Source code for openff.qcsubmit.common_structures

"""
This file contains common starting structures which can be mixed into datasets, results and factories.
"""
import copy
import getpass
import re
from datetime import date, datetime
from enum import Enum
from typing import Any, ClassVar, Dict, List, Optional, Set, Tuple, Union

import numpy as np
import qcportal as ptl
from openff.toolkit.topology import Molecule
from pydantic import (
    BaseModel,
    Field,
    HttpUrl,
    PositiveInt,
    StrictBool,
    StrictFloat,
    StrictInt,
    StrictStr,
    constr,
    validator,
)
from qcelemental import constants
from qcelemental.models.common_models import Model
from qcelemental.models.results import WavefunctionProtocolEnum
from qcportal.models.common_models import DriverEnum

from openff.qcsubmit.exceptions import (
    DatasetInputError,
    PCMSettingError,
    QCSpecificationError,
)
from openff.qcsubmit.utils.smirnoff import split_openff_molecule


[docs]class DatasetConfig(BaseModel): """ The basic configurations for all datasets. """ class Config: arbitrary_types_allowed: bool = True allow_mutation: bool = True validate_assignment: bool = True json_encoders: Dict[str, Any] = { np.ndarray: lambda v: v.flatten().tolist(), Enum: lambda v: v.value, } extra: True
[docs]class ResultsConfig(BaseModel): """ A basic config class for results structures. """ class Config: arbitrary_types_allowed: bool = True allow_mutation: bool = False json_encoders: Dict[str, Any] = { np.ndarray: lambda v: v.flatten().tolist(), Enum: lambda v: v.value, }
[docs]class SCFProperties(str, Enum): """ The type of SCF property that should be extracted from a single point calculation. """ Dipole = "dipole" Quadrupole = "quadrupole" MullikenCharges = "mulliken_charges" LowdinCharges = "lowdin_charges" WibergLowdinIndices = "wiberg_lowdin_indices" MayerIndices = "mayer_indices" MBISCharges = "mbis_charges" @classmethod def _missing_(cls, value): """ overwrite the missing method to handle properties with incorrect capitalization. """ for member in cls.__members__.values(): if member._value_ == value.lower(): return member raise QCSpecificationError( f"{value} is not a valid {cls.__name__} please chose from {cls.__members__.values()}" )
DefaultProperties = ( SCFProperties.Dipole, SCFProperties.Quadrupole, SCFProperties.WibergLowdinIndices, SCFProperties.MayerIndices, )
[docs]class ComponentProperties(BaseModel): """ The workflow properties class which controls if the component can be used in multiprocessing or if the component produces duplicates. """ process_parallel: bool = Field( ..., description="If the component can safely be ran in parallel `True` or not `False`.", ) produces_duplicates: bool = Field( ..., description="If the component is expected to produce duplicate molecules `True` or not `False`.", ) class Config: allow_mutation: bool = False extra = "forbid"
[docs]class TDSettings(DatasetConfig): """ A replacement of the TDKeywords class in the QCFractal which drops the dihedrals field as this is moved up the model. The settings here overwrite the global dataset and allow the user to have control over the individual scans. """ grid_spacing: Optional[List[int]] = Field( None, description="List of grid spacings for the dihedral scan in degrees." ) dihedral_ranges: Optional[List[Tuple[int, int]]] = Field( None, description="A list of the dihedral scan limits of the form (lower, upper)", ) energy_decrease_thresh: Optional[float] = Field( None, description="The threshold of the smallest energy decrease amount to trigger activating optimizations from " "grid point.", ) energy_upper_limit: Optional[float] = Field( None, description="The threshold if the energy of a grid point that is higher than the current global minimum, to " "start new optimizations, in unit of a.u. I.e. if energy_upper_limit = 0.05, current global " "minimum energy is -9.9 , then a new task starting with energy -9.8 will be skipped.", ) additional_keywords: Dict[str, Any] = Field( {}, description="Additional keywords to add to the torsiondrive's optimization runs", )
