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]

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]
  ADJUST_IGNOREALL = rdkit.Chem.rdmolops.AdjustQueryWhichFlags.A...
  ADJUST_IGNORECHAINS = rdkit.Chem.rdmolops.AdjustQueryWhichFlag...
  ADJUST_IGNOREDUMMIES = rdkit.Chem.rdmolops.AdjustQueryWhichFla...
  ADJUST_IGNORENONDUMMIES = rdkit.Chem.rdmolops.AdjustQueryWhich...
  ADJUST_IGNORENONE = rdkit.Chem.rdmolops.AdjustQueryWhichFlags....
  ADJUST_IGNORERINGS = rdkit.Chem.rdmolops.AdjustQueryWhichFlags...
  ALLOW_CHARGE_SEPARATION = rdkit.Chem.rdchem.ResonanceFlags.ALL...
  ALLOW_INCOMPLETE_OCTETS = rdkit.Chem.rdchem.ResonanceFlags.ALL...
  AROMATICITY_CUSTOM = rdkit.Chem.rdmolops.AromaticityModel.AROM...
  AROMATICITY_DEFAULT = rdkit.Chem.rdmolops.AromaticityModel.ARO...
  AROMATICITY_RDKIT = rdkit.Chem.rdmolops.AromaticityModel.AROMA...
  AROMATICITY_SIMPLE = rdkit.Chem.rdmolops.AromaticityModel.AROM...
  AllProps = rdkit.Chem.rdchem.PropertyPickleOptions.AllProps
  AtomProps = rdkit.Chem.rdchem.PropertyPickleOptions.AtomProps
  BondProps = rdkit.Chem.rdchem.PropertyPickleOptions.BondProps
  CHI_OTHER = rdkit.Chem.rdchem.ChiralType.CHI_OTHER
  CHI_TETRAHEDRAL_CCW = rdkit.Chem.rdchem.ChiralType.CHI_TETRAHE...
  CHI_TETRAHEDRAL_CW = rdkit.Chem.rdchem.ChiralType.CHI_TETRAHED...
  CHI_UNSPECIFIED = rdkit.Chem.rdchem.ChiralType.CHI_UNSPECIFIED
  COMPOSITE_AND = rdkit.Chem.rdchem.CompositeQueryType.COMPOSITE...
  COMPOSITE_OR = rdkit.Chem.rdchem.CompositeQueryType.COMPOSITE_OR
  COMPOSITE_XOR = rdkit.Chem.rdchem.CompositeQueryType.COMPOSITE...
  ComputedProps = rdkit.Chem.rdchem.PropertyPickleOptions.Comput...
  KEKULE_ALL = rdkit.Chem.rdchem.ResonanceFlags.KEKULE_ALL
  LayeredFingerprint_substructLayers = 7
  MolProps = rdkit.Chem.rdchem.PropertyPickleOptions.MolProps
  NoProps = rdkit.Chem.rdchem.PropertyPickleOptions.NoProps
  PrivateProps = rdkit.Chem.rdchem.PropertyPickleOptions.Private...
  QueryAtomData = rdkit.Chem.rdchem.PropertyPickleOptions.QueryA...
  SANITIZE_ADJUSTHS = rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE...
  SANITIZE_ALL = rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_ALL
  SANITIZE_CLEANUP = rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_...
  SANITIZE_CLEANUPCHIRALITY = rdkit.Chem.rdmolops.SanitizeFlags....
  SANITIZE_FINDRADICALS = rdkit.Chem.rdmolops.SanitizeFlags.SANI...
  SANITIZE_KEKULIZE = rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE...
  SANITIZE_NONE = rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_NONE
  SANITIZE_PROPERTIES = rdkit.Chem.rdmolops.SanitizeFlags.SANITI...
  SANITIZE_SETAROMATICITY = rdkit.Chem.rdmolops.SanitizeFlags.SA...
  SANITIZE_SETCONJUGATION = rdkit.Chem.rdmolops.SanitizeFlags.SA...
  SANITIZE_SETHYBRIDIZATION = rdkit.Chem.rdmolops.SanitizeFlags....
  SANITIZE_SYMMRINGS = rdkit.Chem.rdmolops.SanitizeFlags.SANITIZ...
  UNCONSTRAINED_ANIONS = rdkit.Chem.rdchem.ResonanceFlags.UNCONS...
  UNCONSTRAINED_CATIONS = rdkit.Chem.rdchem.ResonanceFlags.UNCON...
  __package__ = 'rdkit.Chem'

