
+    name: "💻-${{matrix.os }} 🐍-${{ matrix.python-version }} 🗃️${{ matrix.pydantic-version }} oechem: ${{ matrix.openeye }}"
     strategy:
       fail-fast: false
       matrix:
@@ -35,13 +35,21 @@ jobs:
           - "3.9"
           - "3.10"
           - "3.11"
+        openeye: ["no"]
         include:
           - os: "macos"
             python-version: "3.11"
             pydantic-version: ">1"
           - os: "ubuntu"
             python-version: "3.11"
             pydantic-version: "<2"
+          - os: "ubuntu"
+            python-version: "3.11"
+            pydantic-version: ">1"
+            openeye: "yes"
+
+    env:
+      OE_LICENSE: ${{ github.workspace }}/oe_license.txt
 
     steps:
       - uses: actions/checkout@v4
@@ -66,6 +74,16 @@ jobs:
             pydantic=${{ matrix.pydantic-version }}
           init-shell: bash
 
+      - name: "Install OpenEye"
+        if: ${{ !github.event.pull_request.head.repo.fork
+                && matrix.openeye == 'yes' }}
+        env:
+          OE_LICENSE_TEXT: ${{ secrets.OE_LICENSE }}
+        run: |
+          echo "${OE_LICENSE_TEXT}" > ${OE_LICENSE}
+          micromamba install -c openeye openeye-toolkits
+          python -c "import openeye; assert openeye.oechem.OEChemIsLicensed(), 'oechem license check failed!'"
+
       - name: "Install GUFE from main@HEAD"
         run: python -m pip install --no-deps git+https://github.com/OpenFreeEnergy/gufe@main
 

diff --git a/.gitignore b/.gitignore
@@ -170,3 +170,9 @@ docs/ExampleNotebooks/
 
 # duecredit
 .duecredit.p
+
+# Some charge stuff
+*.model.pt
+
+# Rever
+rever/
diff --git a/docs/CHANGELOG.rst b/docs/CHANGELOG.rst
@@ -0,0 +1,5 @@
+=================
+openfe Change Log
+=================
+
+.. current developments
diff --git a/docs/conf.py b/docs/conf.py
@@ -103,9 +103,10 @@
 
 autodoc_mock_imports = [
     "matplotlib",
-    "openmmtools",
     "mdtraj",
     "openmmforcefields",
+    "openmmtools",
+    "pymbar",
 ]
 
 # Extensions for the myst parser

diff --git a/docs/cookbook/creating_atom_mappings.rst b/docs/cookbook/creating_atom_mappings.rst
@@ -5,7 +5,7 @@ Creating Atom Mappings
 
 Once your :ref:`data has been loaded<Loading Molecules>`
 we can now proceed to defining how Components in these Systems correspond.
-``Mapping`` objects are used to defined how ``Component`` objects from different :class:`ChemicalSystems` are related.
+``Mapping`` objects are used to defined how ``Component`` objects from different :class:`.ChemicalSystem` objects are related.
 This guide will show how this concept applies to the case of a pair of ligands we wish to transform between.
 
 Generating Mappings

diff --git a/docs/index.rst b/docs/index.rst
@@ -65,13 +65,13 @@ The **OpenFE** toolkit provides open-source frameworks for calculating alchemica
 
         Reference guide on using the OpenFE CLI.
 
-    .. grid-item-card:: OpenFE Showcase
+    .. grid-item-card:: Changelog
         :img-top: _static/Showcase.svg
         :text-align: center
-        :link: tutorials/showcase_notebook
+        :link: CHANGELOG
         :link-type: doc
 
-        Tutorial notebook showing the sorts of things OpenFE can do.
+        Any notable changes in the package for each released version
 
     .. grid-item-card:: Relative Free Energy Protocol
         :img-top: _static/Rocket.svg
@@ -92,6 +92,7 @@ The **OpenFE** toolkit provides open-source frameworks for calculating alchemica
    guide/index
    cookbook/index
    reference/index
+   CHANGELOG
 
 Indices and tables
 ------------------

diff --git a/docs/reference/api/atom_mappers.rst b/docs/reference/api/atom_mappers.rst
@@ -0,0 +1,80 @@
+.. _Atom Mappers:
+
+Atom Mappings
+=============
+
+Tools for mapping atoms in one molecule to those in another. Used to generate efficient ligand networks.
+
+.. module:: openfe.setup.atom_mapping
+
+.. rubric:: Abstract Base Class
+
+.. autosummary::
+    :nosignatures:
+    :toctree: generated/
+
+    LigandAtomMapper
+
+.. rubric:: Implementations
+
+.. autosummary::
+    :nosignatures:
+    :toctree: generated/
+
+    LomapAtomMapper
+    PersesAtomMapper
+
+.. rubric:: Data Types
+
+.. autosummary::
+    :nosignatures:
+    :toctree: generated/
+
+    LigandAtomMapping
+
+.. _Atom Map Scorers:
+
+Atom Map Scorers
+----------------
+
+Scoring functions for a mapping between ligands. These are used as objective functions for :any:`Ligand Network Planners`.
+
+
+Lomap Scorers
+~~~~~~~~~~~~~
+
+Scorers implemented by the `LOMAP <https://github.com/OpenFreeEnergy/Lomap>`_ package.
+
+.. apparently we need the atom_mapping because internally autofunction is
+    trying ``import openfe.setup.lomap_scorers``, which doesn't work (whereas
+    ``from openfe.setup import lomap_scorers`` does)
+.. module:: openfe.setup.atom_mapping.lomap_scorers
+
+.. autosummary::
+    :nosignatures:
+    :toctree: generated/
+
+    default_lomap_score
+    ecr_score
+    mcsr_score
+    mncar_score
+    atomic_number_score
+    hybridization_score
+    sulfonamides_score
+    heterocycles_score
+    transmuting_methyl_into_ring_score
+    transmuting_ring_sizes_score
+
+
+Perses Scorers
+~~~~~~~~~~~~~~
+
+Scorers implemented by the `Perses <https://github.com/choderalab/perses>`_ package.
+
+.. module:: openfe.setup.atom_mapping.perses_scorers
+
+.. autosummary::
+    :nosignatures:
+    :toctree: generated/
+
+    default_perses_scorer
diff --git a/docs/reference/api/data.rst b/docs/reference/api/data.rst
diff --git a/docs/reference/api/index.rst b/docs/reference/api/index.rst
@@ -6,10 +6,11 @@ OpenFE API Reference
 .. toctree::
     :maxdepth: 2
 