[docs]class PCMSettings(ResultsConfig): """ A class to handle PCM settings which can be used with PSi4. """ units: str = Field( ..., description="The units used in the input options atomic units are used by default.", ) codata: int = Field( 2010, description="The set of fundamental physical constants to be used in the module.", ) cavity_Type: str = Field( "GePol", description="Completely specifies type of molecular surface and its discretization.", ) cavity_Area: float = Field( 0.3, description="Average area (weight) of the surface partition for the GePol cavity in the specified units. By default this is in AU.", ) cavity_Scaling: bool = Field( True, description="If true, the radii for the spheres will be scaled by 1.2. For finer control on the scaling factor for each sphere, select explicit creation mode.", ) cavity_RadiiSet: str = Field( "Bondi", description="Select set of atomic radii to be used. Currently Bondi-Mantina Bondi, UFF and Allinger’s MM3 sets available. Radii in Allinger’s MM3 set are obtained by dividing the value in the original paper by 1.2, as done in the ADF COSMO implementation We advise to turn off scaling of the radii by 1.2 when using this set.", ) cavity_MinRadius: float = Field( 100, description="Minimal radius for additional spheres not centered on atoms. An arbitrarily big value is equivalent to switching off the use of added spheres, which is the default in AU.", ) cavity_Mode: str = Field( "Implicit", description="How to create the list of spheres for the generation of the molecular surface.", ) medium_SolverType: str = Field( "IEFPCM", description="Type of solver to be used. All solvers are based on the Integral Equation Formulation of the Polarizable Continuum Model.", ) medium_Nonequilibrium: bool = Field( False, description="Initializes an additional solver using the dynamic permittivity. To be used in response calculations.", ) medium_Solvent: str = Field( ..., description="Specification of the dielectric medium outside the cavity. Note this will always be converted to the molecular formula to aid parsing via PCM.", ) medium_MatrixSymm: bool = Field( True, description="If True, the PCM matrix obtained by the IEFPCM collocation solver is symmetrized.", ) medium_Correction: float = Field( 0.0, description="Correction, k for the apparent surface charge scaling factor in the CPCM solver.", ge=0, ) medium_DiagonalScaling: float = Field( 1.07, description="Scaling factor for diagonal of collocation matrices, values commonly used in the literature are 1.07 and 1.0694.", ge=0, ) medium_ProbeRadius: float = Field( 1.0, description="Radius of the spherical probe approximating a solvent molecule. Used for generating the solvent-excluded surface (SES) or an approximation of it. Overridden by the built-in value for the chosen solvent. Default in AU.", ) _solvents: ClassVar[Dict[str, str]] = { "water": "H2O", "dimethylsulfoxide": "DMSO", "nitromethane": "CH3NO2", "acetonitrile": "CH3CN", "methanol": "CH3OH", "ethanol": "CH3CH2OH", "1,2-dichloroethane": "C2H4CL2", "methylenechloride": "CH2CL2", "tetrahydrofurane": "THF", "aniline": "C6H5NH2", "chlorobenzene": "C6H5CL", "chloroform": "CHCL3", "toluene": "C6H5CH3", "1,4-dioxane": "C4H8O2", "carbon tetrachloride": "CCL4", "cyclohexane": "C6H12", "n-heptane": "C7H16", } @validator("units") def _check_units(cls, unit: str) -> str: """ Make sure the units are a valid option. """ units = ["au", "angstrom"] if unit.lower() not in units: raise PCMSettingError(f"{unit} is not valid only {units} are supported.") return unit @validator("codata") def _check_codata(cls, codata: int) -> int: """ Make sure the codata is a valid option in PCM. """ datasets = [2010, 2006, 2002, 1998] if codata not in datasets: raise PCMSettingError( f"{codata} is not valid only {datasets} are supported." ) return codata @validator("cavity_Type") def _check_cavity_type(cls, cavity: str) -> str: """ Make sure the cavity type is GePol as this is the only kind supported. """ if cavity.lower() != "gepol": raise PCMSettingError( f"{cavity} is not a supported type only GePol is available." ) return "GePol" @validator("cavity_RadiiSet") def _check_radii_set(cls, radiiset: str) -> str: """ Make sure a valid radii set is passed. """ radiisets = ["bondi", "uff", "allinger"] if radiiset.lower() not in radiisets: raise PCMSettingError( f"{radiiset} is not a supported set please chose from {radiisets}" ) return radiiset @validator("cavity_Mode") def _check_cavity_mode(cls, cavity: str) -> str: """ Make sure that a valid cavity mode is passed. """ if cavity.lower() != "implicit": raise PCMSettingError( f"{cavity} is not supported via QCSubmit only implicit can be used for collection based calculations." ) return "Implicit" @validator("medium_SolverType") def _check_solver(cls, solver: str) -> str: """ Make sure valid solver is passed. """ solvers = ["IEFPCM", "CPCM"] if solver.upper() not in solvers: raise PCMSettingError(f"{solver} not supported please chose from {solvers}") return solver.upper() @validator("medium_Solvent") def _check_solvent(cls, solvent: str) -> str: """ Make sure that a valid solvent from the list of supported values is passed. """ solvent_formula = cls._solvents.get(solvent.lower(), solvent.upper()) if solvent_formula not in cls._solvents.values(): raise PCMSettingError( f"The solvent {solvent} is not supported please chose from the following solvents or formulas {cls._solvents.items()}" ) return solvent_formula def __init__(self, **kwargs): """ Fully validate the model making sure options are compatible and convert any defaults to the give unit system. """ # convert all inputs to the correct units units = kwargs.get("units", None) if units is not None and units.lower() == "angstrom": # we need to convert the default values only which have length scales if "medium_ProbeRadius" not in kwargs: medium_ProbeRadius = ( self.__fields__["medium_ProbeRadius"].default * constants.bohr2angstroms ) kwargs["medium_ProbeRadius"] = medium_ProbeRadius if "cavity_MinRadius" not in kwargs: cavity_MinRadius = ( self.__fields__["cavity_MinRadius"].default * constants.bohr2angstroms ) kwargs["cavity_MinRadius"] = cavity_MinRadius if "cavity_Area" not in kwargs: cavity_Area = ( self.__fields__["cavity_Area"].default * constants.bohr2angstroms**2 ) kwargs["cavity_Area"] = cavity_Area super(PCMSettings, self).__init__(**kwargs)
[docs] def to_string(self) -> str: """ Generate the formated PCM settings string which can be ingested by psi4 via the qcschema interface. """ # format the medium keywords medium_str, cavity_str = "", "" for prop in self.__fields__.keys(): if "medium" in prop: medium_str += f"\n {prop[7:]} = {getattr(self, prop)}" elif "cavity" in prop: cavity_str += f"\n {prop[7:]} = {getattr(self, prop)}" # format the cavity keywords pcm_string = f""" Units = {self.units} CODATA = {self.codata} Medium {{{medium_str }}} Cavity {{{cavity_str}}}""" return pcm_string
[docs]class QCSpec(ResultsConfig): method: constr(strip_whitespace=True) = Field( "B3LYP-D3BJ", description="The name of the computational model used to execute the calculation. This could be the QC method or the forcefield name.", ) basis: Optional[constr(strip_whitespace=True)] = Field( "DZVP", description="The name of the basis that should be used with the given method, outside of QC this can be the parameterization ie antechamber or None.", ) program: constr(strip_whitespace=True) = Field( "psi4", description="The name of the program that will be used to perform the calculation.", ) spec_name: constr(strip_whitespace=True) = Field( "default", description="The name the specification will be stored under in QCArchive.", ) spec_description: str = Field( "Standard OpenFF optimization quantum chemistry specification.", description="The description of the specification which will be stored in QCArchive.", ) store_wavefunction: WavefunctionProtocolEnum = Field( WavefunctionProtocolEnum.none, description="The level of wavefunction detail that should be saved in QCArchive. Note that this is done for every calculation and should not be used with optimizations.", ) implicit_solvent: Optional[PCMSettings] = Field( None, description="If PCM is to be used with psi4 this is the full description of the settings that should be used.", ) maxiter: PositiveInt = Field( 200, description="The maximum number of SCF iterations in QM calculations this will be ignored by programs where this does not make sense.", ) scf_properties: Optional[List[SCFProperties]] = Field( [ SCFProperties.Dipole, SCFProperties.Quadrupole, SCFProperties.WibergLowdinIndices, SCFProperties.MayerIndices, ], description="The SCF properties which should be extracted after every single point calculation.", ) keywords: Optional[ Dict[ str, Union[StrictStr, StrictInt, StrictFloat, StrictBool, List[StrictFloat]] ] ] = Field( None, description="An optional set of program specific computational keywords that " "should be passed to the program. These may include, for example, DFT grid " "settings.", ) def __init__( self, method: constr(strip_whitespace=True) = "B3LYP-D3BJ", basis: Optional[constr(strip_whitespace=True)] = "DZVP", program: constr(strip_whitespace=True) = "psi4", spec_name: constr(strip_whitespace=True) = "default", spec_description: str = "Standard OpenFF optimization quantum chemistry specification.", store_wavefunction: WavefunctionProtocolEnum = WavefunctionProtocolEnum.none, implicit_solvent: Optional[PCMSettings] = None, maxiter: PositiveInt = 200, scf_properties: List[SCFProperties] = DefaultProperties, keywords: Optional[ Dict[ str, Union[StrictStr, StrictInt, StrictFloat, StrictBool, List[StrictFloat]], ] ] = None, ): """ Validate the combination of method, basis and program. """ from openff.toolkit.typing.engines.smirnoff import get_available_force_fields try: from openmmforcefields.generators.template_generators import ( GAFFTemplateGenerator, ) gaff_forcefields = GAFFTemplateGenerator.INSTALLED_FORCEFIELDS except ModuleNotFoundError: gaff_forcefields = [ "gaff-1.4", "gaff-1.8", "gaff-1.81", "gaff-2.1", "gaff-2.11", ] # set up the valid method basis and program combinations ani_methods = {"ani1x", "ani1ccx", "ani2x"} openff_forcefields = list( ff.split(".offxml")[0].lower() for ff in get_available_force_fields() ) openmm_forcefields = { "smirnoff": openff_forcefields, "antechamber": gaff_forcefields, } xtb_methods = { "gfn0-xtb", "gfn0xtb", "gfn1-xtb", "gfn1xtb", "gfn2-xtb", "gfn2xtb", "gfn-ff", "gfnff", } rdkit_methods = {"uff", "mmff94", "mmff94s"} settings = { "openmm": openmm_forcefields, "torchani": {None: ani_methods}, "xtb": {None: xtb_methods}, "rdkit": {None: rdkit_methods}, "psi4": {}, } if program.lower() != "psi4": # make sure PCM is not set if implicit_solvent is not None: raise QCSpecificationError( "PCM can only be used with PSI4 please set implicit solvent to None." ) # we need to make sure it is valid in the above list program_settings = settings.get(program.lower(), None) if program_settings is None: raise QCSpecificationError( f"The program {program.lower()} is not supported please use one of the following {settings.keys()}" ) allowed_methods = program_settings.get(basis, None) if allowed_methods is None: raise QCSpecificationError( f"The Basis {basis} is not supported for the program {program}, chose from {program_settings.keys()}" ) # now we need to check the methods # strip the offxml if present method = method.split(".offxml")[0].lower() if method not in allowed_methods: raise QCSpecificationError( f"The method {method} is not supported for the program {program} with basis {basis}, please chose from {allowed_methods}" ) super().__init__( method=method, basis=basis, program=program.lower(), spec_name=spec_name, spec_description=spec_description, store_wavefunction=store_wavefunction, implicit_solvent=implicit_solvent, maxiter=maxiter, scf_properties=scf_properties, keywords=keywords, )
[docs] def dict( self, *, include: Union["AbstractSetIntStr", "MappingIntStrAny"] = None, exclude: Union["AbstractSetIntStr", "MappingIntStrAny"] = None, by_alias: bool = False, skip_defaults: bool = None, exclude_unset: bool = False, exclude_defaults: bool = False, exclude_none: bool = False, ) -> "DictStrAny": data = super().dict( include=include, exclude=exclude, by_alias=by_alias, skip_defaults=skip_defaults, exclude_defaults=exclude_defaults, exclude_unset=exclude_unset, exclude_none=exclude_none, ) if "store_wavefunction" in data: data["store_wavefunction"] = self.store_wavefunction.value if "scf_properties" in data: data["scf_properties"] = [prop.value for prop in self.scf_properties] return data
