genui.compounds.initializers package

Submodules

genui.compounds.initializers.base module

base

Created by: Martin Sicho On: 18-12-19, 11:32

class genui.compounds.initializers.base.ChEMBLStandardizer[source]: Bases: Standardizer

class genui.compounds.initializers.base.MolSetInitializer(instance: MolSet, progress_recorder=None, standardizer=None)[source]

Bases: ABC

exception DuplicateChemicalEntityWarning(entity, duplicates, compound_set, *args)[source]

Bases: GenUIWarning

getData()[source]

addMoleculeFromSMILES(smiles: str, molecule_class=<class 'genui.compounds.models.Molecule'>, create_kwargs=None)[source]

createChemicalEntity(smiles)[source]

createMolecule(entity, molecule_class, create_kwargs=None)[source]

getInstance()[source]

property instance

abstract populateInstance() → int[source]

standardizeFromSMILES(smiles)[source]

abstract updateInstance() → int[source]

class genui.compounds.initializers.base.Standardizer[source]: Bases: ABC

genui.compounds.initializers.exceptions module

exceptions

Created by: Martin Sicho On: 12/27/19, 7:41 PM

exception genui.compounds.initializers.exceptions.CompoundImportException(original, *args, **kwargs)[source]: Bases: GenUIException

exception genui.compounds.initializers.exceptions.InconsistentIdentifiersException(original, attemptedIdentifiers, existingIdentifiers, *args)[source]

Bases: GenUIException

getData()[source]

exception genui.compounds.initializers.exceptions.SMILESParsingError(bad_smiles: str, original, *args)[source]

Bases: GenUIException

getData()[source]

exception genui.compounds.initializers.exceptions.StandardizationError(original, *args, **kwargs)[source]: Bases: GenUIException

Module contents

__init__

Created by: Martin Sicho On: 2/9/20, 4:23 PM