-    data
     systems_and_components
+    atom_mappers
     ligand_network
     alchemical_network_planning
     defining_and_executing_simulations
     openmm_rfe
     openmm_solvation_afe
+    openmm_md
diff --git a/docs/reference/api/ligand_network.rst b/docs/reference/api/ligand_network.rst
@@ -52,83 +52,3 @@ Functions to load a :class:`.LigandNetwork` from equivalent classes in other pac
     load_orion_network
     load_fepplus_network
 
-.. _Atom Mappers:
-
-Atom Mappings
--------------
-
-Tools for mapping atoms in one molecule to those in another. Used to generate efficient ligand networks.
-
-.. module:: openfe.setup.atom_mapping
-
-.. rubric:: Abstract Base Class
-
-.. autosummary::
-    :nosignatures:
-    :toctree: generated/
-
-    LigandAtomMapper
-
-.. rubric:: Implementations
-
-.. autosummary::
-    :nosignatures:
-    :toctree: generated/
-
-    LomapAtomMapper
-    PersesAtomMapper
-
-.. rubric:: Data Types
-
-.. autosummary::
-    :nosignatures:
-    :toctree: generated/
-
-    LigandAtomMapping
-
-.. _Atom Map Scorers:
-
-Atom Map Scorers
-----------------
-
-Scoring functions for a mapping between ligands. These are used as objective functions for :any:`Ligand Network Planners`.
-
-
-Lomap Scorers
-~~~~~~~~~~~~~
-
-Scorers implemented by the `LOMAP <https://github.com/OpenFreeEnergy/Lomap>`_ package.
-
-.. apparently we need the atom_mapping because internally autofunction is
-    trying ``import openfe.setup.lomap_scorers``, which doesn't work (whereas
-    ``from openfe.setup import lomap_scorers`` does)
-.. module:: openfe.setup.atom_mapping.lomap_scorers
-
-.. autosummary::
-    :nosignatures:
-    :toctree: generated/
-
-    default_lomap_score
-    ecr_score
-    mcsr_score
-    mncar_score
-    atomic_number_score
-    hybridization_score
-    sulfonamides_score
-    heterocycles_score
-    transmuting_methyl_into_ring_score
-    transmuting_ring_sizes_score
-
-
-Perses Scorers
-~~~~~~~~~~~~~~
-
-Scorers implemented by the `Perses <https://github.com/choderalab/perses>`_ package.
-
-.. module:: openfe.setup.atom_mapping.perses_scorers
-
-.. autosummary::
-    :nosignatures:
-    :toctree: generated/
-
-    default_perses_scorer
diff --git a/docs/reference/api/openmm_md.rst b/docs/reference/api/openmm_md.rst
@@ -0,0 +1,21 @@
+OpenMM Molecular Dynamics Protocol
+==================================
+
+This Protocol implements a standard MD execution for a solvated protein system.
+
+Protocol Settings
+-----------------
+
+.. module:: openfe.protocols.openmm_md
+
+.. autopydantic_model:: PlainMDProtocolSettings
+   :model-show-json: False
+   :model-show-field-summary: False
+   :model-show-config-member: False
+   :model-show-config-summary: False
+   :model-show-validator-members: False
+   :model-show-validator-summary: False
+   :field-list-validators: False
+   :inherited-members: SettingsBaseModel
+   :exclude-members: get_defaults
+   :member-order: bysource
diff --git a/docs/reference/api/systems_and_components.rst b/docs/reference/api/systems_and_components.rst
@@ -10,11 +10,10 @@ We describe a chemical system as being made up of one or more "components," e.g.
     :nosignatures:
     :toctree: generated/
 
-    Component
-	SmallMoleculeComponent
- 	ProteinComponent
- 	SolventComponent
- 	ChemicalSystem
+    SmallMoleculeComponent
+    ProteinComponent
+    SolventComponent
+    ChemicalSystem
 
 
 Chemical System Generators

diff --git a/environment.yml b/environment.yml
@@ -19,6 +19,7 @@ dependencies:
   - coverage
   - cinnabar ==0.3.0
   - openff-toolkit>=0.13.0
+  - openff-nagl-base >=0.3.3
   - openff-units==0.2.0
   - pint<0.22
   - openff-models>=0.0.5
@@ -42,4 +43,6 @@ dependencies:
   - sphinx-click
   - pip:
     - sphinx-toolbox
+    - espaloma_charge
+    - openff-nagl-models>=0.1.2
     - git+https://github.com/OpenFreeEnergy/gufe@main
diff --git a/news/TEMPLATE.rst b/news/TEMPLATE.rst
@@ -0,0 +1,23 @@
+**Added:**
+
+* <news item>
+
+**Changed:**
+
+* <news item>
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* <news item>
+
+**Security:**
+
+* <news item>