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
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QuickSmartsMatch(smi,
sma,
unique=True,
display=False) |
source code
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SupplierFromFilename(fileN,
delim='
' ,
**kwargs) |
source code
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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
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Imports:
rdBase,
RDConfig,
DataStructs,
rdGeometry,
pyPeriodicTable,
rdchem,
_HasSubstructMatchStr,
AddHs,
AddRecursiveQuery,
AdjustQueryParameters,
AdjustQueryProperties,
AdjustQueryWhichFlags,
AssignAtomChiralTagsFromStructure,
AssignRadicals,
AssignStereochemistry,
Atom,
AtomMonomerInfo,
AtomMonomerType,
AtomPDBResidueInfo,
Bond,
BondDir,
BondStereo,
BondType,
CanonicalRankAtoms,
CanonicalRankAtomsInFragment,
ChiralType,
Cleanup,
CombineMols,
CompositeQueryType,
Conformer,
DeleteSubstructs,
EditableMol,
FastFindRings,
FindAllPathsOfLengthN,
FindAllSubgraphsOfLengthMToN,
FindAllSubgraphsOfLengthN,
FindAtomEnvironmentOfRadiusN,
FindUniqueSubgraphsOfLengthN,
ForwardSDMolSupplier,
FragmentOnBRICSBonds,
FragmentOnBonds,
FragmentOnSomeBonds,
Get3DDistanceMatrix,
GetAdjacencyMatrix,
GetDistanceMatrix,
GetFormalCharge,
GetMolFrags,
GetPeriodicTable,
GetSSSR,
GetShortestPath,
GetSymmSSSR,
HybridizationType,
InchiReadWriteError,
InchiToInchiKey,
Kekulize,
LayeredFingerprint,
LogErrorMsg,
LogWarningMsg,
MergeQueryHs,
Mol,
MolAddRecursiveQueries,
MolFragmentToSmiles,
MolFromFASTA,
MolFromHELM,
MolFromInchi,
MolFromMol2Block,
MolFromMol2File,
MolFromMolBlock,
MolFromMolFile,
MolFromPDBBlock,
MolFromPDBFile,
MolFromSequence,
MolFromSmarts,
MolFromSmiles,
MolFromTPLBlock,
MolFromTPLFile,
MolToFASTA,
MolToHELM,
MolToInchi,
MolToInchiAndAuxInfo,
MolToMolBlock,
MolToMolFile,
MolToPDBBlock,
MolToPDBFile,
MolToSVG,
MolToSequence,
MolToSmarts,
MolToSmiles,
MolToTPLBlock,
MolToTPLFile,
MurckoDecompose,
PDBWriter,
ParseMolQueryDefFile,
PathToSubmol,
PatternFingerprint,
PeriodicTable,
QueryAtom,
QueryBond,
RDKFingerprint,
RWMol,
RemoveHs,
RemoveStereochemistry,
RenumberAtoms,
ReplaceCore,
ReplaceSidechains,
ReplaceSubstructs,
ResonanceFlags,
ResonanceMolSupplier,
RingInfo,
SDMolSupplier,
SDWriter,
SanitizeFlags,
SanitizeMol,
SetAromaticity,
SetConjugation,
SetHybridization,
SmilesMolSupplier,
SmilesMolSupplierFromText,
SmilesWriter,
SplitMolByPDBChainId,
SplitMolByPDBResidues,
TDTMolSupplier,
TDTWriter,
UnfoldedRDKFingerprintCountBased,
WedgeMolBonds,
WrapLogs,
inchi,
rdinchi,
rdmolfiles,
rdmolops,
tossit
FindMolChiralCenters(mol,
force=True,
includeUnassigned=False)
| source code
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>>> 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')]
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ADJUST_EMPTY
- Value:
rdkit.Chem.rdmolops.AdjustQueryWhichFlags.ADJUST_EMPTY
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ADJUST_IGNOREDUMMIES
- Value:
rdkit.Chem.rdmolops.AdjustQueryWhichFlags.ADJUST_IGNOREDUMMIES
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ADJUST_RINGSONLY
- Value:
rdkit.Chem.rdmolops.AdjustQueryWhichFlags.ADJUST_RINGSONLY
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ADJUST_SETALL
- Value:
rdkit.Chem.rdmolops.AdjustQueryWhichFlags.ADJUST_SETALL
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ALLOW_CHARGE_SEPARATION
- Value:
rdkit.Chem.rdchem.ResonanceFlags.ALLOW_CHARGE_SEPARATION
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ALLOW_INCOMPLETE_OCTETS
- Value:
rdkit.Chem.rdchem.ResonanceFlags.ALLOW_INCOMPLETE_OCTETS
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CHI_TETRAHEDRAL_CCW
- Value:
rdkit.Chem.rdchem.ChiralType.CHI_TETRAHEDRAL_CCW
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CHI_TETRAHEDRAL_CW
- Value:
rdkit.Chem.rdchem.ChiralType.CHI_TETRAHEDRAL_CW
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COMPOSITE_AND
- Value:
rdkit.Chem.rdchem.CompositeQueryType.COMPOSITE_AND
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COMPOSITE_XOR
- Value:
rdkit.Chem.rdchem.CompositeQueryType.COMPOSITE_XOR
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SANITIZE_ADJUSTHS
- Value:
rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_ADJUSTHS
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SANITIZE_CLEANUP
- Value:
rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_CLEANUP
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SANITIZE_CLEANUPCHIRALITY
- Value:
rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_CLEANUPCHIRALITY
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SANITIZE_FINDRADICALS
- Value:
rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_FINDRADICALS
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SANITIZE_KEKULIZE
- Value:
rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_KEKULIZE
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SANITIZE_PROPERTIES
- Value:
rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_PROPERTIES
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SANITIZE_SETAROMATICITY
- Value:
rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_SETAROMATICITY
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SANITIZE_SETCONJUGATION
- Value:
rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_SETCONJUGATION
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SANITIZE_SETHYBRIDIZATION
- Value:
rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_SETHYBRIDIZATION
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SANITIZE_SYMMRINGS
- Value:
rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_SYMMRINGS
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UNCONSTRAINED_ANIONS
- Value:
rdkit.Chem.rdchem.ResonanceFlags.UNCONSTRAINED_ANIONS
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UNCONSTRAINED_CATIONS
- Value:
rdkit.Chem.rdchem.ResonanceFlags.UNCONSTRAINED_CATIONS
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