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/2019-1/NB/build-139/mmshare-v4.5/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)
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)