openff.toolkit.typing.chemistry.ChemicalEnvironment
- class openff.toolkit.typing.chemistry.ChemicalEnvironment(smirks=None, label=None, validate_parsable=True, validate_valence_type=True, toolkit_registry=None)[source]
Chemical environment abstract base class used for validating SMIRKS
- __init__(smirks=None, label=None, validate_parsable=True, validate_valence_type=True, toolkit_registry=None)[source]
Initialize a chemical environment abstract base class.
- smirks = string, optional
if smirks is not None, a chemical environment is built from the provided SMIRKS string
- label = anything, optional
intended to be used to label this chemical environment could be a string, int, or float, or anything
- validate_parsable: bool, optional, default=True
If specified, ensure the provided smirks is parsable
- validate_valence_typebool, optional, default=True
If specified, ensure the tagged atoms are appropriate to the specified valence type
- toolkit_registry = string or ToolkitWrapper or ToolkitRegistry. Default = None
Either a ToolkitRegistry, ToolkitWrapper, or the strings ‘openeye’ or ‘rdkit’, indicating the backend to use for validating the correct connectivity of the SMIRKS during initialization. If None, this function will use the GLOBAL_TOOLKIT_REGISTRY
- Raises
- SMIRKSParsingError
if smirks was unparsable
- SMIRKSMismatchError
if smirks did not have expected connectivity between tagged atoms and validate_valence_type=True
Methods
__init__
([smirks, label, validate_parsable, ...])Initialize a chemical environment abstract base class.
get_type
([toolkit_registry])Return the valence type implied by the connectivity of the bound atoms in this ChemicalEnvironment.
validate
([validate_valence_type, ...])Returns True if the underlying smirks is the correct valence type, False otherwise.
validate_smirks
(smirks[, validate_parsable, ...])Check the provided SMIRKS string is valid, and if requested, tags atoms appropriate to the specified valence type.
- validate(validate_valence_type=True, toolkit_registry=None)[source]
Returns True if the underlying smirks is the correct valence type, False otherwise. If the expected type is None, this method always returns True.
- validate_valence_typebool, optional, default=True
If specified, ensure the tagged atoms are appropriate to the specified valence type
- toolkit_registry = ToolkitWrapper or ToolkitRegistry. Default = None
Either a ToolkitRegistry or ToolkitWrapper, indicating the backend to use for validating the correct connectivity of the SMIRKS during initialization. If None, this function will use the GLOBAL_TOOLKIT_REGISTRY
- Raises
- SMIRKSParsingError
if smirks was unparsable
- SMIRKSMismatchError
if smirks did not have expected connectivity between tagged atoms and validate_valence_type=True
- classmethod validate_smirks(smirks, validate_parsable=True, validate_valence_type=True, toolkit_registry=None)[source]
Check the provided SMIRKS string is valid, and if requested, tags atoms appropriate to the specified valence type.
- Parameters
- smirksstr
The SMIRKS expression to validate
- validate_parsable: bool, optional, default=True
If specified, ensure the provided smirks is parsable
- validate_valence_typebool, optional, default=True
If specified, ensure the tagged atoms are appropriate to the specified valence type
- toolkit_registry = string or ToolkitWrapper or ToolkitRegistry. Default = None
Either a ToolkitRegistry, ToolkitWrapper, or the strings ‘openeye’ or ‘rdkit’, indicating the backend to use for validating the correct connectivity of the SMIRKS during initialization. If None, this function will use the GLOBAL_TOOLKIT_REGISTRY
- Raises
- SMIRKSParsingError
if smirks was unparsable
- SMIRKSMismatchError
if smirks did not have expected connectivity between tagged atoms and validate_valence_type=True
- get_type(toolkit_registry=None)[source]
Return the valence type implied by the connectivity of the bound atoms in this ChemicalEnvironment.
- Parameters
- toolkit_registryopenff.toolkit.utils.ToolkitRegistry or openff.toolkit.utils.ToolkitWrapper
The cheminformatics toolkit to use for parsing the smirks
- Returns
- valence_typestr
One of “Atom”, “Bond”, “Angle”, “ProperTorsion”, “ImproperTorsion”, or None. If tagged atoms are not connected in a known pattern this method will return None.
- Raises
- SMIRKSParsingError
if smirks was unparsable