Package rdkit :: Package Chem

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# Package Chem

source code

    A module for molecules and stuff

    see Chem/index.html in the doc tree for documentation

Submodules | [hide private]

- 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.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.SimilarityMaps
  - rdkit.Chem.Draw.aggCanvas
  - rdkit.Chem.Draw.cairoCanvas
  - rdkit.Chem.Draw.canvasbase
  - rdkit.Chem.Draw.mplCanvas
  - rdkit.Chem.Draw.qtCanvas
  - 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.Fraggle
  - rdkit.Chem.Fraggle.FraggleSim
- 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.MCS
- 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.PandasTools: Importing pandasTools enables several features that allow for using RDKit molecules as columns of a Pandas dataframe.
- 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.SimpleEnum
  - rdkit.Chem.SimpleEnum.Enumerator
- 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.TorsionFingerprints: Torsion Fingerprints (Deviation) (TFD) According to a paper from Schulz-Gasch et al., JCIM, 52, 1499-1512 (2012).
- rdkit.Chem.fmcs: Actual implementation of the FMCS algorithm...
  - rdkit.Chem.fmcs.fmcs: FMCS - Find Maximum Common Substructure
- rdkit.Chem.inchi

Functions | [hide private]

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 | [hide private]

| _HasSubstructMatchStr = `rdchem._HasSubstructMatchStr`

Imports: rdBase, RDConfig, DataStructs, rdGeometry, pyPeriodicTable, rdchem

Function Details | [hide private]

### 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,force=True)
    [(1, 'S')]

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

    The handling of unassigned stereocenters for 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'), (4, '?'), (6, 'R')]