Namespaces
namespace	detail

Classes
class	AtomCompareFunctor

struct	bondholder

struct	canon_atom

class	ChiralAtomCompareFunctor

class	MolStackElem
	these are the actual elements in the molecular stack More...

union	MolStackUnion
	used to store components in the molecular stack More...

class	SpecialChiralityAtomCompareFunctor

class	SpecialSymmetryAtomCompareFunctor

Typedefs
typedef std::vector< MolStackElem >	MolStack

typedef std::tuple< int, int, Bond * >	PossibleType
	used to represent possible branches from an atom

Enumerations
enum	AtomColors { WHITE_NODE = 0 , GREY_NODE , BLACK_NODE }
	used in traversals of the molecule More...

enum	MolStackTypes { MOL_STACK_ATOM = 0 , MOL_STACK_BOND , MOL_STACK_RING , MOL_STACK_BRANCH_OPEN , MOL_STACK_BRANCH_CLOSE }
	used to indicate types of entries in the molecular stack: More...

Functions
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

RDKIT_GRAPHMOL_EXPORT bool	chiralAtomNeedsTagInversion (const RDKit::ROMol &mol, const RDKit::Atom *atom, bool isAtomFirst, size_t numClosures)

RDKIT_GRAPHMOL_EXPORT void	canonicalizeEnhancedStereo (ROMol &mol, const std::vector< unsigned int > *atomRanks=nullptr)
	Canonicalizes the atom stereo labels in enhanced stereo groups.

RDKIT_GRAPHMOL_EXPORT void	updateAtomNeighborIndex (canon_atom *atoms, std::vector< bondholder > &nbrs)

RDKIT_GRAPHMOL_EXPORT void	updateAtomNeighborNumSwaps (canon_atom *atoms, std::vector< bondholder > &nbrs, unsigned int atomIdx, std::vector< std::pair< unsigned int, unsigned int > > &result)

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)

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)

RDKIT_GRAPHMOL_EXPORT void	CreateSinglePartition (unsigned int nAtoms, int order, int count, canon_atom *atoms)

RDKIT_GRAPHMOL_EXPORT void	ActivatePartitions (unsigned int nAtoms, int order, int count, int &activeset, int next, int changed)

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)

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)

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)

RDKIT_GRAPHMOL_EXPORT void	chiralRankMolAtoms (const ROMol &mol, std::vector< unsigned int > &res)

RDKIT_GRAPHMOL_EXPORT void	initCanonAtoms (const ROMol &mol, std::vector< Canon::canon_atom > &atoms, bool includeChirality=true, bool includeStereoGroups=true)

Variables
const int	MAX_NATOMS = 5000
	used in the canonical traversal code

const int	MAX_CYCLES = 1000
	used in the canonical traversal code

const int	MAX_BONDTYPE = 32
	used in the canonical traversal code

const unsigned int	ATNUM_CLASS_OFFSET = 10000

Typedef Documentation

◆ MolStack

typedef std::vector<MolStackElem> RDKit::Canon::MolStack

Definition at line 95 of file Canon.h.

◆ PossibleType

typedef std::tuple<int, int, Bond *> RDKit::Canon::PossibleType

used to represent possible branches from an atom

Definition at line 98 of file Canon.h.

Enumeration Type Documentation

◆ AtomColors

enum RDKit::Canon::AtomColors

used in traversals of the molecule

Enumerator
WHITE_NODE	not visited
GREY_NODE	visited, but not finished
BLACK_NODE	visited and finished

Definition at line 30 of file Canon.h.

◆ MolStackTypes

enum RDKit::Canon::MolStackTypes

used to indicate types of entries in the molecular stack:

Enumerator
MOL_STACK_ATOM	an Atom
MOL_STACK_BOND	a Bond
MOL_STACK_RING	a ring closure
MOL_STACK_BRANCH_OPEN	beginning of a branch
MOL_STACK_BRANCH_CLOSE	end of a branch

Definition at line 37 of file Canon.h.

Function Documentation

◆ ActivatePartitions()

RDKIT_GRAPHMOL_EXPORT void RDKit::Canon::ActivatePartitions	(	unsigned int	nAtoms,
		int *	order,
		int *	count,
		int &	activeset,
		int *	next,
		int *	changed
	)

◆ BreakTies()

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
	)

Definition at line 754 of file new_canon.h.

References RDKit::Canon::canon_atom::degree, RDKit::ROMol::getNumAtoms(), RDKit::Canon::canon_atom::index, RDKit::Canon::canon_atom::nbrIds, RDKit::rdvalue_is(), and RefinePartitions().

◆ canonicalizeEnhancedStereo()

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.

