Fixes for issues and assorted cleanups to generators (#391)

* Cleanups:

* Remove residue_atoms argument of generate_residue_template() methods: fixes #379

* OpenMMSystemMixin.convert_system_to_ffxml improper_atom_ordering was silently ignored

* Removal of unused kwargs that could cause misspelled parameters to be silently ignored

* Removal of some unused local variables

* DummySystemGenerator: was broken due to early return

* Consolidate custom classproperty implementation

* Docstrings: parameters out of order, errors, formatting

* Fix OpenFF units import for older openff-toolkit version compatible with espaloma

* Fix broken DummySystemGenerator feature

* Partial charge normalization

* Use common logic for checking user-specified partial charges sum to
  total formal charge, and raising a warning if so

* GAFFTemplateGenerator no longer silently adjusts user-specified
  partial charges if they don't sum to the formal charge: fixes #373

* Cleanups to test cases:

* Consolidate propagate_dynamics() implementations into
  TemplateGeneratorBaseCase

* Remove charges_from_system(), charges_are_equal(), compute_energy(),
  and compare_energies() from TestGAFFTemplateGenerator since identical
  implementations are available in TemplateGeneratorBaseCase

* Bump CI OpenMM versions

* Testing template generator user charge feature:

* Ensure warnings are raised / not raised as appropriate (GAFF, SMIRNOFF)

* SMIRNOFF should accept user charges not matching once we warn about it

* Make template_generator_kwargs explicit

* ruff format

* Remove unused imports

* Formatting, remove unused local assignments

* Remove references to and tests for DummySystemGenerator

* Style update: import classproperty

---------

Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com>

Author: epretti

.github/workflows/test_charmm.yaml

@@ -25,7 +25,7 @@ jobs:
       matrix:
         os: [ubuntu-latest]
         python-version: ["3.12"]
-        openmm-version: ["8.2.0dev1"]
+        openmm-version: ["8.3.1"]
 
     steps:
     - uses: actions/checkout@v4

openmmforcefields/generators/system_generators.py

@@ -1,32 +1,22 @@
 """
 System generators that build an OpenMM System object from a Topology object.
-
 """
 
+from openmmforcefields.utils import classproperty
+
 ################################################################################
 # LOGGER
 ################################################################################
 
 import logging
 
-_logger = logging.getLogger("openmmforcefields.system_generators")
+_logger = logging.getLogger("openmmforcefields.generators.system_generators")
 
 ################################################################################
 # System generator base class
 ################################################################################
 
 
-class classproperty(property):
-    def __get__(self, obj, objtype=None):
-        return super().__get__(objtype)
-
-    def __set__(self, obj, value):
-        super().__set__(type(obj), value)
-
-    def __delete__(self, obj):
-        super().__delete__(type(obj))
-
-
 class SystemGenerator:
     """
     Common interface for generating OpenMM Systems from OpenMM Topology objects
@@ -97,7 +87,7 @@ def __init__(
         ----------
         forcefields : list of str, optional, default=None
             List of the names of ffxml files that will be used in System creation for the biopolymer.
-        small_molecule_forcefield : str, optional, default='openff-1.0.0'
+        small_molecule_forcefield : str, optional, default='openff-2.2.0'
             Small molecule force field to use.
             Must be supported by one of the registered template generators:
                 [GAFFTemplateGenerator, SMIRNOFFTemplateGenerator]
@@ -113,7 +103,7 @@ def __init__(
         periodic_forcefield_kwargs : NonbondedMethod, optional, default={'nonbondedMethod' : PME}
             Keyword arguments added to forcefield_kwargs when the Topology is periodic.
         template_generator_kwargs : dict, optional, default=None
-            Keyword arguments to be passed to subclasses of
+            The value of an extra keyword argument called `template_generator_kwargs` to be passed to subclasses of
             ``openmmforcefields.generators.template_generators.SmallMoleculeTemplateGenerator``.
             Currently only used for ``openmmforcefields.generators.template_generators.EspalomaTemplateGenerator``.
         barostat : openmm.MonteCarloBarostat, optional, default=None
@@ -202,7 +192,6 @@ def __init__(
         >>> system_generator.particle_epsilons = False # will zero out Lennard-Jones particle-particle interactions
         >>> system_generator.particle_exceptions = False # will zero out all 1-4 Lennard-Jones interactions
         >>> system_generator.torsions = False # will zero out all torsion terms
-
         """  # noqa
 
         # Initialize
@@ -301,8 +290,8 @@ def add_molecules(self, molecules):
             Can also be a list of Molecule objects or objects that can be used to construct a Molecule.
             If specified, these molecules will be recognized and parameterized as needed.
             The parameters will be cached in case they are encountered again the future.
-
         """
+
         if self.template_generator is None:
             raise ValueError(
                 "You must have a small molecule residue template generator registered to add small molecules"
@@ -314,6 +303,7 @@ def _modify_forces(self, system):
         """
         Add barostat and modify forces if requested.
         """
+
         # Add barostat if requested and the system uses periodic boundary conditions
         if (self.barostat is not None) and system.usesPeriodicBoundaryConditions():
             import numpy as np
@@ -368,21 +358,21 @@ def create_system(self, topology, molecules=None):
 
         Parameters
         ----------
-        topology : openmmtools.topology.Topology object
+        topology : openmm.app.Topology object
             The topology describing the system to be created
         molecules : openff.toolkit.topology.Molecule or list of Molecules, optional, default=None
             Can alternatively be an object (such as an OpenEye OEMol or RDKit Mol or SMILES string) that can be used
             to construct a Molecule.
             Can also be a list of Molecule objects or objects that can be used to construct a Molecule.
-            If specified, these molecules will be recognized and parameterized with antechamber as needed.
+            If specified, these molecules will be recognized and parameterized as needed.
             The parameters will be cached in case they are encountered again the future.
 
         Returns
         -------
         system : openmm.System
             A system object generated from the topology
-
         """
+
         # Inform the template generator about any specified molecules
         if (self.template_generator is not None) and (molecules is not None):
             self.template_generator.add_molecules(molecules)