schrodinger.application.matsci.smartsutils module

Utilities for working with SMARTS patterns

Copyright Schrodinger, LLC. All rights reserved.

class schrodinger.application.matsci.smartsutils.SMARTSGroupData(number, name, pattern, indexes)

Bases: tuple

__contains__

Return key in self.

__init__

Initialize self. See help(type(self)) for accurate signature.

__len__

Return len(self).

count(value) → integer -- return number of occurrences of value

index(value[, start[, stop]]) → integer -- return first index of value.

Raises ValueError if the value is not present.

indexes

Alias for field number 3

name

Alias for field number 1

number

Alias for field number 0

pattern

Alias for field number 2

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

exception schrodinger.application.matsci.smartsutils.SMARTSGroupError

Bases: Exception

Class for exceptions related to SMARTS group finding

__init__

Initialize self. See help(type(self)) for accurate signature.

args

with_traceback()

Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

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

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 on Return type:dict Returns:A dictionary. Keys are smarts group numbers, values are SMARTSGroupData named tuples for the SMARTS group with that number Raises:SMARTSGroupError – If something in the data is not consistent

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

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