rdkit.Chem

Package Chem

A module for molecules and stuff see Chem/index.html in the doc tree for documentation

Submodules

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rdkit.Chem.AllChem: Import all RDKit chemistry modules...
rdkit.Chem.AtomPairs
- rdkit.Chem.AtomPairs.Pairs: Contains an implementation of Atom-pair fingerprints, as described in:
- rdkit.Chem.AtomPairs.Torsions: Contains an implementation of Topological-torsion fingerprints, as described in:
- rdkit.Chem.AtomPairs.Utils
rdkit.Chem.AvailDescriptors: DEPRECATED...
rdkit.Chem.BRICS: Implementation of the BRICS algorithm from Degen et al.
rdkit.Chem.BuildFragmentCatalog: command line utility for working with FragmentCatalogs (CASE-type analysis)
rdkit.Chem.ChemUtils
- rdkit.Chem.ChemUtils.AlignDepict
- rdkit.Chem.ChemUtils.BulkTester
- rdkit.Chem.ChemUtils.SDFToCSV
- rdkit.Chem.ChemUtils.TemplateExpand
rdkit.Chem.ChemicalFeatures
rdkit.Chem.ChemicalForceFields
rdkit.Chem.Crippen: Atom-based calculation of LogP and MR using Crippen's approach
rdkit.Chem.DSViewer: uses DSViewer to interact with molecules
rdkit.Chem.Descriptors
rdkit.Chem.Draw
- rdkit.Chem.Draw.IPythonConsole
- rdkit.Chem.Draw.MolDrawing
- rdkit.Chem.Draw.aggCanvas
- rdkit.Chem.Draw.cairoCanvas
- rdkit.Chem.Draw.canvasbase
- rdkit.Chem.Draw.spingCanvas
rdkit.Chem.EState: A module for Kier and Hall's EState Descriptors
- rdkit.Chem.EState.AtomTypes: contains SMARTS definitions and calculators for EState atom types
- rdkit.Chem.EState.EState: Basic EState definitions
- rdkit.Chem.EState.EState_VSA: Hybrid EState-VSA descriptors (like the MOE VSA descriptors)
- rdkit.Chem.EState.Fingerprinter: EState fingerprinting
rdkit.Chem.FastSDMolSupplier
rdkit.Chem.FeatFinderCLI
rdkit.Chem.FeatMaps
- rdkit.Chem.FeatMaps.FeatMapParser
- rdkit.Chem.FeatMaps.FeatMapPoint
- rdkit.Chem.FeatMaps.FeatMapUtils
- rdkit.Chem.FeatMaps.FeatMaps
rdkit.Chem.Features
- rdkit.Chem.Features.FeatDirUtilsRD
- rdkit.Chem.Features.ShowFeats
rdkit.Chem.Fingerprints
- rdkit.Chem.Fingerprints.ClusterMols: utility functionality for clustering molecules using fingerprints includes a command line app for clustering
- rdkit.Chem.Fingerprints.DbFpSupplier: Supplies a class for working with fingerprints from databases...
- rdkit.Chem.Fingerprints.FingerprintMols: utility functionality for fingerprinting sets of molecules includes a command line app for working with fingerprints and databases
- rdkit.Chem.Fingerprints.MolSimilarity: utility functionality for molecular similarity includes a command line app for screening databases
- rdkit.Chem.Fingerprints.SimilarityScreener: class definitions for similarity screening
rdkit.Chem.FragmentCatalog
rdkit.Chem.FragmentMatcher: exposes a class for matching fragments of molecules.
rdkit.Chem.Fragments: functions to match a bunch of fragment descriptors from a file
rdkit.Chem.FunctionalGroups
rdkit.Chem.GraphDescriptors: Calculation of topological/topochemical descriptors.
rdkit.Chem.Graphs: Python functions for manipulating molecular graphs
rdkit.Chem.Lipinski: Calculation of Lipinski parameters for molecules
rdkit.Chem.MACCSkeys: SMARTS definitions for the publically available MACCS keys and a MACCS fingerprinter
rdkit.Chem.MolCatalog
rdkit.Chem.MolDb
- rdkit.Chem.MolDb.FingerprintUtils
- rdkit.Chem.MolDb.Loader
- rdkit.Chem.MolDb.Loader_orig
- rdkit.Chem.MolDb.Loader_sa
rdkit.Chem.MolSurf: Exposes functionality for MOE-like approximate molecular surface area descriptors.
rdkit.Chem.PeriodicTable
rdkit.Chem.PeriodicTable': periodic table data, **obsolete**
rdkit.Chem.Pharm2D: module with functionality for 2D pharmacophores
- rdkit.Chem.Pharm2D.Generate: generation of 2D pharmacophores
- rdkit.Chem.Pharm2D.Gobbi_Pharm2D: Definitions for 2D Pharmacophores from: Gobbi and Poppinger, Biotech.
- rdkit.Chem.Pharm2D.LazyGenerator
- rdkit.Chem.Pharm2D.Matcher: functionality for finding pharmacophore matches in molecules
- rdkit.Chem.Pharm2D.SigFactory: contains factory class for producing signatures
- rdkit.Chem.Pharm2D.Utils: utility functionality for the 2D pharmacophores code
rdkit.Chem.Pharm3D
- rdkit.Chem.Pharm3D.EmbedLib
- rdkit.Chem.Pharm3D.ExcludedVolume
- rdkit.Chem.Pharm3D.Pharmacophore
rdkit.Chem.PropertyMol
rdkit.Chem.PyMol: uses pymol to interact with molecules
rdkit.Chem.Randomize
rdkit.Chem.Recap: Implementation of the RECAP algorithm from Lewell et al.
rdkit.Chem.SATIS: Functionality for SATIS typing atoms
rdkit.Chem.SaltRemover
rdkit.Chem.Scaffolds
- rdkit.Chem.Scaffolds.MurckoScaffold: Generation of Murcko scaffolds from a molecule
rdkit.Chem.ShowMols
rdkit.Chem.Subshape
- rdkit.Chem.Subshape.BuilderUtils
- rdkit.Chem.Subshape.SubshapeAligner
- rdkit.Chem.Subshape.SubshapeBuilder
- rdkit.Chem.Subshape.SubshapeObjects
rdkit.Chem.Suppliers
- rdkit.Chem.Suppliers.DbMolSupplier: Supplies a class for working with molecules from databases...
- rdkit.Chem.Suppliers.MolSupplier: Supplies an abstract class for working with sequences of molecules
rdkit.Chem.TemplateAlign
rdkit.Chem.inchi
rdkit.Chem.rdChemReactions: Module containing classes and functions for working with chemical reactions.
rdkit.Chem.rdChemicalFeatures: Module containing free chemical feature functionality These are feature that are not associated with molecules.
rdkit.Chem.rdDepictor: Module containing the functionality to compute 2D coordinates for a molecule
rdkit.Chem.rdDistGeom: Module containing functions to compute atomic coordinates in 3D using distance geometry
rdkit.Chem.rdForceFieldHelpers: Module containing functions to handle molecular force fields (currently UFF)
rdkit.Chem.rdMolAlign: Module containing functions to align a molecule to a second molecule
rdkit.Chem.rdMolCatalog
rdkit.Chem.rdMolChemicalFeatures: Module containing from chemical feature and functions to generate the
rdkit.Chem.rdMolDescriptors: Module containing functions to compute molecular descriptors
rdkit.Chem.rdMolTransforms: Module containing functions to perform 3D operations like rotate and translate conformations
rdkit.Chem.rdPartialCharges: Module containing functions to set partial charges - currently Gasteiger Charges
rdkit.Chem.rdSLNParse: Module containing classes and functions for working with Sybyl line notation (SLN).
rdkit.Chem.rdShapeHelpers: Module containing functions to encode ans compre the shapes of molecules
rdkit.Chem.rdchem: Module containing the core chemistry functionality of the RDKit
rdkit.Chem.rdfragcatalog
rdkit.Chem.rdinchi
rdkit.Chem.rdmolfiles: Module containing RDKit functionality for working with molecular file formats.
rdkit.Chem.rdmolops: Module containing RDKit functionality for manipulating and querying molecules.

