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RDKIT_GRAPHMOL_EXPORT void | canonicalizeFragment (ROMol &mol, int atomIdx, std::vector< AtomColors > &colors, const std::vector< unsigned int > &ranks, MolStack &molStack, const boost::dynamic_bitset<> *bondsInPlay=nullptr, const std::vector< std::string > *bondSymbols=nullptr, bool doIsomericSmiles=false, bool doRandom=false, bool doChiralInversions=true) |
| constructs the canonical traversal order for a molecular fragment
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RDKIT_GRAPHMOL_EXPORT bool | chiralAtomNeedsTagInversion (const RDKit::ROMol &mol, const RDKit::Atom *atom, bool isAtomFirst, size_t numClosures) |
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RDKIT_GRAPHMOL_EXPORT void | canonicalizeEnhancedStereo (ROMol &mol, const std::vector< unsigned int > *atomRanks=nullptr) |
| Canonicalizes the atom stereo labels in enhanced stereo groups.
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RDKIT_GRAPHMOL_EXPORT void | updateAtomNeighborIndex (canon_atom *atoms, std::vector< bondholder > &nbrs) |
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RDKIT_GRAPHMOL_EXPORT void | updateAtomNeighborNumSwaps (canon_atom *atoms, std::vector< bondholder > &nbrs, unsigned int atomIdx, std::vector< std::pair< unsigned int, unsigned int > > &result) |
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template<typename CompareFunc > |
void | RefinePartitions (const ROMol &mol, canon_atom *atoms, CompareFunc compar, int mode, int *order, int *count, int &activeset, int *next, int *changed, char *touchedPartitions) |
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template<typename CompareFunc > |
void | BreakTies (const ROMol &mol, canon_atom *atoms, CompareFunc compar, int mode, int *order, int *count, int &activeset, int *next, int *changed, char *touchedPartitions) |
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RDKIT_GRAPHMOL_EXPORT void | CreateSinglePartition (unsigned int nAtoms, int *order, int *count, canon_atom *atoms) |
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RDKIT_GRAPHMOL_EXPORT void | ActivatePartitions (unsigned int nAtoms, int *order, int *count, int &activeset, int *next, int *changed) |
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RDKIT_GRAPHMOL_EXPORT void | rankMolAtoms (const ROMol &mol, std::vector< unsigned int > &res, bool breakTies=true, bool includeChirality=true, bool includeIsotopes=true, bool includeAtomMaps=true, bool includeChiralPresence=false, bool includeStereoGroups=true, bool useNonStereoRanks=false) |
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RDKIT_GRAPHMOL_EXPORT void | rankFragmentAtoms (const ROMol &mol, std::vector< unsigned int > &res, const boost::dynamic_bitset<> &atomsInPlay, const boost::dynamic_bitset<> &bondsInPlay, const std::vector< std::string > *atomSymbols, const std::vector< std::string > *bondSymbols, bool breakTies, bool includeChirality, bool includeIsotope, bool includeAtomMaps, bool includeChiralPresence) |
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void | rankFragmentAtoms (const ROMol &mol, std::vector< unsigned int > &res, const boost::dynamic_bitset<> &atomsInPlay, const boost::dynamic_bitset<> &bondsInPlay, const std::vector< std::string > *atomSymbols=nullptr, bool breakTies=true, bool includeChirality=true, bool includeIsotopes=true, bool includeAtomMaps=true, bool includeChiralPresence=false) |
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RDKIT_GRAPHMOL_EXPORT void | chiralRankMolAtoms (const ROMol &mol, std::vector< unsigned int > &res) |
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RDKIT_GRAPHMOL_EXPORT void | initCanonAtoms (const ROMol &mol, std::vector< Canon::canon_atom > &atoms, bool includeChirality=true, bool includeStereoGroups=true) |
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