Imports: rdBase, RDConfig, DataStructs, rdGeometry, pyPeriodicTable, rdchem, _HasSubstructMatchStr, MolToInchi, InchiToInchiKey, MolFromInchi, MolToInchiAndAuxInfo, InchiReadWriteError, INCHI_AVAILABLE, AddHs, AddRecursiveQuery, AdjustQueryParameters, AdjustQueryProperties, AdjustQueryWhichFlags, AromaticityModel, AssignAtomChiralTagsFromStructure, AssignRadicals, AssignStereochemistry, Atom, AtomMonomerInfo, AtomMonomerType, AtomPDBResidueInfo, Bond, BondDir, BondStereo, BondType, CanonicalRankAtoms, CanonicalRankAtomsInFragment, ChiralType, Cleanup, CombineMols, CompositeQueryType, Conformer, DeleteSubstructs, DetectBondStereoChemistry, EditableMol, FastFindRings, FindAllPathsOfLengthN, FindAllSubgraphsOfLengthMToN, FindAllSubgraphsOfLengthN, FindAtomEnvironmentOfRadiusN, FindPotentialStereoBonds, FindUniqueSubgraphsOfLengthN, ForwardSDMolSupplier, FragmentOnBRICSBonds, FragmentOnBonds, FragmentOnSomeBonds, Get3DDistanceMatrix, GetAdjacencyMatrix, GetAtomAlias, GetAtomRLabel, GetAtomValue, GetDefaultPickleProperties, GetDistanceMatrix, GetFormalCharge, GetMolFrags, GetPeriodicTable, GetSSSR, GetShortestPath, GetSupplementalSmilesLabel, GetSymmSSSR, HybridizationType, Kekulize, LayeredFingerprint, LogErrorMsg, LogWarningMsg, MergeQueryHs, Mol, MolAddRecursiveQueries, MolFragmentToSmiles, MolFromFASTA, MolFromHELM, MolFromMol2Block, MolFromMol2File, MolFromMolBlock, MolFromMolFile, MolFromPDBBlock, MolFromPDBFile, MolFromSequence, MolFromSmarts, MolFromSmiles, MolFromTPLBlock, MolFromTPLFile, MolToFASTA, MolToHELM, MolToMolBlock, MolToMolFile, MolToPDBBlock, MolToPDBFile, MolToSVG, MolToSequence, MolToSmarts, MolToSmiles, MolToTPLBlock, MolToTPLFile, MurckoDecompose, PDBWriter, ParseMolQueryDefFile, PathToSubmol, PatternFingerprint, PeriodicTable, PropertyPickleOptions, QueryAtom, QueryBond, RDKFingerprint, RWMol, RemoveHs, RemoveStereochemistry, RenumberAtoms, ReplaceCore, ReplaceSidechains, ReplaceSubstructs, ResonanceFlags, ResonanceMolSupplier, RingInfo, SDMolSupplier, SDWriter, SanitizeFlags, SanitizeMol, SetAromaticity, SetAtomAlias, SetAtomRLabel, SetAtomValue, SetConjugation, SetDefaultPickleProperties, SetHybridization, SetSupplementalSmilesLabel, SmilesMolSupplier, SmilesMolSupplierFromText, SmilesParserParams, SmilesWriter, SplitMolByPDBChainId, SplitMolByPDBResidues, TDTMolSupplier, TDTWriter, UnfoldedRDKFingerprintCountBased, WedgeMolBonds, WrapLogs, inchi, rdinchi, rdmolfiles, rdmolops, tossit


