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__(key, /)

Return key in self.

__len__()

Return len(self).

count(value, /)

Return number of occurrences of value.

index(value, start=0, stop=9223372036854775807, /)

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.defines_integer_atom_props(st)[source]

Return True if the given structure has SMARTS-related integer atom properties defined. These properties were originally used when each atom was forced to belong to a single SMARTS group. That condition has been relaxed but these properties are kept for backwards compatibility.

Parameters

st (schrodinger.structure.Structure) – the structure

Return type

bool

Returns

True if such properties are defined

schrodinger.application.matsci.smartsutils.get_group_names(atom)[source]

Return a list of group names for the given atom.

Parameters

atom (schrodinger.structure._StructureAtom) – the atom

Return type

list

Returns

group names

schrodinger.application.matsci.smartsutils.get_group_atom_indices(atom)[source]

Return a list of group atom indices for the given atom.

Parameters

atom (schrodinger.structure._StructureAtom) – the atom

Return type

list

Returns

group atom indices

schrodinger.application.matsci.smartsutils.get_group_numbers(atom)[source]

Return a list of group numbers for the given atom.

Parameters

atom (schrodinger.structure._StructureAtom) – the atom

Return type

list

Returns

group numbers

schrodinger.application.matsci.smartsutils.append_property(atom, key, value)[source]

Append the given property to the atom.

Parameters
schrodinger.application.matsci.smartsutils.validate_name(name)[source]

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[source]

Bases: Exception

Class for exceptions related to SMARTS group finding

__init__(*args, **kwargs)

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)[source]

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)[source]

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)[source]

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)[source]

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

class schrodinger.application.matsci.smartsutils.SMARTSGroup(name, pattern, logger=None)[source]

Bases: object

Handles matching and record-keeping for a SMARTS patter

__init__(name, pattern, logger=None)[source]

Create a SMARTSGroup object

Parameters

  • name (str) – The name of this SMARTS group

  • pattern (str) – The SMARTS pattern for this group

Raises

  • ValueError – If name has invalid characters

  • ValueError – If the SMARTS is invalid

nextNumber(numbers_used)[source]

Get the next unused group number

Parameters

numbers_used (set) – Each member is a number that has already been used for a group and is unavailable. The number returned by this function is added to the numbers_used set.

Return type

int

Returns

The lowest available number. This number will have been added to the numbers_used set.

orderedMatches(struct, backbone_atoms)[source]

Evaluate the smarts pattern matches, where matches are ordered to follow network sequence. Consider backbone atoms matches first in the sequence and the side chian matches are then ordered according to atom index.

Parameters

  • struct (schrodinger.structure.Structure) – The structure to delete properties from

  • backbone_atoms (dict) – dictionary with key as molecule number and backbone atoms index ordered in a list

Return list(list)

List of list containing the smart pattern matches

match(struct, numbers_used, backbone_atoms, allow_partial_overlap=False)[source]

Find all the SMARTS groups matching the SMARTS pattern and mark them with the appropriate properties

Parameters

  • struct (schrodinger.structure.Structure) – The structure to delete properties from

  • numbers_used (set) – A set of all the group numbers that have been used and are unavailable

  • backbone_atoms (dict) – dictionary with key as molecule number and backbone atoms index ordered in a list

  • allow_partial_overlap (bool) – whether atoms can belong to multiple groups