Functions

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QuickSmartsMatch(smi, sma, unique=True, display=False)

source code

CanonSmiles(smi, useChiral=1)

source code

SupplierFromFilename(fileN, delim='', **kwargs) source code

FindMolChiralCenters(mol, force=True, includeUnassigned=False)
>>> from rdkit import Chem >>> mol = Chem.MolFromSmiles('[C@H](Cl)(F)Br') >>> FindMolChiralCenters(mol) [(0, 'R')] >>> mol = Chem.MolFromSmiles('[C@@H](Cl)(F)Br') >>> FindMolChiralCenters(mol) [(0, 'S')]

source code

_test()

source code

Variables

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LayeredFingerprint_substructLayers = 7

__package__ = 'rdkit.Chem'

Function Details

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FindMolChiralCenters(mol, force=True, includeUnassigned=False)

source code


>>> from rdkit import Chem
>>> mol = Chem.MolFromSmiles('[C@H](Cl)(F)Br')
>>> FindMolChiralCenters(mol)
[(0, 'R')]
>>> mol = Chem.MolFromSmiles('[C@@H](Cl)(F)Br')
>>> FindMolChiralCenters(mol)
[(0, 'S')]

>>> FindMolChiralCenters(Chem.MolFromSmiles('CCC'))
[]

By default unassigned stereo centers are not reported:
>>> mol = Chem.MolFromSmiles('C[C@H](F)C(F)(Cl)Br')
>>> FindMolChiralCenters(mol)
[(1, 'S')]

but this can be changed:
>>> FindMolChiralCenters(mol,includeUnassigned=True)
[(1, 'S'), (3, '?')]

The handling of dependent stereochemistry is not correct:
>>> Chem.FindMolChiralCenters(Chem.MolFromSmiles('C1CC(C)C(C)C(C)C1'),includeUnassigned=True)
[(2, '?'), (6, '?')]
>>> Chem.FindMolChiralCenters(Chem.MolFromSmiles('C1C[C@H](C)C(C)[C@H](C)C1'),includeUnassigned=True)
[(2, 'S'), (6, 'R')]