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')]


Variables Details [hide private]

ADJUST_IGNOREALL

Value:
rdkit.Chem.rdmolops.AdjustQueryWhichFlags.ADJUST_IGNOREALL

ADJUST_IGNORECHAINS

Value:
rdkit.Chem.rdmolops.AdjustQueryWhichFlags.ADJUST_IGNORECHAINS

ADJUST_IGNOREDUMMIES

Value:
rdkit.Chem.rdmolops.AdjustQueryWhichFlags.ADJUST_IGNOREDUMMIES

ADJUST_IGNORENONDUMMIES

Value:
rdkit.Chem.rdmolops.AdjustQueryWhichFlags.ADJUST_IGNORENONDUMMIES

ADJUST_IGNORENONE

Value:
rdkit.Chem.rdmolops.AdjustQueryWhichFlags.ADJUST_IGNORENONE

ADJUST_IGNORERINGS

Value:
rdkit.Chem.rdmolops.AdjustQueryWhichFlags.ADJUST_IGNORERINGS

ALLOW_CHARGE_SEPARATION

Value:
rdkit.Chem.rdchem.ResonanceFlags.ALLOW_CHARGE_SEPARATION

ALLOW_INCOMPLETE_OCTETS

Value:
rdkit.Chem.rdchem.ResonanceFlags.ALLOW_INCOMPLETE_OCTETS

AROMATICITY_CUSTOM

Value:
rdkit.Chem.rdmolops.AromaticityModel.AROMATICITY_CUSTOM

AROMATICITY_DEFAULT

Value:
rdkit.Chem.rdmolops.AromaticityModel.AROMATICITY_DEFAULT

AROMATICITY_RDKIT

Value:
rdkit.Chem.rdmolops.AromaticityModel.AROMATICITY_RDKIT

AROMATICITY_SIMPLE

Value:
rdkit.Chem.rdmolops.AromaticityModel.AROMATICITY_SIMPLE

CHI_TETRAHEDRAL_CCW

Value:
rdkit.Chem.rdchem.ChiralType.CHI_TETRAHEDRAL_CCW

CHI_TETRAHEDRAL_CW

Value:
rdkit.Chem.rdchem.ChiralType.CHI_TETRAHEDRAL_CW

COMPOSITE_AND

Value:
rdkit.Chem.rdchem.CompositeQueryType.COMPOSITE_AND

COMPOSITE_XOR

Value:
rdkit.Chem.rdchem.CompositeQueryType.COMPOSITE_XOR

ComputedProps

Value:
rdkit.Chem.rdchem.PropertyPickleOptions.ComputedProps

PrivateProps

Value:
rdkit.Chem.rdchem.PropertyPickleOptions.PrivateProps

QueryAtomData

Value:
rdkit.Chem.rdchem.PropertyPickleOptions.QueryAtomData

SANITIZE_ADJUSTHS

Value:
rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_ADJUSTHS

SANITIZE_CLEANUP

Value:
rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_CLEANUP

SANITIZE_CLEANUPCHIRALITY

Value:
rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_CLEANUPCHIRALITY

SANITIZE_FINDRADICALS

Value:
rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_FINDRADICALS

SANITIZE_KEKULIZE

Value:
rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_KEKULIZE

SANITIZE_PROPERTIES

Value:
rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_PROPERTIES

SANITIZE_SETAROMATICITY

Value:
rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_SETAROMATICITY

SANITIZE_SETCONJUGATION

Value:
rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_SETCONJUGATION

SANITIZE_SETHYBRIDIZATION

Value:
rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_SETHYBRIDIZATION

SANITIZE_SYMMRINGS

Value:
rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_SYMMRINGS

UNCONSTRAINED_ANIONS

Value:
rdkit.Chem.rdchem.ResonanceFlags.UNCONSTRAINED_ANIONS

UNCONSTRAINED_CATIONS

Value:
rdkit.Chem.rdchem.ResonanceFlags.UNCONSTRAINED_CATIONS