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RDKit
Open-source cheminformatics and machine learning.
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Namespaces | |
namespace | detail |
Classes | |
struct | BondWedgingParameters |
struct | StereoInfo |
Enumerations | |
enum class | StereoType { Unspecified , Atom_Tetrahedral , Atom_SquarePlanar , Atom_TrigonalBipyramidal , Atom_Octahedral , Bond_Double , Bond_Cumulene_Even , Bond_Atropisomer } |
enum class | StereoDescriptor { None , Tet_CW , Tet_CCW , Bond_Cis , Bond_Trans } |
enum class | StereoSpecified { Unspecified , Specified , Unknown } |
Variables | |
constexpr unsigned int | minRingSizeForDoubleBondStereo = 8 |
double bond stereo will be ignored/removed for rings smaller than this: | |
constexpr auto | nonTetrahedralStereoEnvVar = "RDK_ENABLE_NONTETRAHEDRAL_STEREO" |
constexpr auto | useLegacyStereoEnvVar = "RDK_USE_LEGACY_STEREO_PERCEPTION" |
constexpr bool | nonTetrahedralStereoDefaultVal |
whether or not nontetrahedral stereo is perceived by default | |
constexpr bool | useLegacyStereoDefaultVal |
RDKIT_GRAPHMOL_EXPORT bool | useLegacyStereoPerception |
Enumerator | |
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None | |
Tet_CW | |
Tet_CCW | |
Bond_Cis | |
Bond_Trans |
Definition at line 98 of file Chirality.h.
Enumerator | |
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Unspecified | |
Specified | |
Unknown |
Definition at line 100 of file Chirality.h.
Enumerator | |
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Unspecified | |
Atom_Tetrahedral | |
Atom_SquarePlanar | |
Atom_TrigonalBipyramidal | |
Atom_Octahedral | |
Bond_Double | |
Bond_Cumulene_Even | |
Bond_Atropisomer |
Definition at line 87 of file Chirality.h.
RDKIT_GRAPHMOL_EXPORT void RDKit::Chirality::assignLegacyCIPLabels | ( | ROMol & | mol, |
bool | flagPossibleStereoCenters = false |
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calls the approximate legacy code for assigning CIP labels
RDKIT_GRAPHMOL_EXPORT void RDKit::Chirality::cleanupStereoGroups | ( | ROMol & | mol | ) |
removes atoms without specified chirality from stereo groups
RDKIT_GRAPHMOL_EXPORT void RDKit::Chirality::clearMolBlockWedgingInfo | ( | ROMol & | mol | ) |
Remove MolBlock bond wedging information from molecule.
mol | molecule to modify |
RDKIT_GRAPHMOL_EXPORT std::vector< StereoInfo > RDKit::Chirality::findPotentialStereo | ( | const ROMol & | mol | ) |
overload
RDKIT_GRAPHMOL_EXPORT std::vector< StereoInfo > RDKit::Chirality::findPotentialStereo | ( | ROMol & | mol, |
bool | cleanIt, | ||
bool | flagPossible = true |
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identifies potential stereoatoms and stereobonds in a molecule
Note that this function is still somewhat experimental and the API and results may change in a future release.
