openforcefield.typing.chemistry.ChemicalEnvironment¶
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class
openforcefield.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
Methods
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.
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__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.
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