mcdlutil.cpp File Reference

#include <openbabel/babelconfig.h>
#include <openbabel/mol.h>
#include <openbabel/atom.h>
#include <openbabel/bond.h>
#include <openbabel/mcdlutil.h>
#include <openbabel/data.h>
#include <openbabel/obconversion.h>
#include <openbabel/stereo/stereo.h>
#include <openbabel/stereo/cistrans.h>
#include <cmath>

Namespaces
	OpenBabel

Macros
#define	CONNMAX   15
#define	PI   3.141592653589793238462
#define	blDenominator   4.0
#define	nRotBondsMax   10
#define	NEXACTATOMS   21
#define	NALKALYATOMS   5
#define	NALKALYEARTHATOMS   5
#define	NTRIVALENTATOMS   31
#define	NTITANATOMS   3
#define	NVANADIUMATOMS   3
#define	NCHROMIUMATOMS   3
#define	NMANGANESEATOMS   3
#define	NLIKEFEATOMS   2
#define	NPLATINUMATOMS   6
#define	NCOPPERATOMS   3
#define	NZINKATOMS   2
#define	NMETALS   78
#define	NHALOGENS   5
#define	NHETERO   10
#define	NAROMMAX   9
#define	NLIGHT_METALS   20
#define	NHEAVY_METALS   58
#define	DEUTERIUM_ATOM   104
#define	METALL_ATOM   111
#define	HALOGEN_ATOM   112
#define	ANY_ATOM   113
#define	HETERO_ATOM   114
#define	ANY_BOND   8
#define	RUNDEF   -1.2345678E9
#define	DEFAULTBONDLENGTH   1.44
#define	NDATABASE_MOLECULES   148
#define	NBONDTYPES   11

Typedefs
typedef struct OpenBabel::adjustedlist	adjustedlist
typedef adjustedlist	neighbourlist