For example, after calling this function the chiral centers in the molecules C[C@H](F)Cl |&1:1| and C[C@@H](F)Cl |&1:1| will have the same chiral tags.

◆ canonicalizeFragment()

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

Parameters

mol	the ROMol we're working on
atomIdx	the index of the atom to start the traversal from
colors	the traversal status of each atom in `mol`
ranks	the assigned rank of each atom in `mol`
molStack	the current traversal stack (used to return the results)

Notes

mol will, in general, be modified by this operation as bond directions and the like are changed to fit the canonical traversal order

◆ chiralAtomNeedsTagInversion()

RDKIT_GRAPHMOL_EXPORT bool RDKit::Canon::chiralAtomNeedsTagInversion	(	const RDKit::ROMol &	mol,
		const RDKit::Atom *	atom,
		bool	isAtomFirst,
		size_t	numClosures
	)

Check if a chiral atom needs to have its tag flipped after reading or before writing SMILES

◆ chiralRankMolAtoms()

RDKIT_GRAPHMOL_EXPORT void RDKit::Canon::chiralRankMolAtoms	(	const ROMol &	mol,
		std::vector< unsigned int > &	res
	)

◆ CreateSinglePartition()

RDKIT_GRAPHMOL_EXPORT void RDKit::Canon::CreateSinglePartition	(	unsigned int	nAtoms,
		int *	order,
		int *	count,
		canon_atom *	atoms
	)

◆ initCanonAtoms()

RDKIT_GRAPHMOL_EXPORT void RDKit::Canon::initCanonAtoms	(	const ROMol &	mol,
		std::vector< Canon::canon_atom > &	atoms,
		bool	includeChirality = `true`,
		bool	includeStereoGroups = `true`
	)

◆ rankFragmentAtoms() [1/2]

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
	)

Referenced by rankFragmentAtoms().

◆ rankFragmentAtoms() [2/2]

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`
	)

inline

Definition at line 828 of file new_canon.h.

References rankFragmentAtoms(), and RDKit::rdvalue_is().

◆ rankMolAtoms()

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`
	)

◆ RefinePartitions()

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
	)

Definition at line 657 of file new_canon.h.

References RDKit::Canon::canon_atom::degree, RDKit::ROMol::getNumAtoms(), RDKit::hanoisort(), RDKit::Canon::canon_atom::index, RDKit::Canon::canon_atom::nbrIds, and RDKit::rdvalue_is().

Referenced by BreakTies().

◆ updateAtomNeighborIndex()

RDKIT_GRAPHMOL_EXPORT void RDKit::Canon::updateAtomNeighborIndex	(	canon_atom *	atoms,
		std::vector< bondholder > &	nbrs
	)

Referenced by RDKit::Canon::SpecialChiralityAtomCompareFunctor::operator()(), RDKit::Canon::SpecialSymmetryAtomCompareFunctor::operator()(), and RDKit::Canon::AtomCompareFunctor::operator()().

◆ updateAtomNeighborNumSwaps()

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
	)

Referenced by RDKit::Canon::SpecialChiralityAtomCompareFunctor::operator()().

Variable Documentation

◆ ATNUM_CLASS_OFFSET

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

Definition at line 530 of file new_canon.h.

Referenced by RDKit::Canon::ChiralAtomCompareFunctor::operator()().

◆ MAX_BONDTYPE

const int RDKit::Canon::MAX_BONDTYPE = 32

used in the canonical traversal code

Definition at line 27 of file Canon.h.

◆ MAX_CYCLES

const int RDKit::Canon::MAX_CYCLES = 1000

used in the canonical traversal code

Definition at line 26 of file Canon.h.

◆ MAX_NATOMS

const int RDKit::Canon::MAX_NATOMS = 5000

used in the canonical traversal code

Definition at line 25 of file Canon.h.

Namespaces

Classes

Typedefs

Enumerations

Functions

Variables

Typedef Documentation

◆ MolStack

◆ PossibleType

Enumeration Type Documentation

◆ AtomColors

◆ MolStackTypes

Function Documentation

◆ ActivatePartitions()

◆ BreakTies()

◆ canonicalizeEnhancedStereo()

◆ canonicalizeFragment()

◆ chiralAtomNeedsTagInversion()

◆ chiralRankMolAtoms()

◆ CreateSinglePartition()

◆ initCanonAtoms()

◆ rankFragmentAtoms() [1/2]

◆ rankFragmentAtoms() [2/2]

◆ rankMolAtoms()

◆ RefinePartitions()

◆ updateAtomNeighborIndex()

◆ updateAtomNeighborNumSwaps()

Variable Documentation

◆ ATNUM_CLASS_OFFSET

◆ MAX_BONDTYPE

◆ MAX_CYCLES

◆ MAX_NATOMS