mol | the molecule to look for stereo in |
cleanIt | remove chirality/stereo specifications from atoms/bonds that cannot be chiral/stereo |
RDKIT_GRAPHMOL_EXPORT INT_VECT RDKit::Chirality::findStereoAtoms | ( | const Bond * | bond | ) |
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extern |
RDKIT_GRAPHMOL_EXPORT Atom * RDKit::Chirality::getChiralAcrossAtom | ( | const Atom * | center, |
const Atom * | qry | ||
) |
RDKIT_GRAPHMOL_EXPORT Atom * RDKit::Chirality::getChiralAcrossAtom | ( | const Atom * | center, |
const Bond * | qry | ||
) |
RDKIT_GRAPHMOL_EXPORT Bond * RDKit::Chirality::getChiralAcrossBond | ( | const Atom * | center, |
const Atom * | qry | ||
) |
RDKIT_GRAPHMOL_EXPORT Bond * RDKit::Chirality::getChiralAcrossBond | ( | const Atom * | center, |
const Bond * | qry | ||
) |
RDKIT_GRAPHMOL_EXPORT unsigned int RDKit::Chirality::getChiralPermutation | ( | const Atom * | center, |
const INT_LIST & | probe | ||
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RDKIT_GRAPHMOL_EXPORT double RDKit::Chirality::getIdealAngleBetweenLigands | ( | const Atom * | center, |
const Atom * | lig1, | ||
const Atom * | lig2 | ||
) |
RDKIT_GRAPHMOL_EXPORT Atom * RDKit::Chirality::getTrigonalBipyramidalAxialAtom | ( | const Atom * | center, |
int | which = 0 |
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RDKIT_GRAPHMOL_EXPORT Bond * RDKit::Chirality::getTrigonalBipyramidalAxialBond | ( | const Atom * | center, |
int | which = 0 |
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which | if this is -1 then the second axial bond will be returned, otherwise the first |
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extern |
RDKIT_GRAPHMOL_EXPORT bool RDKit::Chirality::hasNonTetrahedralStereo | ( | const Atom * | center | ) |
RDKIT_GRAPHMOL_EXPORT void RDKit::Chirality::invertMolBlockWedgingInfo | ( | ROMol & | mol | ) |
Invert bond wedging information read from a mol block (if present).
mol | molecule to modify |
RDKIT_GRAPHMOL_EXPORT int RDKit::Chirality::isTrigonalBipyramidalAxialAtom | ( | const Atom * | center, |
const Atom * | qry | ||
) |
RDKIT_GRAPHMOL_EXPORT int RDKit::Chirality::isTrigonalBipyramidalAxialBond | ( | const Atom * | center, |
const Bond * | qry | ||
) |
RDKIT_GRAPHMOL_EXPORT std::ostream & RDKit::Chirality::operator<< | ( | std::ostream & | oss, |
const StereoSpecified & | s | ||
) |
RDKIT_GRAPHMOL_EXPORT std::ostream & RDKit::Chirality::operator<< | ( | std::ostream & | oss, |
const StereoType & | s | ||
) |
RDKIT_GRAPHMOL_EXPORT INT_MAP_INT RDKit::Chirality::pickBondsToWedge | ( | const ROMol & | mol, |
const BondWedgingParameters * | params = nullptr |
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) |
picks the bonds which should be wedged
RDKIT_GRAPHMOL_EXPORT void RDKit::Chirality::reapplyMolBlockWedging | ( | ROMol & | mol | ) |
Clears existing bond wedging and forces use of atom wedging from MolBlock.
mol | molecule to have its wedges altered |
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extern |
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extern |
RDKIT_GRAPHMOL_EXPORT void RDKit::Chirality::wedgeBond | ( | Bond * | bond, |
unsigned int | fromAtomIdx, | ||
const Conformer * | conf | ||
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RDKIT_GRAPHMOL_EXPORT void RDKit::Chirality::wedgeMolBonds | ( | ROMol & | mol, |
const Conformer * | conf = nullptr , |
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const BondWedgingParameters * | params = nullptr |
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double bond stereo will be ignored/removed for rings smaller than this:
Definition at line 30 of file Chirality.h.
whether or not nontetrahedral stereo is perceived by default
Definition at line 34 of file Chirality.h.
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constexpr |
Definition at line 32 of file Chirality.h.
whether or not the legacy stereo perception code is used by default
Definition at line 36 of file Chirality.h.
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constexpr |
Definition at line 33 of file Chirality.h.
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extern |
Toggle usage of the legacy stereo perception code
Definition at line 51 of file Chirality.h.