Functions
string	intToStr (int k)
double	xDistPoint (double x1, double y1, double x2, double y2, double x0, double y0)
bool	overlapped (double x1A, double y1A, double x2A, double y2A, double x1B, double y1B, double x2B, double y2B, double delta)
int	sproduct (TSimpleMolecule &sm, int br, int i1, int i2)
bool	compareAtoms (int a1, int a2, const std::vector< std::vector< int > *> aeqList)
bool	incrementValues (std::vector< int > &currentValues, const std::vector< int > maxValues)
bool	CompareRotor (const pair< int, int > &a, const pair< int, int > &b)
void	deleteIntElement (std::vector< int > *source, int index)
int	hydrogenValency (int na)
int	maxValency (int na)
static int	findAlternateSinglets (const std::vector< int >iA1, const std::vector< int >iA2, const std::vector< int > nH, const std::vector< int > hydrogenValency, std::vector< int > &bondOrder, int nAtoms, int nBonds)
static void	makeAssignment (const std::vector< int > iA1, const std::vector< int > iA2, const std::vector< int > nH, const std::vector< int > hydrogenValency, const std::vector< int > bondAssignment, const std::vector< int > specialFlag, std::vector< int > &bondOrder, int nAtoms, int nBonds, int &nAss)
static bool	analyzeOK (const std::vector< int > iA1, const std::vector< int > iA2, const std::vector< int > nH, const std::vector< int > hydrogenValency, const std::vector< int > maxValency, const std::vector< int > bondOrder, const std::vector< int > atomCheckFlag, int nAtoms, int nBonds, int &nGtMax, int &nNEH, int &nOddEven, bool testExceedHydrogen, bool oddEvenCheck)
static bool	incrementAssignment (std::vector< int > &bondAssignment, int nAss)
static int	determineBondsOrder (const std::vector< int > iA1, const std::vector< int > iA2, const std::vector< int > nH, const std::vector< int > maxValency, std::vector< int > &bondOrder, std::vector< int > &hydrogenValency, int nAtoms, int nBonds, bool oddEvenViolate)
int	alternate (const std::vector< int > aPosition, const std::vector< int > aCharge, const std::vector< int > aRad, const std::vector< int > nHydr, const std::vector< int > iA1, const std::vector< int > iA2, std::vector< int > &bondOrders, int nAtoms, int nBonds)
int	alternate (OBMol *pmol, const std::vector< int > nH, std::vector< int > &bondOrders)
bool	ptInRect (const Rect r, const Point p)
void	generateDiagram (OBMol *pmol, std::ostream &ofs)
void	generateDiagram (OBMol *pmol)
void	generateDiagram (const std::vector< int > iA1, const std::vector< int > iA2, std::vector< double > &rx, std::vector< double > &ry, int nAtoms, int nBonds)
bool	fragmentSearch (OBMol *query, OBMol *structure)
bool	fragmentSearch (const std::vector< int > aPositionQuery, const std::vector< int > iA1Query, const std::vector< int > iA2Query, const std::vector< int > bondTypesQuery, const std::vector< int > aPositionStructure, const std::vector< int > iA1Structure, const std::vector< int > iA2Structure, const std::vector< int > bondTypesStructure, int nAtomsQuery, int nBondsQuery, int nAtomsStructure, int nBondsStructure)
void	equivalenceList (const std::vector< int > aPosition, const std::vector< int > aCharge, const std::vector< int > aRad, const std::vector< int > iA1, const std::vector< int > iA2, const std::vector< int > bondTypes, std::vector< int > &eqList, int nAtoms, int nBonds)
void	equivalenceList (OBMol *pmol, std::vector< int > &eqList)
void	addFragment (OBMol *molecule, OBMol *fragment, int molAN, int fragAN, int molBN, int fragBN, bool isAddition)
void	createStereoLists (OBMol *pmol, std::vector< int > &bondStereoList, std::vector< int > &atomStereoList, std::vector< int > &eqList)
int	compareStringsNumbers (string s1, string s2)
std::string	getAtomSymbol (TSimpleMolecule &sm, int atAtom, int atEx, int priority, string ndData)
std::string	getAtomSymbol (TSimpleMolecule &sm, int atAtom)
int	indexOf (const string instring, const string substring, int fromPos=0)
std::string	removeZeroeth (std::string instring)
int	analizeParity (string data)
int	analizeParityBond (string data)
std::string	changeParity (std::string data)
std::string	changeParityBond (std::string data)
std::string	getAtomMCDL (OBMol *pmol, int ntatoms, const std::vector< int > ix, const std::vector< int > aNumber, const std::vector< int > atomStereoList, const std::vector< int > eqList)
bool	bondEquivalent (int bn1, int bn2, const std::vector< int > eqList, TSimpleMolecule &sm)
std::string	getBondMCDL (OBMol *pmol, int nbStore, int ntatoms, const std::vector< int > ix, const std::vector< int > aNumber, int bonds[MAXBONDS][4], const std::vector< int > bondStereoList, const std::vector< int > eqList)
std::string	addZeroeth (std::string instring, std::string stringAdd)
void	setUpDownBonds (int atomNo, int parity, TSimpleMolecule &sm, std::vector< int > &iA1, std::vector< int > &iA2, std::vector< int > &stereoBonds)
void	implementAtomStereo (std::vector< int > &iA1, std::vector< int > &iA2, std::vector< int > &stereoBonds, const std::vector< double >rx, const std::vector< double > ry, int acount, int bcount, std::string astereo)
void	implementBondStereo (const std::vector< int > iA1, const std::vector< int > iA2, std::vector< double > &rx, std::vector< double > &ry, int acount, int bcount, std::string bstereo)
int	groupRedraw (OBMol *pmol, int bondN, int atomN, bool atomNInGroup)
bool	parseFormula (const std::string formulaString, std::vector< int > &enumber, int &valency)
int	canonizeMCDL (const std::string atomBlock, std::vector< std::string > &structureList)
void	prepareTest (OBMol *pmol, std::ostream &ofs)

Variables
const int	hVal [NELEMMCDL]
const int	maxVal [NELEMMCDL]
const int	chargeVal [NELEMMCDL]
const string	aSymb [NELEMMCDL]
const int	exactAtom [NEXACTATOMS] ={6,14,5,50,82,8,16,34,52,7,15,33,51,9,17,35,53,32,13,26,80}
const int	alkaly [NALKALYATOMS] ={3,11,19,37,55}
const int	alkalyEarth [NALKALYEARTHATOMS] ={4,12,20,38,56}
const int	trivalent [NTRIVALENTATOMS] ={21,31,39,49,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,81,89,90,91,92,93,94,95,96,97,98,99}
const int	titan [NTITANATOMS] ={22,40,72}
const int	vanadium [NVANADIUMATOMS] ={23,41,73}
const int	cromium [NCHROMIUMATOMS] ={24,42,74}
const int	manganeze [NMANGANESEATOMS] ={25,43,75}
const int	likeFe [NLIKEFEATOMS] ={27,28}
const int	platinum [NPLATINUMATOMS] ={44,45,46,76,77,78}
const int	copper [NCOPPERATOMS] ={29,47,79}
const int	zink [NZINKATOMS] ={30,48}
const int	possibleAromatic [NAROMMAX] = {7,8,15,16,33,34,51,52,HETERO_ATOM}
const int	metals [NMETALS]
const int	lightMetals [NLIGHT_METALS]
const int	heavyMetals [NHEAVY_METALS]
const int	halogens [NHALOGENS] = {9,17,35,53,85}
const int	hetero [NHETERO] = {7,8,14,15,16,33,34,51,52,84}
const string	strData [NDATABASE_MOLECULES]
const int	bondValence [NBONDTYPES] = {1,2,3,1,1,0,0,0,1,1,1}
const string	fsastart ="{SA:"
const string	fsbstart ="{SB:"