@property def qc_model(self) -> Model: """Return the qcelmental schema for this method and basis.""" return Model(method=self.method, basis=self.basis) @property def qc_keywords(self) -> Dict[str, Any]: """ Return the formatted keywords for this calculation. """ data = self.dict(include={"maxiter", "scf_properties"}) if self.keywords is not None: data.update(self.keywords) if self.implicit_solvent is not None: if self.program.lower() != "psi4": raise QCSpecificationError( "PCM can only be used with PSI4 please set implicit solvent to None." ) data["pcm"] = True data["pcm__input"] = self.implicit_solvent.to_string() return data
[docs]class QCSpecificationHandler(BaseModel): """ A mixin class for handling the QCSpecification """ qc_specifications: Dict[str, QCSpec] = Field( {"default": QCSpec()}, description="The QCSpecifications which will be computed for this dataset.", )
[docs] def clear_qcspecs(self) -> None: """ Clear out any current QCSpecs. """ self.qc_specifications = {}
[docs] def remove_qcspec(self, spec_name: str) -> None: """ Remove a QCSpec from the dataset. Parameters: spec_name: The name of the spec that should be removed. Note: The QCSpec settings are not mutable and so they must be removed and a new one added to ensure they are fully validated. """ if spec_name in self.qc_specifications.keys(): del self.qc_specifications[spec_name]
@property def n_qc_specs(self) -> int: """ Return the number of QCSpecs on this dataset. """ return len(self.qc_specifications) def _check_qc_specs(self) -> None: if self.n_qc_specs == 0: raise QCSpecificationError( "There are no QCSpecifications for this dataset please add some using `add_qc_spec`" )
[docs] def add_qc_spec( self, method: str, basis: Optional[str], program: str, spec_name: str, spec_description: str, store_wavefunction: str = "none", overwrite: bool = False, implicit_solvent: Optional[PCMSettings] = None, maxiter: PositiveInt = 200, scf_properties: Optional[List[SCFProperties]] = None, keywords: Optional[ Dict[ str, Union[StrictStr, StrictInt, StrictFloat, StrictBool, List[StrictFloat]], ] ] = None, ) -> None: """ Add a new qcspecification to the factory which will be applied to the dataset. Parameters: method: The name of the method to use eg B3LYP-D3BJ basis: The name of the basis to use can also be `None` program: The name of the program to execute the computation spec_name: The name the spec should be stored under spec_description: The description of the spec store_wavefunction: what parts of the wavefunction that should be saved overwrite: If there is a spec under this name already overwrite it implicit_solvent: The implicit solvent settings if it is to be used. maxiter: The maximum number of SCF iterations that should be done. scf_properties: The list of SCF properties that should be extracted from the calculation. keywords: Program specific computational keywords that should be passed to the program """ spec = QCSpec( method=method, basis=basis, program=program, spec_name=spec_name, spec_description=spec_description, store_wavefunction=store_wavefunction, maxiter=maxiter, scf_properties=scf_properties or DefaultProperties, implicit_solvent=implicit_solvent, keywords=keywords, ) if spec_name not in self.qc_specifications: self.qc_specifications[spec.spec_name] = spec elif overwrite: self.qc_specifications[spec.spec_name] = spec else: raise QCSpecificationError( f"A specification is already stored under {spec_name} to replace it set `overwrite=True`." )
