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Backport fix from PR #450 #451

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Merged
lohedges merged 1 commit into from
Sep 23, 2025
Merged

Backport fix from PR #450 #451

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29 changes: 15 additions & 14 deletions python/BioSimSpace/Process/_somd.py
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Original file line number Diff line number Diff line change
Expand Up @@ -238,9 +238,9 @@ def __init__(
self._zero_dummy_impropers = kwargs.get("zero_dummy_impropers", False)
if not isinstance(self._zero_dummy_impropers, bool):
self._zero_dummy_impropers = False
self._no_dummy_modifications = kwargs.get("no_dummy_modifications", False)
if not isinstance(self._no_dummy_modifications, bool):
self._no_dummy_modifications = False
self._dummy_modifications = kwargs.get("dummy_modifications", True)
if not isinstance(self._dummy_modifications, bool):
self._dummy_modifications = True

# The names of the input files.
self._rst_file = _os.path.join(str(self._work_dir), f"{name}.rst7")
Expand Down Expand Up @@ -343,7 +343,7 @@ def _setup(self):
zero_dummy_impropers=self._zero_dummy_impropers,
property_map=self._property_map,
perturbation_type=self._protocol.getPerturbationType(),
no_dummy_modifications=self._no_dummy_modifications,
dummy_modifications=self._dummy_modifications,
)

self._input_files.append(self._pert_file)
Expand Down Expand Up @@ -926,7 +926,7 @@ def _to_pert_file(
print_all_atoms=False,
property_map={},
perturbation_type="full",
no_dummy_modifications=False,
dummy_modifications=True,
):
"""
Write a perturbation file for a perturbable molecule.
Expand Down Expand Up @@ -966,9 +966,10 @@ def _to_pert_file(
"grow_soft" : Perturb all growing soft atom LJ terms (i.e. 0.0->value).
"charge_soft" : Perturb all charging soft atom LJ terms (i.e. 0.0->value).

no_dummy_modifications : bool
Whether to skip modifications to dummy atoms. This is useful when
modifications to dummy atoms have already been applied.
dummy_modifications : bool
Whether to modify bonded interactions involving dummy atoms. It is
useful to disable this when modifications to dummy atom terms have
already been applied to the system externally.

Returns
-------
Expand Down Expand Up @@ -1006,8 +1007,8 @@ def _to_pert_file(
if not isinstance(perturbation_type, str):
raise TypeError("'perturbation_type' must be of type 'str'")

if not isinstance(no_dummy_modifications, bool):
raise TypeError("'no_dummy_modifications' must be of type 'bool'")
if not isinstance(dummy_modifications, bool):
raise TypeError("'dummy_modifications' must be of type 'bool'")

# Convert to lower case and strip whitespace.
perturbation_type = perturbation_type.lower().replace(" ", "")
Expand Down Expand Up @@ -1985,8 +1986,8 @@ def sort_angles(angles, idx):
initial_dummy = _has_dummy(mol, [idx0, idx1, idx2])
final_dummy = _has_dummy(mol, [idx0, idx1, idx2], True)

# Modifications to dummy states.
if not no_dummy_modifications:
# Perform dummy modifications if required.
if dummy_modifications:
# Set the angle parameters of the dummy state to those of
# the non-dummy end state.
if initial_dummy and final_dummy:
Expand Down Expand Up @@ -2329,7 +2330,7 @@ def sort_dihedrals(dihedrals, idx):
all_dummy_final = all(_is_dummy(mol, [idx0, idx1, idx2, idx3], True))

# Perform dummy modifications if required.
if not no_dummy_modifications:
if dummy_modifications:
# Dummies are present in both end states, use null potentials.
if has_dummy_initial and has_dummy_final:
amber_dihedral0 = _SireMM.AmberDihedral()
Expand Down Expand Up @@ -2729,7 +2730,7 @@ def sort_dihedrals(dihedrals, idx):
all_dummy_final = all(_is_dummy(mol, [idx0, idx1, idx2, idx3], True))

# Perform dummy modifications if required.
if not no_dummy_modifications:
if dummy_modifications:
# Dummies are present in both end states, use null potentials.
if has_dummy_initial and has_dummy_final:
amber_dihedral0 = _SireMM.AmberDihedral()
Expand Down