schrodinger.application.matsci.smartsutils module

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

Bases: tuple

indexes

Alias for field number 3

name

Alias for field number 1

number

Alias for field number 0

pattern

Alias for field number 2

exception schrodinger.application.matsci.smartsutils.SMARTSGroupError

Bases: exceptions.Exception

Class for exceptions related to SMARTS group finding

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
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