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Reparse TorsionIndexer if a new mol is returned from the TK #99

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Reparse TorsionIndexer if a new mol is returned from the TK #99

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reparse TorsionIndexer if a new mol is returned from the TK
trevorgokey Feb 4, 2021
52275b5
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trevorgokey Feb 4, 2021
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24 changes: 19 additions & 5 deletions openff/qcsubmit/workflow_components/state_enumeration.py
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Original file line number Diff line number Diff line change
Expand Up @@ -3,17 +3,16 @@
"""
from typing import List

from openforcefield.topology import Molecule
from openforcefield.utils.toolkits import OpenEyeToolkitWrapper
from pydantic import Field

from openff.qcsubmit.common_structures import ComponentProperties
from openff.qcsubmit.common_structures import ComponentProperties, TorsionIndexer
from openff.qcsubmit.datasets import ComponentResult
from openff.qcsubmit.utils import check_missing_stereo
from openff.qcsubmit.workflow_components.base_component import (
CustomWorkflowComponent,
ToolkitValidator,
)
from openforcefield.topology import Molecule
from openforcefield.utils.toolkits import OpenEyeToolkitWrapper
from pydantic import Field


class EnumerateTautomers(ToolkitValidator, CustomWorkflowComponent):
Expand Down Expand Up @@ -58,6 +57,7 @@ def _apply(self, molecules: List[Molecule]) -> ComponentResult:
result = self._create_result()

for molecule in molecules:
dihedrals = molecule.properties.get("dihedrals", None)
try:
tautomers = molecule.enumerate_tautomers(
max_states=self.max_tautomers, toolkit_registry=toolkit
Expand All @@ -67,6 +67,10 @@ def _apply(self, molecules: List[Molecule]) -> ComponentResult:
result.add_molecule(molecule)
else:
for tautomer in tautomers:
if dihedrals is not None:
tautomer.properties["dihedrals"] = TorsionIndexer.parse_obj(
dihedrals
)
result.add_molecule(tautomer)

except Exception:
Expand Down Expand Up @@ -127,6 +131,7 @@ def _apply(self, molecules: List[Molecule]) -> ComponentResult:
result = self._create_result()

for molecule in molecules:
dihedrals = molecule.properties.get("dihedrals", None)
try:
isomers = molecule.enumerate_stereoisomers(
undefined_only=self.undefined_only,
Expand All @@ -138,6 +143,10 @@ def _apply(self, molecules: List[Molecule]) -> ComponentResult:
# now check that each molecule is well defined
for isomer in isomers:
if not check_missing_stereo(isomer):
if dihedrals is not None:
isomer.properties["dihedrals"] = TorsionIndexer.parse_obj(
dihedrals
)
result.add_molecule(isomer)

# now check the input
Expand Down Expand Up @@ -201,10 +210,15 @@ def _apply(self, molecules: List[Molecule]) -> ComponentResult:
if has_oe:

for molecule in molecules:
dihedrals = molecule.properties.get("dihedrals", None)
try:
protomers = molecule.enumerate_protomers(max_states=self.max_states)

for protomer in protomers:
if dihedrals is not None:
protomer.properties["dihedrals"] = TorsionIndexer.parse_obj(
dihedrals
)
result.add_molecule(protomer)
result.add_molecule(molecule)

Expand Down