Canon.h File Reference

#include <RDGeneral/export.h>
#include <boost/dynamic_bitset.hpp>
#include <vector>

Go to the source code of this file.

Classes
union	RDKit::Canon::MolStackUnion
	used to store components in the molecular stack More...
class	RDKit::Canon::MolStackElem
	these are the actual elements in the molecular stack More...

Namespaces
namespace	RDKit
	Std stuff.
namespace	RDKit::Canon

Typedefs
typedef std::vector< MolStackElem >	RDKit::Canon::MolStack
typedef std::tuple< int, int, Bond * >	RDKit::Canon::PossibleType
	used to represent possible branches from an atom

Enumerations
enum	RDKit::Canon::AtomColors { RDKit::Canon::WHITE_NODE = 0 , RDKit::Canon::GREY_NODE , RDKit::Canon::BLACK_NODE }
	used in traversals of the molecule More...
enum	RDKit::Canon::MolStackTypes {   RDKit::Canon::MOL_STACK_ATOM = 0 , RDKit::Canon::MOL_STACK_BOND , RDKit::Canon::MOL_STACK_RING , RDKit::Canon::MOL_STACK_BRANCH_OPEN ,   RDKit::Canon::MOL_STACK_BRANCH_CLOSE }
	used to indicate types of entries in the molecular stack: More...

Functions
RDKIT_GRAPHMOL_EXPORT void	RDKit::Canon::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
RDKIT_GRAPHMOL_EXPORT void	RDKit::Canon::canonicalizeFragment (ROMol &mol, int atomIdx, std::vector< AtomColors > &colors, const std::vector< unsigned int > &ranks, MolStack &molStack, const boost::dynamic_bitset<> *atomsInPlay, const boost::dynamic_bitset<> *bondsInPlay, const std::vector< std::string > *bondSymbols=nullptr, bool doIsomericSmiles=false, bool doRandom=false, bool doChiralInversions=true)
RDKIT_GRAPHMOL_EXPORT bool	RDKit::Canon::chiralAtomNeedsTagInversion (const RDKit::ROMol &mol, const RDKit::Atom *atom, bool isAtomFirst, size_t numClosures)
RDKIT_GRAPHMOL_EXPORT void	RDKit::Canon::canonicalizeEnhancedStereo (ROMol &mol, const std::vector< unsigned int > *atomRanks=nullptr)
	Canonicalizes the atom stereo labels in enhanced stereo groups.

Variables
constexpr int	RDKit::Canon::MAX_NATOMS = 5000
	used in the canonical traversal code
constexpr int	RDKit::Canon::MAX_CYCLES = 1024
	used in the canonical traversal code
constexpr int	RDKit::Canon::MAX_BONDTYPE = 32
	used in the canonical traversal code