Merge branch 'main' into cli_yaml_draft

.github/CONTRIBUTING.md

@@ -0,0 +1,22 @@
+# Contributing to OpenFE
+
+Thanks for contributing to the OpenFE software project!
+Read our [code of conduct](../Code_of_Conduct.md) to understand the standards you must adhere to.
+
+## Questions
+
+If you have any questions on using the OpenFE package, reach out on the "Discussions" tab above to start a conversation!
+We are happy to get you started in using our software.
+
+## Issues
+
+If you think you have encountered a software issue, please raise this on the "Issues" tab in Github.
+In general the more details you can provide the better, 
+we recommend reading section 3.3 of [this article](https://livecomsjournal.org/index.php/livecoms/article/view/v3i1e1473)
+to understand the problem solving process.
+
+## Contributing
+
+We welcome any fixes or code contributions.
+Note that any contributions made must be made under a MIT license.
+Feel free to reach out to the developer team who can assist you in this process.

.github/workflows/ci.yaml

@@ -79,6 +79,7 @@ jobs:
         env:
           # Set the OFE_SLOW_TESTS to True if running a Cron job
           OFE_SLOW_TESTS: ${{ fromJSON('{"false":"false","true":"true"}')[github.event_name != 'pull_request'] }}
+          DUECREDIT_ENABLE: 'yes'
         run: |
           pytest -n auto -v --cov=openfe --cov=openfecli --cov-report=xml --durations=10
 

.gitignore

@@ -1,4 +1,5 @@
 # custom ignores
+.duecredit.p
 .xxrun
 .idea/
 .vscode/

README.md

@@ -1,5 +1,5 @@
 [![Logo](https://img.shields.io/badge/OSMF-OpenFreeEnergy-%23002f4a)](https://openfree.energy/)
-[![build](https://github.com/OpenFreeEnergy/openfe/actions/workflows/ci.yaml/badge.svg)](https://github.com/OpenFreeEnergy/openfe/actions/workflows/ci.yaml)
+[![build](https://github.com/OpenFreeEnergy/openfe/actions/workflows/ci.yaml/badge.svg?event=schedule)](https://github.com/OpenFreeEnergy/openfe/actions/workflows/ci.yaml)
 [![coverage](https://codecov.io/gh/OpenFreeEnergy/openfe/branch/main/graph/badge.svg)](https://codecov.io/gh/OpenFreeEnergy/openfe)
 [![documentation](https://readthedocs.org/projects/openfe/badge/?version=latest)](https://openfe.readthedocs.io/en/latest/?badge=latest)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.8344248.svg)](https://doi.org/10.5281/zenodo.8344248)

docs/conf.py

@@ -103,7 +103,6 @@
 
 autodoc_mock_imports = [
     "matplotlib",
-    "lomap",
     "openmmtools",
     "mdtraj",
     "openmmforcefields",
@@ -137,6 +136,7 @@
         }
     ],
     "accent_color": "DarkGoldenYellow",
+    "navigation_with_keys": False,
 }
 html_logo = "_static/Squaredcircle.svg"
 

docs/environment.yaml

@@ -4,6 +4,7 @@ channels:
 - https://conda.anaconda.org/conda-forge
 dependencies:
 - autodoc-pydantic<2.0
+- lomap2>=3.0.0
 - openff-models>=0.0.5
 - openff-toolkit >=0.13.0
 - openff-units

docs/reference/api/ligand_network.rst

@@ -32,6 +32,9 @@ Functions that build a :class:`.LigandNetwork` from a collection of :class:`Smal
     generate_radial_network
     generate_maximal_network
     generate_minimal_spanning_network
+    generate_minimal_redundant_network
+    generate_lomap_network
+
 
 .. _Ligand Network Loaders:
 
@@ -90,15 +93,15 @@ Atom Map Scorers
 
 Scoring functions for a mapping between ligands. These are used as objective functions for :any:`Ligand Network Planners`.
 
