src

mol.cpp File Reference

Handle molecules. Implementation of OBMol. More...

#include "mol.h"
#include "rotamer.h"
#include "phmodel.h"
#include "bondtyper.h"
#include "math/matrix3x3.h"
#include "obiter.h"
#include <sstream>

Namespaces

namespace  OpenBabel

Defines

#define OBAtomIncrement   100
#define OBAtomIncrement   100
#define OBAtomIncrement   100
#define OBBondIncrement   100

Functions

bool SortVVInt (const vector< int > &a, const vector< int > &b)
bool SortAtomZ (const pair< OBAtom *, double > &a, const pair< OBAtom *, double > &b)
static bool OBComparePairSecond (const pair< OBAtom *, unsigned int > &a, const pair< OBAtom *, unsigned int > &b)
static bool OBComparePairFirst (const pair< OBAtom *, unsigned int > &a, const pair< OBAtom *, unsigned int > &b)
static void ClassCount (vector< pair< OBAtom *, unsigned int > > &vp, unsigned int &count)
 counts the number of unique symmetry classes in a list
static void CreateNewClassVector (vector< pair< OBAtom *, unsigned int > > &vp1, vector< pair< OBAtom *, unsigned int > > &vp2)
static int ValenceSum (OBAtom *atom)
static bool KekulePropagate (OBAtom *atom, vector< int > &visit, vector< int > &ival, int depth)
int GetCurrentValence (OBAtom *atom)
bool ExpandKekule (OBMol &mol, vector< OBNodeBase * > &va, vector< OBNodeBase * >::iterator i, vector< int > &maxv, bool secondpass)
void CorrectBadResonanceForm (OBMol &mol)
bool WriteTitles (ostream &ofs, OBMol &mol)

Variables

bool SwabInt
OBPhModel phmodel
OBAromaticTyper aromtyper
 Global OBAromaticTyper for detecting aromatic atoms and bonds.
OBAtomTyper atomtyper
OBBondTyper bondtyper
 Global OBBondTyper for perception of bond order assignment.

Detailed Description

Handle molecules. Implementation of OBMol.

Define Documentation

#define OBAtomIncrement   100

#define OBAtomIncrement   100

#define OBAtomIncrement   100

#define OBBondIncrement   100