Skip to content

Remove duplicate atom type handling and re-enable GAFF tests #371

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
epretti merged 1 commit into from
Mar 24, 2025
Merged

Remove duplicate atom type handling and re-enable GAFF tests #371

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
20 changes: 0 additions & 20 deletions openmmforcefields/generators/template_generators.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -535,11 +535,6 @@ def __init__(self, molecules=None, forcefield=None, cache=None, **kwargs):

self._database_table_name = os.path.basename(forcefield)

# Track which OpenMM ForceField objects have loaded the relevant GAFF parameters
self._gaff_parameters_loaded = dict()
# Track which atom types we have told OpenMM about
self._gaff_atom_types_observed = set()

@property
def gaff_version(self):
"""The current GAFF version in use"""
Expand Down Expand Up @@ -734,21 +729,6 @@ def generate_residue_template(self, molecule, residue_atoms=None):
if "write_unused" in signature(params.write).parameters:
kwargs["write_unused"] = True

# We need to make sure we don't duplicate atom types we have already told
# OpenMM about. To do this we will keep track of atom types we have already
# seen and ensure we only record new atom types in the xml.

# iterate over a copy of the atom types
for atom_type in params.atom_types.copy().keys():
if atom_type not in self._gaff_atom_types_observed:
self._gaff_atom_types_observed.add(atom_type)
_logger.debug(f"added {atom_type} to set of seen types")
# if we have seen the atom type, delete it from the OG params,
# not the copy!
else:
del params.atom_types[atom_type]
_logger.debug(f"{atom_type} already recorded")

params.write(ffxml, **kwargs)
ffxml_contents = ffxml.getvalue()

Expand Down
2 changes: 1 addition & 1 deletion openmmforcefields/tests/test_template_generators.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -306,7 +306,7 @@ def compute_energy(system, positions):
return openmm_energy, openmm_forces


@pytest.mark.skip(reason="Skip GAFF tests")
@pytest.mark.rungaff
class TestGAFFTemplateGenerator(TemplateGeneratorBaseCase):
TEMPLATE_GENERATOR = GAFFTemplateGenerator

Expand Down