Source code for openff.qcsubmit.workflow_components.conformer_generation

from typing import List, Optional

import simtk.unit as unit
from openff.toolkit.topology import Molecule
from openff.toolkit.utils import ToolkitRegistry
from pydantic import Field
from typing_extensions import Literal

from openff.qcsubmit.common_structures import ComponentProperties
from openff.qcsubmit.workflow_components.base_component import (
from openff.qcsubmit.workflow_components.utils import ComponentResult

[docs]class StandardConformerGenerator(ToolkitValidator, CustomWorkflowComponent): """ Standard conformer generator using the OFFTK and the back end toolkits. """ type: Literal["StandardConformerGenerator"] = "StandardConformerGenerator" rms_cutoff: Optional[float] = Field( None, description="The rms cut off in angstroms to be used when generating the conformers. Passing None will use the default in toolkit of 1.", ) max_conformers: int = Field( 10, description="The maximum number of conformers to be generated per molecule." ) clear_existing: bool = Field( True, description="If any pre-existing conformers should be kept." )
[docs] @classmethod def description(cls) -> str: return "Generate conformations for the given molecules."
[docs] @classmethod def fail_reason(cls) -> str: return "Conformers could not be generated."
[docs] @classmethod def properties(cls) -> ComponentProperties: return ComponentProperties(process_parallel=True, produces_duplicates=False)
def _apply_init(self, result: ComponentResult) -> None: """ Set up the standard conformer filter """ if self.rms_cutoff is not None: self._cache["cutoff"] = self.rms_cutoff * unit.angstrom else: self._cache["cutoff"] = None def _apply( self, molecules: List[Molecule], toolkit_registry: ToolkitRegistry ) -> ComponentResult: """ Generate conformers for the molecules using the selected toolkit backend. Args: molecules: The list of molecules the component should be applied on. toolkit_registry: The openff.toolkit.utils.ToolkitRegistry that declares the available toolkits. Returns: An instance of the [ComponentResult][qcsubmit.datasets.ComponentResult] class which handles collecting together molecules that pass and fail the component """ # create the toolkit result = self._create_result(toolkit_registry=toolkit_registry) rms_cutoff = self._cache["cutoff"] for molecule in molecules: try: # assume input is angstrom until Quantity can be serialized molecule.generate_conformers( n_conformers=self.max_conformers, clear_existing=self.clear_existing, rms_cutoff=rms_cutoff, toolkit_registry=toolkit_registry, ) # need to catch more specific exceptions here. except Exception: result.filter_molecule(molecule) finally: # if we could not produce a conformer then fail the molecule if molecule.n_conformers == 0: result.filter_molecule(molecule) else: result.add_molecule(molecule) return result