-LOMAP Scorers
+
+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::

environment.yml

@@ -3,6 +3,8 @@ channels:
   - jaimergp/label/unsupported-cudatoolkit-shim
   - conda-forge
 dependencies:
+  - duecredit
+  - lomap2>=3.0.0
   - numpy<1.24
   - networkx
   - rdkit

openfe/due.py

@@ -0,0 +1,74 @@
+# emacs: at the end of the file
+# ex: set sts=4 ts=4 sw=4 et:
+# ## ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### #
+"""
+
+Stub file for a guaranteed safe import of duecredit constructs:  if duecredit
+is not available.
+
+To use it, place it into your project codebase to be imported, e.g. copy as
+
+    cp stub.py /path/tomodule/module/due.py
+
+Note that it might be better to avoid naming it duecredit.py to avoid shadowing
+installed duecredit.
+
+Then use in your code as
+
+    from .due import due, Doi, BibTeX, Text
+
+See  https://github.com/duecredit/duecredit/blob/master/README.md for examples.
+
+Origin:     Originally a part of the duecredit
+Copyright:  2015-2021  DueCredit developers
+License:    BSD-2
+"""
+
+__version__ = '0.0.9'
+
+
+class InactiveDueCreditCollector(object):
+    """Just a stub at the Collector which would not do anything"""
+    def _donothing(self, *args, **kwargs):
+        """Perform no good and no bad"""
+        pass
+
+    def dcite(self, *args, **kwargs):
+        """If I could cite I would"""
+        def nondecorating_decorator(func):
+            return func
+        return nondecorating_decorator
+
+    active = False
+    activate = add = cite = dump = load = _donothing
+
+    def __repr__(self):
+        return self.__class__.__name__ + '()'
+
+
+def _donothing_func(*args, **kwargs):
+    """Perform no good and no bad"""
+    pass
+
+
+try:
+    from duecredit import due, BibTeX, Doi, Url, Text  # lgtm [py/unused-import]
+    if 'due' in locals() and not hasattr(due, 'cite'):
+        raise RuntimeError(
+            "Imported due lacks .cite. DueCredit is now disabled")
+except Exception as e:
+    if not isinstance(e, ImportError):
+        import logging
+        logging.getLogger("duecredit").error(
+            "Failed to import duecredit due to %s" % str(e))
+    # Initiate due stub
+    due = InactiveDueCreditCollector()
+    BibTeX = Doi = Url = Text = _donothing_func
+
+# Emacs mode definitions
+# Local Variables:
+# mode: python
+# py-indent-offset: 4
+# tab-width: 4
+# indent-tabs-mode: nil
+# End:

openfe/protocols/openmm_afe/base.py

@@ -27,6 +27,7 @@
 import openmm
 from openff.units import unit
 from openff.units.openmm import from_openmm, to_openmm, ensure_quantity
+from openff.toolkit.topology import Molecule as OFFMolecule
 from openmmtools import multistate
 from openmmtools.states import (SamplerState,
                                 ThermodynamicState,
@@ -71,7 +72,7 @@ def __init__(self, *,
                  stateA: ChemicalSystem,
                  stateB: ChemicalSystem,
                  settings: settings.Settings,
-                 alchemical_components: Dict[str, List[str]],
+                 alchemical_components: dict[str, list[Component]],
                  generation: int = 0,
                  repeat_id: int = 0,
                  name: Optional[str] = None,):
@@ -89,6 +90,8 @@ def __init__(self, *,
           constructed by calling the
           :class:`AbsoluteTransformProtocol.get_default_settings` method
           to get a default set of settings.
+        alchemical_components : dict[str, Component]
+          the alchemical components for each state in this Unit
         name : str, optional
           Human-readable identifier for this Unit
         repeat_id : int, optional
@@ -110,24 +113,24 @@ def __init__(self, *,
 
     @staticmethod
     def _get_alchemical_indices(omm_top: openmm.Topology,
-                                comp_resids: Dict[str, npt.NDArray],
-                                alchem_comps: Dict[str, List[Component]]
-                                ) -> List[int]:
+                                comp_resids: dict[Component, npt.NDArray],
+                                alchem_comps: dict[str, list[Component]]
+                                ) -> list[int]:
         """
         Get a list of atom indices for all the alchemical species
 
         Parameters
         ----------
         omm_top : openmm.Topology
           Topology of OpenMM System.
-        comp_resids : Dict[str, npt.NDArray]
+        comp_resids : dict[Component, npt.NDArray]
           A dictionary of residues for each component in the System.
-        alchem_comps : Dict[str, List[Component]]
+        alchem_comps : dict[str, list[Component]]
           A dictionary of alchemical components for each end state.
 
