Namespaces |
| namespace | OpenBabel |
Defines |
| #define | CONNMAX 15 |
| #define | NATOMSMAX 255 |
| #define | NBONDSMAX 255 |
| #define | PI 3.141592653589793238462 |
| #define | blDenominator 4.0 |
| #define | nRotBondsMax 20 |
| #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 147 |
| #define | NBONDTYPES 11 |
Typedefs |
typedef struct
OpenBabel::adjustedlist | adjustedlist |
| typedef adjustedlist | neigbourlist [NATOMSMAX] |
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) |
| bool | compareAtoms (int a1, int a2, const std::vector< std::vector< int > * > aeqList) |
| bool | incrementValues (std::vector< int > ¤tValues, const std::vector< int > maxValues) |
| 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) |
| int | sproduct (TSimpleMolecule &sm, int br, int i1, int i2) |
| 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) |
| bool | restoreDoubleBonds (TEditedMolecule &sm, bool putEither) |
| 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:" |
2D molecule coordinate generation.
1.7.2.