schrodinger.analysis.transformations module

Module to support chemical transformations defined via reaction SMARTS (RDKit dialect).

Transformations can be applied either individually using apply_transform(), or “en-masse” via apply_transforms() (see below).

TransformsRepository class supports loading of the transformations from files (or text) in JSON format.

class schrodinger.analysis.transformations.TransformsRepository

Bases: object

system_file = '/scr/buildbot/savedbuilds/2018-4/NB/build-145/mmshare-v4.4/data/transformations.json'
validate = <voluptuous.Schema object>
__init__()

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

load(fp)
loads(text)
loadFile(filename)
tags
shared_tags

Tags shared by two or more entries.

getEntries(tags=None)
getSmarts(tags=None)
__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.analysis.transformations', 'system_file': '/scr/buildbot/savedbuilds/2018-4/NB/build-145/mmshare-v4.4/data/transformations.json', 'validate': <voluptuous.Schema object>, '__init__': <function TransformsRepository.__init__>, '_appendEntries': <function TransformsRepository._appendEntries>, 'load': <function TransformsRepository.load>, 'loads': <function TransformsRepository.loads>, 'loadFile': <function TransformsRepository.loadFile>, 'tags': <property object>, 'shared_tags': <property object>, 'getEntries': <function TransformsRepository.getEntries>, 'getSmarts': <function TransformsRepository.getSmarts>, '__dict__': <attribute '__dict__' of 'TransformsRepository' objects>, '__weakref__': <attribute '__weakref__' of 'TransformsRepository' objects>, '__doc__': None})
__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_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.analysis.transformations'
__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).

__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).

__weakref__

list of weak references to the object (if defined)

schrodinger.analysis.transformations.apply_transform(st, rxn, core=None, f3d_engine=None, logger=None)

Applies single transformation and generates (smiles, st, core) tuples for the outcomes.

Parameters:
  • st (Structure) – Input structure.
  • rxn (ChemicalReaction instance.) – Reaction to be performed.
  • core (iterable) – Indices of the atoms that must be kept unchanged.
  • f3d_engine (fast3d.SingleConformerEngine instance.) – fast3d handle to be used for 3d coordinates generation (omitted if None).
schrodinger.analysis.transformations.apply_transforms(st, transforms, core=None, f3d_engine=None, logger=None)

Applies transformations to structure.

Generator of the (Structure, smiles, core, route) tuples.

Parameters:
  • st (Structure) – Input structure.
  • transforms (list of lists of ChemicalReaction instances.) – List of lists of reactions to be performed.
  • core (iterable) – Indices of the atoms that must be kept unchanged.
  • f3d_engine (fast3d.SingleConformerEngine instance.) – fast3d handle to be used for 3d coordinates generation (omitted if None).
schrodinger.analysis.transformations.structure_to_rdkit_smiles(st)
schrodinger.analysis.transformations.rdkit_reaction_from_smarts(smarts)