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fix devtools partial charge assignment variation

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This commit is contained in:
IAlibay
2024-02-10 00:43:11 +00:00
parent 1487ae2228
commit 1b455cb410
3 changed files with 16 additions and 6 deletions
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18
devtools/data/gen-serialized-results.py
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@@ -14,7 +14,12 @@ import json
import logging
import pathlib
import tempfile
from openff.toolkit import Molecule
from openff.toolkit import (
Molecule, RDKitToolkitWrapper, AmberToolsToolkitWrapper
)
from openff.toolkit.utils.toolkit_registry import (
toolkit_registry_manager, ToolkitRegistry
)
from openff.units import unit
from kartograf.atom_aligner import align_mol_shape
from kartograf import KartografAtomMapper
@@ -31,11 +36,16 @@ logger = logging.getLogger(__name__)
LIGA = "[H]C([H])([H])C([H])([H])C(=O)C([H])([H])C([H])([H])[H]"
LIGB = "[H]C([H])([H])C(=O)C([H])([H])C([H])([H])C([H])([H])[H]"
amber_rdkit = ToolkitRegistry(
[RDKitToolkitWrapper(), AmberToolsToolkitWrapper()]
)
def get_molecule(smi, name):
m = Molecule.from_smiles(smi)
m.generate_conformers()
m.assign_partial_charges(partial_charge_method="am1bcc")
with toolkit_registry_manager(amber_rdkit):
m = Molecule.from_smiles(smi)
m.generate_conformers()
m.assign_partial_charges(partial_charge_method="am1bcc")
return openfe.SmallMoleculeComponent.from_openff(m, name=name)