Merge pull request #302 from OpenBioSim/fix_zero_dummy_torsions

Expose torsion modification kwargs

python/BioSimSpace/Process/_somd.py

@@ -226,6 +226,14 @@ def __init__(
  else:
  raise IOError("SOMD executable doesn't exist: '%s'" % exe)
 
+ # Validate torsion modification kwargs.
+ self._zero_dummy_dihedrals = kwargs.get("zero_dummy_dihedrals", False)
+ if not isinstance(self._zero_dummy_dihedrals, bool):
+ self._zero_dummy_dihedrals = False
+ self._zero_dummy_impropers = kwargs.get("zero_dummy_impropers", False)
+ if not isinstance(self._zero_dummy_impropers, bool):
+ self._zero_dummy_impropers = False
+
  # The names of the input files.
  self._rst_file = _os.path.join(str(self._work_dir), f"{name}.rst7")
  self._top_file = _os.path.join(str(self._work_dir), f"{name}.prm7")
@@ -322,7 +330,9 @@ def _setup(self):
  # to the lambda = 0 state.
  pert_mol = _to_pert_file(
  pert_mol,
- self._pert_file,
+ filename=self._pert_file,
+ zero_dummy_dihedrals=self._zero_dummy_dihedrals,
+ zero_dummy_impropers=self._zero_dummy_impropers,
  property_map=self._property_map,
  perturbation_type=self._protocol.getPerturbationType(),
  )