Detailed Description

2D molecule coordinate generation.

utilities for mcdl format, might be useful for another

Macro Definition Documentation

CONNMAX

#define CONNMAX   15

Referenced by OpenBabel::intToStr().

PI

#define PI   3.141592653589793238462

Referenced by OpenBabel::alternate(), OpenBabel::intToStr(), and OpenBabel::ptInRect().

blDenominator

#define blDenominator   4.0

Referenced by OpenBabel::incrementValues().

nRotBondsMax

#define nRotBondsMax   10

Referenced by OpenBabel::CompareRotor(), and OpenBabel::incrementValues().

NEXACTATOMS

#define NEXACTATOMS   21

Referenced by OpenBabel::intToStr().

NALKALYATOMS

#define NALKALYATOMS   5

Referenced by OpenBabel::intToStr().

NALKALYEARTHATOMS

#define NALKALYEARTHATOMS   5

Referenced by OpenBabel::intToStr().

NTRIVALENTATOMS

#define NTRIVALENTATOMS   31

Referenced by OpenBabel::intToStr().

NTITANATOMS

#define NTITANATOMS   3

Referenced by OpenBabel::intToStr().

NVANADIUMATOMS

#define NVANADIUMATOMS   3

Referenced by OpenBabel::intToStr().

NCHROMIUMATOMS

#define NCHROMIUMATOMS   3

Referenced by OpenBabel::intToStr().

NMANGANESEATOMS

#define NMANGANESEATOMS   3

Referenced by OpenBabel::intToStr().

NLIKEFEATOMS

#define NLIKEFEATOMS   2

Referenced by OpenBabel::intToStr().

NPLATINUMATOMS

#define NPLATINUMATOMS   6

Referenced by OpenBabel::intToStr().

NCOPPERATOMS

#define NCOPPERATOMS   3

Referenced by OpenBabel::intToStr().

NZINKATOMS

#define NZINKATOMS   2

Referenced by OpenBabel::intToStr().

NMETALS

#define NMETALS   78

Referenced by OpenBabel::intToStr(), and OBAtom::IsMetal().

NHALOGENS

#define NHALOGENS   5

Referenced by OpenBabel::intToStr().

NHETERO

#define NHETERO   10

Referenced by OpenBabel::intToStr().

NAROMMAX

#define NAROMMAX   9

Referenced by OpenBabel::intToStr().

NLIGHT_METALS

#define NLIGHT_METALS   20

NHEAVY_METALS

#define NHEAVY_METALS   58

DEUTERIUM_ATOM

#define DEUTERIUM_ATOM   104

METALL_ATOM

#define METALL_ATOM   111

Referenced by OpenBabel::intToStr().

HALOGEN_ATOM

#define HALOGEN_ATOM   112

Referenced by OpenBabel::intToStr().

ANY_ATOM

#define ANY_ATOM   113

Referenced by OpenBabel::alternate(), and OpenBabel::intToStr().

HETERO_ATOM

#define HETERO_ATOM   114

Referenced by OpenBabel::intToStr().

ANY_BOND

#define ANY_BOND   8

Referenced by OpenBabel::alternate(), and OpenBabel::intToStr().

RUNDEF

#define RUNDEF   -1.2345678E9

Referenced by OpenBabel::alternate(), and OpenBabel::ptInRect().

DEFAULTBONDLENGTH

#define DEFAULTBONDLENGTH   1.44

Referenced by OpenBabel::alternate().

NDATABASE_MOLECULES

#define NDATABASE_MOLECULES   148

Referenced by OpenBabel::alternate().

NBONDTYPES

#define NBONDTYPES   11

Referenced by OpenBabel::intToStr().