/* * File: chemPropSet.h * Author: flong * * Created on July 3, 2014, 1:27 PM */ #ifndef CHEMPROPSET_H #define CHEMPROPSET_H #ifndef KERNEL_H #include "kernel.h" #endif #ifndef ATOM_H #include "atom.h" #endif #ifndef BOND_H #include "bond.h" #endif #ifndef ANGLE_H #include "angle.h" #endif #ifndef TORSION_H #include "torsion.h" #endif #ifndef RESIDUE_H #include "residue.h" #endif #ifndef RING_H #include "ring.h" #endif #ifndef PLANE_H #include "plane.h" #endif #ifndef CHAIN_H #include "chain.h" #endif #ifndef MOLECULE_H #include "molecule.h" #endif #ifndef LIBG_MODEL_H #include "libgmodel.h" #endif #ifndef SSBOND_H #include "ssbond.h" #endif #ifndef LIBG_LINK_H #include "libglink.h" #endif #ifndef CRYSTINFO_H #include "crystInfo.h" #endif #ifndef SECONDARYSTRUCTURES_H #include "secondaryStructures.h" #endif #ifndef CODCLASSIFY_H #include "codClassify.h" #endif #ifndef UTILITY_H #include "utility.h" #endif #ifndef TRANSCOORD_H #include "TransCoord.h" #endif #ifndef MOLSDFFILE_H #include "MolSdfFile.h" #endif #ifndef PERIODICTABLE_H #include "periodicTable.h" #endif namespace LIBMOL { class Atom; class AtomDict; class Bond; class BondDict; class Ring; class RingDict; class Angle; class AngleDict; class Torsion; class TorsionDict; class Chiral; class ChiralDict; class Plane; class PlaneDict; class Molecule; class CodClassify; class CCP4AtomType; class MolSdfFile; class PeriodicTable; extern bool assignElementType(PeriodicTable & tP, std::string tStr, std::vector::iterator tAtom); extern int getNumOxyConnect(std::vector & tAtoms, std::vector::iterator iA); extern void getHydroAtomConnect(std::vector & tAtoms); extern void mdChiralByClasses(std::vector::iterator iAt, std::vector & tAtoms); // Two stages for sp hybridization (They will be merged to the same // function once the second one passes tests // 1. Currently used one (originally in codClassify.h and .cpp) extern void setAtomsBondingAndChiralCenter(std::vector & tAtoms); // 2. For modAtomsBondingAndChiralCenter // tMode 0 : not use coordinates (in dictionary generation stage) // tMode 1 : definitely have reliable coordinates (in DB molecule generation stage) extern void modAtomsBondingAndChiralCenter(std::vector & tAtoms, std::vector & tBonds, std::vector & tAngles, std::vector & tRings, int tMode); extern void setAtomsNB1NB2_SP(std::vector & tAtoms); extern void setAtomsNB1NB2_exElectrons(std::vector & tAtoms); extern void setBondsAndAngles_NB1NB2_SP(std::vector & tAtoms, std::vector & tBonds, std::vector & tAngles); extern void setBondsAndAngles_NB1NB2_EE(std::vector & tAtoms, std::vector & tBonds, std::vector & tAngles); extern void reIndexAtomInRing(std::vector & tAtoms, std::vector & tRings); extern void setAnglesSPSigns(std::vector & tAtoms, std::vector & tAngles); extern bool confirmPlaneByChiralVol(std::vector & tAtoms, std::vector::iterator tA); extern bool confirmPlaneByAngle(std::vector & tAtoms, std::vector::iterator tA, REAL tCri); // a function transfer int sp to a string extern std::string strTransSP(int tSP); extern bool checkBridgeStruct(std::vector & tAtoms, std::vector & tRings, int tAnchIdx); // extern REAL checkProtonateO(std::vector::iterator tIA, REAL tTolBondOrder); extern REAL checkProtonateO(std::vector::iterator tIA, Molecule & tMol); extern REAL checkProtonateO(std::vector::iterator tIA, Molecule & tMol, REAL tPka, REAL tPh); extern REAL checkProtonateN(std::vector::iterator tIA, REAL tTolBondOrder, std::vector &tAllAtoms); extern REAL checkProtonateN(std::vector::iterator tIA, Molecule & tMol); extern REAL checkProtonateAll(std::vector::iterator tIA, Molecule & tMol, PeriodicTable & tTab); extern REAL checkProtonateAll(std::vector::iterator tIA, std::vector & tAtoms, std::vector & tBonds, PeriodicTable & tTab); // The following function replaces the previous function addHAtomToMols(). extern void ProtonateFunctionGroupInOneMol(std::vector & tA, std::vector & tBonds, std::vector & tAddHIdx); extern REAL checkProtonateAll(std::vector::iterator tIA, Molecule & tMol, PeriodicTable & tTab); extern REAL checkProtonateN(std::vector::iterator tIA, Molecule & tMol, REAL tPka, REAL tPh); extern REAL checkProtonateS(std::vector::iterator tIA, REAL tTolBondOrder); extern REAL checkProtonateS(std::vector::iterator tIA, Molecule & tMol); extern REAL checkProtonateS(std::vector::iterator tIA, Molecule & tMol, REAL tPka, REAL tPh); extern REAL checkProtonateC(std::vector::iterator tIA, REAL tTolBondOrder); extern REAL checkProtonateC(std::vector::iterator tIA, Molecule & tMol); extern REAL checkProtonateC(std::vector::iterator tIA, Molecule & tMol, REAL tPka, REAL tPh); // Function groups at the moment. extern void checkProtonatedCarBoxylicTerminus(std::vector::iterator tIA, std::vector & tAtoms, std::vector & tBonds, REAL tPH, REAL tPka, std::vector tDoneAtoms); extern void checkProtonatedSulfuricAcids(std::vector::iterator tIA, std::vector & tAtoms, std::vector & tBonds, REAL tPH, std::vector tDoneAtoms); extern void checkProtonatedAminoTerminus(std::vector::iterator tIA, std::vector & tAtoms, std::vector & tBonds, REAL tPH, REAL tPka, std::vector tDoneAtoms); extern void checkProtonatedPAcids(std::vector::iterator tIA, std::vector & tAtoms, std::vector & tBonds, REAL tPH, std::vector tDoneAtoms); // The following function overwrites addHAtoms in MolSdfFile class extern void adjustHAtoms(std::vector & tAtoms, std::vector & tBonds, int tAtmIdx, int tAddH, std::vector & tHAtmIdxs); extern void setAllAddedHAtomCoords(std::vector & tAtoms, std::vector & tHAtmIdxs); // Bond order sections extern REAL getTotalBondOrder(Molecule & tMol, std::vector::iterator tIA); extern REAL getTotalBondOrder(std::vector & tBonds, std::vector & tAtoms, std::vector::iterator tIA); extern REAL getTotalBondOrder(std::vector & tBonds, std::vector & tAtoms, int tIA); extern void modifyBondOrderAR(std::vector & tBonds, std::vector & tAtoms, int tIdxB1, int tIdxB2, int tAtCen, int tAt1, int tAt2, PeriodicTable & tTab); extern REAL getFixedBondOrder(std::vector & tBonds, std::vector & tAtoms, int tAtmIdx); extern REAL getBondOrder(Molecule & tMol, int tIdx1, int tIdx2); extern REAL getBondOrder(std::vector & tBonds, int tIdx1, int tIdx2); extern REAL getBondOrderOneAtom(std::vector tBonds, std::vector tAtoms, int tIdx1, int tIdx2); extern void setAllBondOrders(std::vector & tAtoms, std::vector & tBonds); extern void kekulizeRings(std::vector & tAtoms, std::vector & tBonds, std::vector & tRings); extern void kekulizeOneRing(std::vector & tAtoms, std::vector & tBonds, RingDict & tRing, int tStartIdx, PeriodicTable & tTab); extern void setOneHAtomCoords(); extern void setOneHAtomCoordsSP3(std::vector & tAtoms, std::vector::iterator