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.
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class
schrodinger.analysis.transformations.
TransformsRepository
¶ Bases:
object
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system_file
= '/scr/buildbot/savedbuilds/2020-3/NB/build-133/mmshare-v5.1/data/transformations.json'¶
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validate
= <voluptuous.Schema object>¶
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__init__
()¶ Initialize self. See help(type(self)) for accurate signature.
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load
(fp)¶
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loads
(text)¶
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loadFile
(filename)¶
Tags shared by two or more entries.
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getEntries
(tags=None)¶
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getSmarts
(tags=None)¶
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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).
- st (
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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).
- st (
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schrodinger.analysis.transformations.
structure_to_rdkit_smiles
(st)¶
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schrodinger.analysis.transformations.
rdkit_reaction_from_smarts
(smarts)¶