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new_canon.h File Reference
`#include <RDGeneral/export.h>`
`#include <RDGeneral/hanoiSort.h>`
`#include <GraphMol/ROMol.h>`
`#include <GraphMol/RingInfo.h>`
`#include <GraphMol/StereoGroup.h>`
`#include <RDGeneral/BoostStartInclude.h>`
`#include <cstdint>`
`#include <boost/dynamic_bitset.hpp>`
`#include <RDGeneral/BoostEndInclude.h>`
`#include <cstring>`
`#include <iostream>`
`#include <cassert>`
`#include <vector>`

Go to the source code of this file.

## Classes

struct | RDKit::Canon::bondholder
struct | RDKit::Canon::canon_atom
class | RDKit::Canon::SpecialChiralityAtomCompareFunctor
class | RDKit::Canon::SpecialSymmetryAtomCompareFunctor
class | RDKit::Canon::AtomCompareFunctor
class | RDKit::Canon::ChiralAtomCompareFunctor

## Namespaces

namespace | RDKit
| Std stuff.
namespace | RDKit::Canon
namespace | RDKit::Canon::detail

## Functions

RDKIT_GRAPHMOL_EXPORT void | RDKit::Canon::updateAtomNeighborIndex (canon_atom *atoms, std::vector< bondholder > &nbrs)
RDKIT_GRAPHMOL_EXPORT void | RDKit::Canon::updateAtomNeighborNumSwaps (canon_atom *atoms, std::vector< bondholder > &nbrs, unsigned int atomIdx, std::vector< std::pair< unsigned int, unsigned int > > &result)
template<typename CompareFunc >
void | RDKit::Canon::RefinePartitions (const ROMol &mol, canon_atom *atoms, CompareFunc compar, int mode, int *order, int *count, int &activeset, int *next, int *changed, char *touchedPartitions)
template<typename CompareFunc >
void | RDKit::Canon::BreakTies (const ROMol &mol, canon_atom *atoms, CompareFunc compar, int mode, int *order, int *count, int &activeset, int *next, int *changed, char *touchedPartitions)
RDKIT_GRAPHMOL_EXPORT void | RDKit::Canon::CreateSinglePartition (unsigned int nAtoms, int *order, int *count, canon_atom *atoms)
RDKIT_GRAPHMOL_EXPORT void | RDKit::Canon::ActivatePartitions (unsigned int nAtoms, int *order, int *count, int &activeset, int *next, int *changed)
RDKIT_GRAPHMOL_EXPORT void | RDKit::Canon::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)

RDKIT_GRAPHMOL_EXPORT void

RDKit::Canon::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)

void | RDKit::Canon::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)
RDKIT_GRAPHMOL_EXPORT void | RDKit::Canon::chiralRankMolAtoms (const ROMol &mol, std::vector< unsigned int > &res)
RDKIT_GRAPHMOL_EXPORT void | RDKit::Canon::initCanonAtoms (const ROMol &mol, std::vector< Canon::canon_atom > &atoms, bool includeChirality=true, bool includeStereoGroups=true)
void | RDKit::Canon::detail::initFragmentCanonAtoms (const ROMol &mol, std::vector< Canon::canon_atom > &atoms, bool includeChirality, const std::vector< std::string > *atomSymbols, const std::vector< std::string > *bondSymbols, const boost::dynamic_bitset<> &atomsInPlay, const boost::dynamic_bitset<> &bondsInPlay, bool needsInit)
template<typename T >
void | RDKit::Canon::detail::rankWithFunctor (T &ftor, bool breakTies, int *order, bool useSpecial=false, bool useChirality=false, const boost::dynamic_bitset<> *atomsInPlay=nullptr, const boost::dynamic_bitset<> *bondsInPlay=nullptr)

## Variables

const unsigned int | RDKit::Canon::ATNUM_CLASS_OFFSET = 10000