canon.cpp File Reference

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

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

Include dependency graph for canon.cpp:


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, unsigned int nfragatoms, unsigned 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())))

#define NO_SYMCLASS   0x7FFFFFFF