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

__add__

Return self+value.

__class__

alias of builtins.type

__contains__

Return key in self.

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__getitem__

Return self[key].

__getnewargs__()

Return self as a plain tuple. Used by copy and pickle.

__gt__

Return self>value.

__hash__

Return hash(self).

__init__

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

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__iter__

Implement iter(self).

__le__

Return self<=value.

__len__

Return len(self).

__lt__

Return self<value.

__module__ = 'schrodinger.application.matsci.smartsutils'

__mul__

Return self*value.n

__ne__

Return self!=value.

static __new__(_cls, number, name, pattern, indexes)

Create new instance of SMARTSGroupData(number, name, pattern, indexes)

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__()

Return a nicely formatted representation string

__rmul__

Return self*value.

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__slots__ = ()

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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

__cause__

exception cause

__class__

alias of builtins.type

__context__

exception context

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.matsci.smartsutils', '__doc__': ' Class for exceptions related to SMARTS group finding ', '__weakref__': <attribute '__weakref__' of 'SMARTSGroupError' objects>})

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__

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

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.matsci.smartsutils'

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__setstate__()

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__suppress_context__

__traceback__

__weakref__

list of weak references to the object (if defined)

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