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| RDKIT_GRAPHMOL_EXPORT void | setAllowNontetrahedralChirality (bool val) |
| |
| RDKIT_GRAPHMOL_EXPORT bool | getAllowNontetrahedralChirality () |
| |
| RDKIT_GRAPHMOL_EXPORT void | setUseLegacyStereoPerception (bool val) |
| |
| RDKIT_GRAPHMOL_EXPORT bool | getUseLegacyStereoPerception () |
| |
| RDKIT_GRAPHMOL_EXPORT void | removeNonExplicit3DChirality (ROMol &mol) |
| |
| RDKIT_GRAPHMOL_EXPORT std::vector< StereoInfo > | findPotentialStereo (ROMol &mol, bool cleanIt, bool flagPossible=true) |
| | identifies potential stereoatoms and stereobonds in a molecule
|
| |
| RDKIT_GRAPHMOL_EXPORT std::vector< StereoInfo > | findPotentialStereo (const ROMol &mol) |
| | overload
|
| |
| RDKIT_GRAPHMOL_EXPORT void | cleanupStereoGroups (ROMol &mol) |
| | removes atoms without specified chirality from stereo groups
|
| |
| RDKIT_GRAPHMOL_EXPORT void | assignLegacyCIPLabels (ROMol &mol, bool flagPossibleStereoCenters=false) |
| | calls the approximate legacy code for assigning CIP labels
|
| |
| RDKIT_GRAPHMOL_EXPORT INT_VECT | findStereoAtoms (const Bond *bond) |
| |
| RDKIT_GRAPHMOL_EXPORT std::ostream & | operator<< (std::ostream &oss, const StereoSpecified &s) |
| |
| RDKIT_GRAPHMOL_EXPORT std::ostream & | operator<< (std::ostream &oss, const StereoType &s) |
| |
| RDKIT_GRAPHMOL_EXPORT std::map< int, std::unique_ptr< Chirality::WedgeInfoBase > > | pickBondsToWedge (const ROMol &mol, const BondWedgingParameters *params=nullptr) |
| |
| RDKIT_GRAPHMOL_EXPORT std::map< int, std::unique_ptr< Chirality::WedgeInfoBase > > | pickBondsToWedge (const ROMol &mol, const BondWedgingParameters *params, const Conformer *conf) |
| |
| RDKIT_GRAPHMOL_EXPORT void | wedgeMolBonds (ROMol &mol, const Conformer *conf=nullptr, const BondWedgingParameters *params=nullptr) |
| |
| RDKIT_GRAPHMOL_EXPORT void | wedgeBond (Bond *bond, unsigned int fromAtomIdx, const Conformer *conf) |
| |
| RDKIT_GRAPHMOL_EXPORT bool | shouldBeACrossedBond (const Bond *bond) |
| | Returns true for double bonds which should be shown as a crossed bonds.
|
| |
| RDKIT_GRAPHMOL_EXPORT void | reapplyMolBlockWedging (ROMol &mol, bool allBondTypes=true) |
| | Clears existing bond wedging and forces use of atom wedging from MolBlock.
|
| |
| RDKIT_GRAPHMOL_EXPORT void | clearMolBlockWedgingInfo (ROMol &mol) |
| | Remove MolBlock bond wedging information from molecule.
|
| |
| RDKIT_GRAPHMOL_EXPORT void | invertMolBlockWedgingInfo (ROMol &mol) |
| | Invert bond wedging information read from a mol block (if present).
|
| |
| RDKIT_GRAPHMOL_EXPORT void | GetMolFileBondStereoInfo (const Bond *bond, const std::map< int, std::unique_ptr< RDKit::Chirality::WedgeInfoBase > > &wedgeBonds, const Conformer *conf, int &dirCode, bool &reverse) |
| | gets stereo info for a bond
|
| |
| RDKIT_GRAPHMOL_EXPORT void | GetMolFileBondStereoInfo (const Bond *bond, const std::map< int, std::unique_ptr< RDKit::Chirality::WedgeInfoBase > > &wedgeBonds, const Conformer *conf, Bond::BondDir &dir, bool &reverse) |
| |
| RDKIT_GRAPHMOL_EXPORT void | addStereoAnnotations (ROMol &mol, std::string absLabel="abs ({cip})", std::string orLabel="or{id}", std::string andLabel="and{id}", std::string cipLabel="({cip})", std::string bondLabel="({cip})") |
| | add R/S, relative stereo, and E/Z annotations to atoms and bonds
|
| |
| RDKIT_GRAPHMOL_EXPORT void | simplifyEnhancedStereo (ROMol &mol, bool removeAffectedStereoGroups=true) |
| |
| RDKIT_GRAPHMOL_EXPORT std::vector< std::pair< unsigned int, unsigned int > > | findMesoCenters (const ROMol &mol, bool includeIsotopes=true, bool includeAtomMaps=false) |
| | returns the meso centers in a molecule (if any)
|
| |
|
| RDKIT_GRAPHMOL_EXPORT bool | hasNonTetrahedralStereo (const Atom *center) |
| |
| RDKIT_GRAPHMOL_EXPORT Bond * | getChiralAcrossBond (const Atom *center, const Bond *qry) |
| |
| RDKIT_GRAPHMOL_EXPORT Bond * | getChiralAcrossBond (const Atom *center, const Atom *qry) |
| |
| RDKIT_GRAPHMOL_EXPORT Atom * | getChiralAcrossAtom (const Atom *center, const Bond *qry) |
| |
| RDKIT_GRAPHMOL_EXPORT Atom * | getChiralAcrossAtom (const Atom *center, const Atom *qry) |
| |
| RDKIT_GRAPHMOL_EXPORT Bond * | getTrigonalBipyramidalAxialBond (const Atom *center, int which=0) |
| |
| RDKIT_GRAPHMOL_EXPORT Atom * | getTrigonalBipyramidalAxialAtom (const Atom *center, int which=0) |
| |
| RDKIT_GRAPHMOL_EXPORT int | isTrigonalBipyramidalAxialBond (const Atom *center, const Bond *qry) |
| |
| RDKIT_GRAPHMOL_EXPORT int | isTrigonalBipyramidalAxialAtom (const Atom *center, const Atom *qry) |
| |
| RDKIT_GRAPHMOL_EXPORT double | getIdealAngleBetweenLigands (const Atom *center, const Atom *lig1, const Atom *lig2) |
| |
| RDKIT_GRAPHMOL_EXPORT unsigned int | getChiralPermutation (const Atom *center, const INT_LIST &probe) |
| |
| RDKIT_GRAPHMOL_EXPORT void RDKit::Chirality::addStereoAnnotations |
( |
ROMol & |
mol, |
|
|
std::string |
absLabel = "abs ({cip})", |
|
|
std::string |
orLabel = "or{id}", |
|
|
std::string |
andLabel = "and{id}", |
|
|
std::string |
cipLabel = "({cip})", |
|
|
std::string |
bondLabel = "({cip})" |
|
) |
| |
add R/S, relative stereo, and E/Z annotations to atoms and bonds
- Parameters
-
| mol | molecule to modify |
| absLabel | label for atoms in an ABS stereo group |
| orLabel | label for atoms in an OR stereo group |
| andLabel | label for atoms in an AND stereo group |
| cipLabel | label for chiral atoms that aren't in a stereo group. |
| bondLabel | label for CIP stereochemistry on bonds |
If any label is empty, the corresponding annotations will not be added.
The labels can contain the following placeholders: {id} - the stereo group's index {cip} - the atom or bond's CIP stereochemistry
Note that CIP labels will only be added if CIP stereochemistry has been assigned to the molecule.
1.9.8