Package schrodinger :: Package analysis :: Module transformations

Module transformations

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.

Classes

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TransformsRepository

Functions

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_extract_heavy_and_polar_atoms(st, core=None, logger=None)
Extracts heavy atoms and polar hydrogens, returns (st_noH, core_noH) where st_noH is the substructure of the input st, core_noH is set of the atom indices in st_noH that correspond to the "core" atoms in the input structure.

apply_transform(st, rxn, core=None, f3d_engine=None, logger=None)
Applies single transformation and generates (smiles, st, core) tuples for the outcomes.

apply_transforms(st, transforms, core=None, f3d_engine=None, logger=None)
Applies transformations to structure.

structure_to_rdkit_smiles(st)

rdkit_reaction_from_smarts(smarts)

Variables

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__package__ = 'schrodinger.analysis'

Function Details

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_extract_heavy_and_polar_atoms(st, core=None, logger=None)

Extracts heavy atoms and polar hydrogens, returns (st_noH, core_noH) where st_noH is the substructure of the input st, core_noH is set of the atom indices in st_noH that correspond to the "core" atoms in the input structure.

Parameters:

st (Structure) - Input structure.
core (iterable) - Indices of the atoms that must be kept unchanged.

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.Engine instance.) - fast3d handle to be used for 3d coordinates generation (omitted if None).

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.Engine instance.) - fast3d handle to be used for 3d coordinates generation (omitted if None).