tIA); extern void setOneHAtomCoordsSP2(std::vector & tAtoms, std::vector::iterator tIA); extern void setOneHAtomCoordsSP(std::vector & tAtoms, std::vector::iterator tIA); extern void setAllAtomEXcessElectrons(std::vector & tAtoms); extern int getOneNBAtomExContri(std::vector& tAtoms, int tIdxAtm, int tIdxNB); extern void setAtomRingProps(std::vector & tAtoms, std::vector & tRings); extern void setInitBondOrdersViaExtraElecs(std::vector & tAtoms, std::vector & tBonds); extern int sumExElectrons(std::vector & tAtoms); // atom and bond stereo extern void checkAllStereo(FileName tMdlIn, FileName tPdbIn, FileName tPdbOut); extern void checkStereoOneMol(std::vector::iterator tMol, FileName tPdbOut); // Check aromatic stability of extended ring systems. // using it to decide planes in the systems(molecules or monomers) extern void setAromPlanes(std::vector & tAtoms, std::vector & tRings, std::vector & tPlans); extern void outBoAndChList(FileName tFName, std::vector & tAtoms, std::vector & tBonds); extern void setAtomFormTypes(std::vector & tAtoms); extern void getDandAPair(PeriodicTable & tPTab, std::vector::iterator tAtm, std::vector::iterator jAtm, std::map & tHPropAtom, std::map > & tHCandAtom, double tDist); class HuckelMOSuite { public : HuckelMOSuite(); ~HuckelMOSuite(); void setWorkMode(int tMode); void execute(std::vector & tAtoms, std::vector & tBonds); void execute2(std::vector & tAtoms, std::vector & tBonds, std::vector & tRings); void execute3(std::vector & tAtoms, std::vector & tBonds, std::vector & tRings); void initiaExElecs(std::vector & tAtoms); void initiaExElecs2(std::vector & tAtoms); void PickPiElectrons(std::vector & tAtoms); void PickOddAtoms(std::vector & tAtoms); void setInitBondOrder(std::vector & tAtoms, std::vector & tBonds, std::vector & tCBondIdx, std::map > & tDelConn, std::map & tRemainval); void setProBondOrdersOneLoop(int & nDone, std::vector & tAtoms, std::vector & tBonds, std::vector & tCBondIdx, std::map > & remainConns, std::map > & tDelConn, std::map & tRemainVal); void setBondOrderInSys(std::vector & tAtoms, std::vector & tBonds); void setBondOrderInSys2(std::vector & tAtoms, std::vector & tBonds, std::vector & tRings); void modBondOrderViaAnnEXOneConn(std::vector & tAtoms, std::vector & tBonds); void modBondOrderViaAnnEXOneLoop(std::vector & tAtoms, std::vector & tBonds, int & tNOpr); void checkIsoExAtoms(std::vector & tAtoms); void partitionSysToSubGraphs(std::vector & tAtoms); void checkChargeInSubGraphs(std::vector & tAtoms); int sumExElecsInSubGraph(std::vector & tAtoms, std::vector & tGraph); void assignChargesInSubGraph(std::vector & tAtoms, std::vector & tGraph); void assignChargeOneInSubGraph(std::vector & tAtoms, std::vector & tIdxNs, bool & tL); void setEquivAtoms(std::vector & tAtoms, std::vector & tBonds); void modDelocBondsByEquivAtoms(std::vector & tAtoms, std::vector & tBonds, std::vector & tIdxs); void setHMatrix(std::vector & tAtoms, REAL ** tH, std::vector & tSubGraph); void getBondOrderFromOrb(int tNOrbs, REAL ** tEigenVect, std::vector & tAtoms, std::vector & tSubGraph); void MOSolver(std::vector & tAtoms); void BondTrans(std::vector & tBonds); void outBoAndChList(FileName tFName, std::vector & tAtoms, std::vector & tBonds); void checkUpdate(REAL & tPreV, int & tProV); bool lUpdate; std::map > BondOrderFromMO; std::map