[docs]class IndexCleaner: """ This class offers the ability to clean a molecule index that already has a numeric tag useful for datasets and results. """ @staticmethod def _clean_index(index: str) -> Tuple[str, int]: """ Take an index and clean it by checking if it already has an enumerator in it. Return the core index and any numeric tags. If no tag is found the tag is set to 0. Parameters: index: The index for the entry which should be checked, if no numeric tag can be found return 0. Returns: A tuple of the core index and the numeric tag it starts from. Note: This function allows the dataset to add more conformers to a molecule set so long as the index the molecule is stored under is a new index not in the database for example if 3 conformers for ethane exist then the new index should start from 'CC-3'. """ # tags take the form '-no' match = re.search("-[0-9]+$", index) if match is not None: core = index[: match.span()[0]] # drop the - tag = int(match.group()[1:]) else: core = index tag = 0 return core, tag
[docs]class ClientHandler: """ This mixin class offers the ability to handle activating qcportal Fractal client instances. """ @staticmethod def _activate_client(client) -> ptl.FractalClient: """ Make the fractal client and connect to the requested instance. Parameters: client: The name of the file containing the client information or the client instance. Returns: A qcportal.FractalClient instance. """ try: from qcfractal.interface import FractalClient as QCFractalClient except ModuleNotFoundError: QCFractalClient = None if isinstance(client, ptl.FractalClient): return client elif QCFractalClient is not None and isinstance(client, QCFractalClient): return client elif client == "public": return ptl.FractalClient() else: return ptl.FractalClient.from_file(client)
[docs]class Metadata(DatasetConfig): """ A general metadata class which is required to be filled in before submitting a dataset to the qcarchive. """ submitter: str = Field( getpass.getuser(), description="The name of the submitter/creator of the dataset, this is automatically generated but can be changed.", ) creation_date: date = Field( datetime.today().date(), description="The date the dataset was created on, this is automatically generated.", ) collection_type: Optional[str] = Field( None, description="The type of collection that will be created in QCArchive this is automatically updated when attached to a dataset.", ) dataset_name: Optional[str] = Field( None, description="The name that will be given to the collection once it is put into QCArchive, this is updated when attached to a dataset.", ) short_description: Optional[constr(min_length=8, regex="[a-zA-Z]")] = Field( None, description="A short informative description of the dataset." ) long_description_url: Optional[HttpUrl] = Field( None, description="The url which links to more information about the submission normally a github repo with scripts showing how the dataset was created.", ) long_description: Optional[constr(min_length=8, regex="[a-zA-Z]")] = Field( None, description="A long description of the purpose of the dataset and the molecules within.", ) elements: Set[str] = Field( set(), description="The unique set of elements present in the dataset" )
[docs] def validate_metadata(self, raise_errors: bool = False) -> Optional[List[str]]: """ Before submitting this function should be called to highlight any incomplete fields. """ empty_fields = [] for field in self.__fields__: if field == "long_description_url": # The 'long_description_url' is made optional to more easily facilitate # local or private dataset submissions. continue attr = getattr(self, field) if attr is None: empty_fields.append(field) if empty_fields and raise_errors: raise DatasetInputError( f"The metadata has the following incomplete fields {empty_fields}" ) else: return empty_fields
[docs]class MoleculeAttributes(DatasetConfig): """ A class to hold and validate the molecule attributes associated with a QCArchive entry, All attributes are required to be entered into a dataset. Note: The attributes here are not exhaustive but are based on those given by cmiles and can all be obtain through the openforcefield toolkit Molecule class. """ class Config: extra = "allow" canonical_smiles: str canonical_isomeric_smiles: str canonical_explicit_hydrogen_smiles: str canonical_isomeric_explicit_hydrogen_smiles: str canonical_isomeric_explicit_hydrogen_mapped_smiles: str = Field( ..., description="The fully mapped smiles where every atom should have a numerical tag so that the