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/2024-3/NB/build-133/mmshare-v6.7/data/transformations.json'¶
- validate = <voluptuous.Schema object>¶
- __init__()¶
- load(fp)¶
- loads(text)¶
- loadFile(filename)¶
- property 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)¶