orgAlphas; std::map orgBetas; std::vector zeroExAtomIdxs; std::vector withExAtomIdxs; std::map oddAtomIdxs; std::map > allSubGraphs; private: int workMode; }; class KekulizeMol { public : // Default constructor KekulizeMol(); // Default destructor ~KekulizeMol(); void execute(std::vector & tAtoms, std::vector & tBonds, std::vector & tRings, std::map & tHMap); void executeBC(std::vector & tAtoms, std::vector & tBonds, std::vector & tRings); void setAllMaps(std::vector & tAtoms, std::vector & tBonds, std::vector & tRings, std::map & tCurVal, std::map & tOutEMap, std::map & tChargeMap, std::map & tElemMap, std::map & tIdAtmMap, std::map > & tAllAtmBondingMap); void setSpecStrs(std::vector & tAtoms, std::vector & tBonds, std::vector & tDoneAtoms, std::vector & tDoneFAtoms, std::vector & tDoneBonds, std::map > & tAllAtmBondingMap); void setSpecStrN(std::vector & tAtoms, std::vector & tBonds, std::vector & tDoneAtoms, std::vector & tDoneFAtoms, std::vector & tDoneBonds, std::map > & tAllAtmBondingMap, std::vector::iterator tAt); void setSpecStrCL(std::vector & tAtoms, std::vector & tBonds, std::vector & tDoneAtoms, std::vector & tDoneFAtoms, std::vector & tDoneBonds, std::map > & tAllAtmBondingMap, std::vector::iterator tAt); void setAtomsPlans(std::vector & tAtoms, std::vector & tBonds, std::vector & tRings, std::map & tAtmPlanMap); void setRingsPlans(std::vector & tAtoms, std::vector & tBonds, std::vector & tRings, std::map & tRingPlanMap); void setValOneAtoms(std::vector & tAtoms, std::vector & tBonds, std::map & tCurVal, std::map & tOutEMap, std::map & tChargeMap, std::map & tElemMap, std::map > & tAllAtmBondingMap, std::vector & tDoneAtoms, std::vector & tDoneBonds); void setOneLinkAtoms(std::vector & tAtoms, std::vector & tBonds, std::map & tCurVal, std::map & tOutEMap, std::map & tChargeMap, std::map & tElemMap, std::map > & tAllAtmBondingMap, std::vector & tDoneAtoms, std::vector & tDoneBonds); void setAllMetalBO(std::vector & tAtoms, std::vector & tBonds, std::map & tCurVal, std::map & tOutEMap, std::map & tChargeMap, std::map & tElemMap, std::map > & tAllAtmBondingMap, std::vector & tDoneAtoms, std::vector & tDoneBonds); void PickSingBonds(std::vector & tAtoms, std::vector & tBonds, std::vector & tRings, std::map & tCurVal, std::map & tOutEMap, std::map & tChargeMap, std::map & tElemMap, std::map > & tAllAtmBondingMap, std::vector & tDoneAtoms, std::vector & tDoneBonds); void setIsolateRings(std::vector & tAtoms, std::vector & tBonds, std::vector & tRings, std::map > & tAllAtmBondingMap, std::map & tCurVal, std::vector & tDoneAtoms, std::vector & tDoneFAtoms, std::vector & tDoneBonds, std::vector & tExcFRings); void setOneIsolateC6Ring(std::vector & tAtoms, std::vector & tBonds, RingDict & tRing, std::map > & tAllAtmBondingMap, std::map & tCurVal, std::vector & tDoneAtoms, std::vector & tDoneFAtoms, std::vector & tDoneBonds); void setOneIsolateC5Ring(std::vector & tAtoms, std::vector & tBonds, RingDict & tRing, std::map > & tAllAtmBondingMap, std::vector & tDoneAtoms, std::vector & tDoneFAtoms, std::vector & tDoneBonds); void setOneIsolateC3N2Ring(std::vector & tAtoms, std::vector & tBonds, RingDict & tRing, std::map > & tAllAtmBondingMap, std::map > & tConnMap, std::vector & tDoneAtoms, std::vector & tDoneFAtoms, std::vector & tDoneBonds); void setOneBondFusedRing(std::vector & tAtoms, std::vector & tBonds, std::vector & tRings, std::map > & tAllAtmBondingMap, std::map & tCurVal, std::vector & tDoneAtoms, std::vector & tDoneFAtoms, std::vector & tDoneBonds, std::vector & tExcRings); void adjustC6ChargedRing(std::vector & tAtoms, std::vector & tBonds, std::vector & tRings, std::map > & tAllAtmBondingMap, std::map & tCurVal, std::vector & tDoneAtoms, std::vector & tDoneFAtoms, std::vector & tDoneBonds); void adjustC6Charged2Ring(int tIdxRing, std::vector & tAtoms, std::vector & tBonds, std::vector & tRings, std::map > & tAllAtmBondingMap, std::map & tCurVal, std::vector & tDoneAtoms, std::vector & tDoneFAtoms, std::vector & tDoneBonds); void FurtheAssignBandC(std::vector & tAtoms, std::vector & tBonds, std::vector & tRings, std::map & tCurVal, std::map & tOutEMap, std::map & tChargeMap, std::map & tElemMap, std::map > & tAllAtmBondingMap, std::vector & tDoneAtoms, std::vector & tDoneFAtoms, std::vector & tDoneBonds); // will replace etResValForAtom and getUnsetBondsForAtom void setResValAndUnsetBondsForAtom( AtomDict & tAtom, std::vector & tBonds, std::map > & tAllAtmBondingMap, std::map & tCurVal, int & tResVal, int & tNumUnSetBonds); int getResValForAtom(AtomDict & tAtom, std::vector & tBonds, std::map > & tAllAtmBondingMap, std::map & tCurVal); int getUnsetBondsForAtom(AtomDict & tAtom, std::vector & tBonds, std::map > & tAllAtmBondingMap); void modifCurVal(std::vector::iterator tAtm, std::map & tCurVal); void checkRingCharge(std::vector & tAtoms, std::vector & tBonds, std::vector & tRings, std::map & tCurVal, std::map & tOutEMap, std::map & tChargeMap, std::map & tElemMap, std::map > & tAllAtmBondingMap, std::vector & tDoneAtoms, std::vector & tDoneBonds); void finalAdjustBandC(std::vector & tAtoms, std::vector & tBonds, std::vector & tRings, std::map & tCurVal, std::map > & tAllAtmBondingMap, std::vector & tDoneAtoms, std::vector & tDoneFAtoms, std::vector & tDoneBonds); void modAromRings(std::vector & tRings); bool checkIfAROMBs(std::vector & tBonds); void setAromBondOrderInSys(std::vector & tAtoms, std::vector & tBonds, std::vector & tRings, std::map & hMap); void modChargeAndBOforSpecialCases( std::vector & tAtoms, std::vector & tBonds, std::vector & tRings); void preStage1(std::vector & tAtoms, std::vector & tBonds, std::vector & tRings, std::map & tDoneAtoms, std::map & doneBonds, std::map & tCurVal, std::map & tChargeMap, std::map & tElemMap, std::map & tIdAtmMap, std::map > & tAllAtmBondingMap, std::map > & tAromAtmMap, std::map & tHMap); void setAllMaps(std::vector & tAtoms, std::vector & tBonds, std::map & tCurVal, std::map & tChargeMap, std::map & tElemMap, std::map & tIdAtmMap, std::map > & tAllAtmBondingMap, std::map > & tAromAtmMap, std::map & tHMap); void preStage2(std::vector & tAtoms, std::vector & tBonds, std::vector & tRings, std::map & tDoneAtoms, std::map & doneBonds, std::map & tCurVal, std::map & tChargeMap, std::map & tElemMap, std::map & tIdAtmMap, std::map > & tAllAtmBondingMap, std::map > & tAromAtmMap, std::map & tHMap); void setRingBonds(std::vector & tAtoms, std::vector & tBonds, std::vector & tRings, std::vector & tAromRingIdxs); void setAtomPiInARing(std::vector & tAtoms, std::vector & tBonds, RingDict & tRing, int tRIdx, std::map > & tAllAtmBondingMap, std::map & tPiInOneAromRing ); int getPiInAAtom(std::vector