Merge pull request #725 from OpenFreeEnergy/doc_drive_2

Doc drive 2
OpenFreeEnergy · Feb 16, 2024 · 7b3c2fe · 7b3c2fe
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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/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