/* * File: MolSdfFile.h * Author: flong * * Created on October 31, 2012, 9:18 PM */ #ifndef MOLSDFFILE_H #define MOLSDFFILE_H #ifndef KERNEL_H #include "kernel.h" #endif #ifndef FILE_H #include "file.h" #endif #ifndef ATOM_H #include "atom.h" #endif #ifndef LIBG_ATOMASSEMBLY_H #include "atomAssembly.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 CHAIN_H #include "chain.h" #endif #ifndef CHIRAL_H #include "chiral.h" #endif #ifndef MOLECULE_H #include "molecule.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 PERIODICTABLE_H #include "periodicTable.h" #endif #ifndef CCP4ATOMTYPE_H #include "CCP4AtomType.h" #endif #ifndef CHEMPROPSET_H #include "chemPropSet.h" #endif #ifndef UTILITY_H #include "utility.h" #endif #ifndef TRANSCOORD_H #include "TransCoord.h" #endif #ifndef CRYSTINFO_H #include "crystInfo.h" #endif namespace LIBMOL { class Atom; class AtomDict; class Residue; class ResidueDict; class Chain; class Bond; class BondDict; class Angle; class AngleDict; class Torsion; class TorsionDict; class Chiral; class ChiralDict; class Ring; class RingDict; class Molecule; class CrystInfo; class Link; class PeriodicTable; class CCP4AtomType; class MolSdfFile : public File { public : // Default constructor MolSdfFile(); // Constructor using a file name MolSdfFile(Name tFname, std::ios_base::openmode tOpenMode); MolSdfFile(FileName tFname, std::ios_base::openmode tOpenMode); MolSdfFile(FileName tInSDFName); // destructor ~MolSdfFile(); void setupSystem(); void setupSystemSimp(); void createCurMol(); void deleteCurMol(); void addHAtomToMols(int tIdxMol); void setHAtomCoordsMols(int tIdxMol); REAL checkProtonated(std::vector::iterator tIA, int tMolIdx); // This is a temp function. the other // overloaded function should be a // proper one REAL checkProtonated(std::vector::iterator tIA, int tMolIdx, REAL tTotalVal, REAL tPka, REAL tPh); void setAtomsCCP4Type(int idxMol); void addHAtoms(int tIdxMol, int tIdxAtm, REAL tNumH); void reNameHAtoms(int tIdxMol); /* REAL getTotalBondOrder(int tIdxMol, std::vector::iterator tIA); REAL getBondOrder(int tIdxMol, int tIdx1, int tIdx2); */ int getNumOxyConnect(int tIdxMol, std::vector::iterator iA); void setAtomsBondingAndChiralCenterMol(int tIdxMol); void setChiral(int tIdxMol); ID molName; ID creatProg; bool hasCoords; bool hasConnect; bool hasH; bool containMetal; std::vector allMols; std::ofstream outFile; std::ifstream inFile; private: Molecule * itsCurMol; }; // should be added to separated chemistry part of source codes. /* 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 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); extern REAL getTotalBondOrder(Molecule & tMol, std::vector::iterator tIA); extern REAL getBondOrder(Molecule & tMol, int tIdx1, int tIdx2); 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); */ class SYBLMol2File: public File { public: // Default constructor SYBLMol2File(); // The constructor using a string as the file name SYBLMol2File(Name tFname, std::ios_base::openmode tOpenMode); // The constructor using an char* as the file name SYBLMol2File(FileName tFname, std::ios_base::openmode tOpenMode); // Default destructor ~SYBLMol2File(); void setupSystem(); void setBlock(std::string tL); // Get information from the input file void getAtomInfo(std::string tLine); void getBondInfo(std::string tLine); void getCrysInfo(std::string tLine); void getRingInfo(); void setAtomsCCP4Type(); void addAllHAtoms(); void addHAtoms(int tIdxAtm, REAL tNumH); void reNameHAtoms(); /* REAL getTotalBondOrder(int tIdxMol, std::vector::iterator tIA); REAL getBondOrder(int tIdxMol, int tIdx1, int tIdx2); */ int getNumOxyConnect(std::vector::iterator iA); // void setAtomsBondingAndChiralCenter(); void setChiral(); void iniDict(); bool hasCoords; bool hasConnect; bool hasH; bool containMetal; std::vector atoms; std::map atomSYBYLTypes; std::vector extraHAtoms; std::vector bonds; std::vector chirals; std::vector rings; std::ofstream outFile; std::ifstream inFile; std::map mol2Dict; }; extern void accumInfoMols(ID tMolId, std::vector & tAllAtomsOneMol, std::vector & tAllBondsOneMol, std::vector & tAllAnglesOneMol, std::map > & tAllAtomTypes, std::vector & tAllBondLines, std::vector & tAllAngleLines); } #endif /* MOLSDFFILE_H */