         Return
         ------
-        atom_ids : List[int]
+        atom_ids : list[int]
           A list of atom indices for the alchemical species
         """
 
@@ -208,7 +211,10 @@ def _set_optional_path(basepath):
         self.shared_basepath = _set_optional_path(shared_basepath)
 
     @abc.abstractmethod
-    def _get_components(self):
+    def _get_components(self) -> tuple[dict[str, list[Component]],
+                                       Optional[gufe.SolventComponent],
+                                       Optional[gufe.ProteinComponent],
+                                       dict[SmallMoleculeComponent, OFFMolecule]]:
         """
         Get the relevant components to create the alchemical system with.
 
@@ -280,7 +286,7 @@ def _get_modeller(
         self,
         protein_component: Optional[ProteinComponent],
         solvent_component: Optional[SolventComponent],
-        smc_components: list[SmallMoleculeComponent],
+        smc_components: dict[SmallMoleculeComponent, OFFMolecule],
         system_generator: SystemGenerator,
         solvation_settings: SolvationSettings
     ) -> tuple[app.Modeller, dict[Component, npt.NDArray]]:
@@ -294,8 +300,8 @@ def _get_modeller(
           Protein Component, if it exists.
         solvent_component : Optional[ProteinCompoinent]
           Solvent Component, if it exists.
-        smc_components : list[SmallMoleculeComponents]
-          List of SmallMoleculeComponents to add.
+        smc_components : list[openff.toolkit.topology.Molecule]
+          List of openff Molecules to add.
         system_generator : openmmforcefields.generator.SystemGenerator
           System Generator to parameterise this unit.
         solvation_settings : SolvationSettings
@@ -317,10 +323,17 @@ def _get_modeller(
         # of solvating the system.
         # Note by default this is cached to ctx.shared/db.json which should
         # reduce some of the costs.
-        for comp in smc_components:
-            offmol = comp.to_openff()
+        for mol in smc_components.values():
+            # don't do this if we have user charges
+            if not (mol.partial_charges is not None and np.any(mol.partial_charges)):
+                # due to issues with partial charge generation in ambertools
+                # we default to using the input conformer for charge generation
+                mol.assign_partial_charges(
+                    'am1bcc', use_conformers=mol.conformers
+                )
+
             system_generator.create_system(
-                offmol.to_topology().to_openmm(), molecules=[offmol]
+                mol.to_topology().to_openmm(), molecules=[mol]
             )
 
         # get OpenMM modeller + dictionary of resids for each component
@@ -338,7 +351,7 @@ def _get_omm_objects(
         self,
         system_modeller: app.Modeller,
         system_generator: SystemGenerator,
-        smc_components: list[SmallMoleculeComponent],
+        smc_components: list[OFFMolecule],
     ) -> tuple[app.Topology, openmm.unit.Quantity, openmm.System]:
         """
         Get the OpenMM Topology, Positions and System of the
@@ -351,8 +364,8 @@ def _get_omm_objects(
           parametrized.
         system_generator : SystemGenerator
           SystemGenerator object to create a System with.
-        smc_components : list[SmallMoleculeComponent]
-          A list of SmallMoleculeComponents to add to the system.
+        smc_components : list
+          A list of openff Molecules to add to the system.
 
         Returns
         -------
@@ -368,7 +381,7 @@ def _get_omm_objects(
         positions = to_openmm(from_openmm(system_modeller.getPositions()))
         system = system_generator.create_system(
             system_modeller.topology,
-            molecules=[s.to_openff() for s in smc_components]
+            molecules=smc_components,
         )
         return topology, system, positions
 
@@ -551,7 +564,7 @@ def _get_reporter(
         )
 
         nc = self.shared_basepath / simulation_settings.output_filename
-        chk = self.shared_basepath / simulation_settings.checkpoint_storage
+        chk = simulation_settings.checkpoint_storage
 
         reporter = multistate.MultiStateReporter(
             storage=nc,
@@ -841,7 +854,7 @@ def run(self, dry=False, verbose=True,
 
         # 5. Get OpenMM topology, positions and system
         omm_topology, omm_system, positions = self._get_omm_objects(
-            system_modeller, system_generator, smc_comps
+            system_modeller, system_generator, list(smc_comps.values())
         )
 
         # 6. Pre-minimize System (Test + Avoid NaNs)
@@ -915,7 +928,7 @@ def run(self, dry=False, verbose=True,
 
         if not dry:
             nc = self.shared_basepath / settings['simulation_settings'].output_filename
-            chk = self.shared_basepath / settings['simulation_settings'].checkpoint_storage
+            chk = settings['simulation_settings'].checkpoint_storage
             return {
                 'nc': nc,
                 'last_checkpoint': chk,