Package schrodinger :: Package application :: Package matsci :: Module smartsutils

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Module smartsutils

Classes

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SMARTSGroupData
SMARTSGroupData(number, name, pattern, indexes)

SMARTSGroupError
Class for exceptions related to SMARTS group finding

Functions

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bool

validate_name(name)
Make sure name has the correct set of characters

delete_group_properties(struct)
Delete all SMARTS group properties (structure and atom) from the structure

dict

find_group_data(struct)
Find an SMARTS group data on the structure

rdkit.Chem.rdchem._ROAtomSeq

get_rdkit_atoms(smarts)
Return a collection of rdkit atoms for the given SMARTS.

bool

is_smarts_bonding_pair(smarts)
Return True if the given SMARTS would match a bonding pair, False otherwise.

Variables

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_doc__ = '\nUtilities for working with SMARTS patterns\n\nCopy...

GROUP_STRUCT_PROP_BASE = 's_matsci_smarts_group_%s'

GROUP_STRUCT_COUNT = 'i_matsci_smarts_group_matches_%s'

GROUP_NAME_PROP = 's_matsci_smarts_group_name'

GROUP_ATOM_INDEX_PROP = 'i_matsci_smarts_group_atom_index'

GROUP_NUMBER_PROP = 'i_matsci_smarts_group_number'

VALID_NAME_PUNCTUATION = '_-()[]'

VALID_NAME_CHARS = set(['(', ')', '-', '0', '1', '2', '3', '4'...

VALID_NAME_DESC_TEXT = 'letters, numbers and the special chara...

__package__ = 'schrodinger.application.matsci'

Function Details

[hide private]

validate_name(name)

Make sure name has the correct set of characters

Parameters:

name (str) - The string to check

Returns: bool

True if name has no invalid characters, False if any characters are invalid

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

find_group_data(struct)

Find an SMARTS group data on the structure

Parameters:

struct (schrodinger.structure.Structure) - The structure to find groups on

Returns: dict

A dictionary. Keys are smarts group numbers, values are SMARTSGroupData named tuples for the SMARTS group with that number

@raise SMARTSGroupError: If something in the data is not consistent

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

Returns: rdkit.Chem.rdchem._ROAtomSeq

the rdkit atoms

Raises:

RuntimeError - if rdkit has a problem with the SMARTS

is_smarts_bonding_pair(smarts)

Return True if the given SMARTS would match a bonding pair, False otherwise.

Parameters:

smarts (str) - the SMARTS pattern

Returns: bool

True if the SMARTS would match a bonding pair, False otherwise

Variables Details

[hide private]

_doc__

Value:

'''
Utilities for working with SMARTS patterns

Copyright Schrodinger, LLC. All rights reserved.
'''

VALID_NAME_CHARS

Value:

set(['(',
     ')',
     '-',
     '0',
     '1',
     '2',
     '3',
     '4',
...

VALID_NAME_DESC_TEXT

Value:

'letters, numbers and the special characters _-()[]'