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
[source]¶ Bases:
object
-
system_file
= '/scr/buildbot/savedbuilds/2021-2/NB/build-118/mmshare-v5.4/data/transformations.json'¶
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validate
= <voluptuous.Schema object>¶
Tags shared by two or more entries.
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schrodinger.analysis.transformations.
apply_transform
(st, rxn, core=None, f3d_engine=None, logger=None)[source]¶ 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)[source]¶ 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).