molecule can be rebuilt to match the order of the coordinates.", ) molecular_formula: str = Field( ..., description="The hill formula of the molecule as given by the openfftoolkit.", ) standard_inchi: str = Field( ..., description="The standard inchi given by the inchi program ie not fixed hydrogen layer.", ) inchi_key: str = Field( ..., description="The standard inchi key given by the inchi program." ) fixed_hydrogen_inchi: Optional[str] = Field( None, description="The non-standard inchi with a fixed hydrogen layer to distinguish tautomers.", ) fixed_hydrogen_inchi_key: Optional[str] = Field( None, description="The non-standard inchikey with a fixed hydrogen layer." ) unique_fixed_hydrogen_inchi_keys: Optional[Set[str]] = Field( None, description="The list of unique non-standard inchikey with a fixed hydrogen layer.", )
[docs] @classmethod def from_openff_molecule(cls, molecule: Molecule) -> "MoleculeAttributes": """Create the Cmiles metadata for an OpenFF molecule object. Parameters: molecule: The molecule for which the cmiles data will be generated. Returns: The Cmiles identifiers generated for the input molecule. Note: The Cmiles identifiers currently include: - `canonical_smiles` - `canonical_isomeric_smiles` - `canonical_explicit_hydrogen_smiles` - `canonical_isomeric_explicit_hydrogen_smiles` - `canonical_isomeric_explicit_hydrogen_mapped_smiles` - `molecular_formula` - `standard_inchi` - `inchi_key` - `fixed_hydrogen_inchi` - `fixed_hydrogen_inchi_key` - `unique_fixed_hydrogen_inchi_keys` """ molecules = split_openff_molecule(molecule=molecule) unique_fixed_hydrogen_inchi_keys = { mol.to_inchikey(fixed_hydrogens=True) for mol in molecules } off_mol = copy.deepcopy(molecule) if "atom_map" in off_mol.properties: del off_mol.properties["atom_map"] cmiles = { "canonical_smiles": off_mol.to_smiles( isomeric=False, explicit_hydrogens=False, mapped=False ), "canonical_isomeric_smiles": off_mol.to_smiles( isomeric=True, explicit_hydrogens=False, mapped=False ), "canonical_explicit_hydrogen_smiles": off_mol.to_smiles( isomeric=False, explicit_hydrogens=True, mapped=False ), "canonical_isomeric_explicit_hydrogen_smiles": off_mol.to_smiles( isomeric=True, explicit_hydrogens=True, mapped=False ), "canonical_isomeric_explicit_hydrogen_mapped_smiles": off_mol.to_smiles( isomeric=True, explicit_hydrogens=True, mapped=True ), "molecular_formula": off_mol.hill_formula, "standard_inchi": off_mol.to_inchi(fixed_hydrogens=False), "inchi_key": off_mol.to_inchikey(fixed_hydrogens=False), "fixed_hydrogen_inchi": off_mol.to_inchi(fixed_hydrogens=True), "fixed_hydrogen_inchi_key": off_mol.to_inchikey(fixed_hydrogens=True), "unique_fixed_hydrogen_inchi_keys": unique_fixed_hydrogen_inchi_keys, } return MoleculeAttributes(**cmiles)
[docs] def to_openff_molecule(self) -> Molecule: """ Create an openff molecule from the CMILES information. """ return Molecule.from_mapped_smiles( mapped_smiles=self.canonical_isomeric_explicit_hydrogen_mapped_smiles, allow_undefined_stereo=True, )
[docs]class CommonBase(DatasetConfig, IndexCleaner, ClientHandler, QCSpecificationHandler): """ A common base structure which the dataset and factory classes derive from. """ driver: DriverEnum = Field( DriverEnum.energy, description="The type of single point calculations which will be computed. Note some services require certain calculations for example optimizations require graident calculations.", ) priority: str = Field( "normal", description="The priority the dataset should be computed at compared to other datasets currently running.", ) dataset_tags: List[str] = Field( ["openff"], description="The dataset tags which help identify the dataset." ) compute_tag: str = Field( "openff", description="The tag the computes tasks will be assigned to, managers wishing to execute these tasks should use this compute tag.", )
[docs] def dict(self, *args, **kwargs): """ Overwrite the dict method to handle any enums when saving to yaml/json via a dict call. """ data = super(CommonBase, self).dict(*args, **kwargs) # now add the enum values if "driver" in data: data["driver"] = self.driver.value return data