canon.cpp File Reference

Canonical numbering of SMILES, molecules and fragments. More...

#include <openbabel/babelconfig.h>
#include <openbabel/mol.h>
#include <openbabel/canon.h>

Namespaces
namespace	OpenBabel
Defines
#define	DEBUG   0
#define	CT_MATCH(b1, b2)   b1->IsUp() ? b2->SetDown() : (b1->IsDown() ? b2->SetUp() : (b2->IsUp() ? b1->SetDown() : (b2->IsDown() ? b1->SetUp() : b1->SetDown())))
#define	NO_SYMCLASS   0x7FFFFFFF
Functions
static bool	CompareUnsigned (const unsigned int &a, const unsigned int &b)
static bool	ComparePairFirst (const pair< OBAtom *, unsigned int > &a, const pair< OBAtom *, unsigned int > &b)
static bool	ComparePairSecond (const pair< OBAtom *, unsigned int > &a, const pair< OBAtom *, unsigned int > &b)
static bool	CompareBondPairSecond (const pair< OBBond *, unsigned int > &a, const pair< OBBond *, unsigned int > &b)
static unsigned int	GetValence (OBAtom *atom, OBBitVec &frag_atoms)
static unsigned int	GetHvyValence (OBAtom *atom, OBBitVec &frag_atoms)
static unsigned int	GetHvyBondSum (OBAtom *atom, OBBitVec &frag_atoms)
static bool	GetGTDVector (OBMol *pmol, OBBitVec &frag_atoms, vector< int > &gtd)
static void	FindRingAtoms (OBMol *pmol, OBBitVec &frag_atoms, OBBitVec &ring_atoms)
static void	GetGIVector (OBMol *pmol, OBBitVec &frag_atoms, vector< unsigned int > &vid)
static void	CreateNewClassVector (vector< pair< OBAtom *, unsigned int > > &vp1, vector< pair< OBAtom *, unsigned int > > &vp2, OBBitVec &frag_atoms, int natoms)
static void	CountAndRenumberClasses (vector< pair< OBAtom *, unsigned int > > &vp, unsigned int &count)
static int	ExtendInvarients (vector< pair< OBAtom *, unsigned int > > &symmetry_classes, OBBitVec &frag_atoms, int nfragatoms, int natoms)
static int	CalculateSymmetry (OBMol *pmol, OBBitVec &frag_atoms, vector< pair< OBAtom *, unsigned int > > &symmetry_classes)
static void	BreakChiralTies (OBMol *pmol, OBBitVec &frag_atoms, int nfragatoms, vector< pair< OBAtom *, unsigned int > > &atom_sym_classes)
static void	FindConjugatedEZBonds (OBAtom *atom, OBBitVec &flip_bonds, OBBitVec &visited_atoms)
static void	FixCisTransBonds (OBMol *pmol, OBBitVec &frag_atoms, vector< unsigned int > &symmetry_classes, vector< unsigned int > &canonical_labels)
void	CanonicalLabels (OBMol *pmol, OBBitVec &frag_atoms, std::vector< unsigned int > &symmetry_classes, std::vector< unsigned int > &canonical_labels)

---

Detailed Description

Canonical numbering of SMILES, molecules and fragments.

---

Define Documentation

#define DEBUG   0

#define CT_MATCH	(	b1,
		b2		)	b1->IsUp() ? b2->SetDown() : (b1->IsDown() ? b2->SetUp() : (b2->IsUp() ? b1->SetDown() : (b2->IsDown() ? b1->SetUp() : b1->SetDown())))

Referenced by OpenBabel::FixCisTransBonds().

#define NO_SYMCLASS   0x7FFFFFFF

Referenced by OpenBabel::CanonicalLabels().