schrodinger.application.matsci.smartsutils module¶
Utilities for working with SMARTS patterns
Copyright Schrodinger, LLC. All rights reserved.
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class
schrodinger.application.matsci.smartsutils.
SMARTSGroupData
(number, name, pattern, indexes)¶ Bases:
tuple
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__contains__
¶ Return key in self.
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__init__
¶ Initialize self. See help(type(self)) for accurate signature.
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__len__
¶ Return len(self).
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count
(value) → integer -- return number of occurrences of value¶
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index
(value[, start[, stop]]) → integer -- return first index of value.¶ Raises ValueError if the value is not present.
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indexes
¶ Alias for field number 3
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name
¶ Alias for field number 1
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number
¶ Alias for field number 0
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pattern
¶ Alias for field number 2
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schrodinger.application.matsci.smartsutils.
validate_name
(name)¶ Make sure name has the correct set of characters
Parameters: name (str) – The string to check Return type: bool Returns: True if name has no invalid characters, False if any characters are invalid
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exception
schrodinger.application.matsci.smartsutils.
SMARTSGroupError
¶ Bases:
Exception
Class for exceptions related to SMARTS group finding
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__init__
¶ Initialize self. See help(type(self)) for accurate signature.
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args
¶
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with_traceback
()¶ Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.
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schrodinger.application.matsci.smartsutils.
delete_group_properties
(struct)¶ Delete all SMARTS group properties (structure and atom) from the structure
Parameters: struct ( schrodinger.structure.Structure
) – The structure to delete properties from
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schrodinger.application.matsci.smartsutils.
find_group_data
(struct)¶ Find an SMARTS group data on the structure
Parameters: struct ( schrodinger.structure.Structure
) – The structure to find groups onReturn type: dict Returns: A dictionary. Keys are smarts group numbers, values are SMARTSGroupData
named tuples for the SMARTS group with that numberRaises: SMARTSGroupError – If something in the data is not consistent
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schrodinger.application.matsci.smartsutils.
get_rdkit_atoms
(smarts)¶ Return a collection of rdkit atoms for the given SMARTS. The return value has the length of a potential match group, for example for ‘cc’ this length is 2, for ‘[$([NH]([CH2])[CH2])]C’ it is 2, for [n-0X2].[n-0X2] it is 2, etc., even though there might be any number of matches if the pattern was matched.
Parameters: smarts (str) – the SMARTS pattern Raises: RuntimeError – if rdkit has a problem with the SMARTS Return type: rdkit.Chem.rdchem._ROAtomSeq Returns: the rdkit atoms
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schrodinger.application.matsci.smartsutils.
is_smarts_bonding_pair
(smarts)¶ Return True if the given SMARTS would match a bonding pair, False otherwise.
Parameters: smarts (str) – the SMARTS pattern Return type: bool Returns: True if the SMARTS would match a bonding pair, False otherwise