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Add optional emle_plus support to OpenFFCreationStrategy #23

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Merged
JMorado merged 1 commit into from
Jul 10, 2026
Merged

Add optional emle_plus support to OpenFFCreationStrategy #23

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9 changes: 6 additions & 3 deletions src/fes_ml/alchemical/strategies/openff_strategy.py
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Original file line number Diff line number Diff line change
Expand Up @@ -446,6 +446,7 @@ def create_alchemical_state(
partial_charges_method: str = "am1bcc",
keep_tmp_files: bool = True,
modifications_kwargs: Optional[Dict[str, Dict[str, Any]]] = None,
emle_plus: bool = False,
*args,
**kwargs,
) -> AlchemicalState:
Expand Down Expand Up @@ -507,6 +508,8 @@ def create_alchemical_state(
The geometry of the ligand.
keep_tmp_files : bool, optional, default=True
Whether to keep the temporary files created by the strategy.
emle_plus : bool, optional, default=False
Whether to use EMLE+ instead of EMLE. If True, the EMLE+ modifications will be applied to the system.
modifications_kwargs : dict
A dictionary of keyword arguments for the modifications.

Expand Down Expand Up @@ -679,9 +682,9 @@ def create_alchemical_state(
for modification_name in emle_instances:
modifications_kwargs[modification_name]["mols"] = sr_mols
modifications_kwargs[modification_name]["parm7"] = alchemical_prm7[0]
# TODO: uncomment for EMLE+
modifications_kwargs[modification_name]["top_file"] = files_prefix + ".top"
modifications_kwargs[modification_name]["crd_file"] = files_prefix + ".gro"
if emle_plus:
modifications_kwargs[modification_name]["top_file"] = files_prefix + ".top"
modifications_kwargs[modification_name]["crd_file"] = files_prefix + ".gro"
modifications_kwargs[modification_name]["mm_charges"] = _np.asarray(
[atom.charge().value() for atom in sr_mols.atoms(alchemical_atoms)]
)
Expand Down
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