/* * File: AllSystem.h * Author: flong * * Created on July 5, 2012, 10:36 AM */ #ifndef ALLSYSTEM_H #define ALLSYSTEM_H #ifndef KERNEL_H #include "kernel.h" #endif #ifndef FILE_H #include "file.h" #endif #ifndef CIFFILE_H #include "DictCifFile.h" #endif #ifndef PDBFILE_H #include "PDBFile.h" #endif #ifndef MOLSDFFILE_H #include "MolSdfFile.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 CHEMPROPSET_H #include "chemPropSet.h" #endif #ifndef CCP4ATOMTYPE_H #include "CCP4AtomType.h" #endif #ifndef CHEMPROPSET_H #include "chemPropSet.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 MolSdfFile; class SYBLMol2File; class DictCifFile; class DictPDBFile; class CodClassify; class CCP4AtomType; class AllSystem { public: // Default constructor AllSystem(); // Copy constructor AllSystem(const AllSystem & tAllSys); // No need for copy constructor. AllSystem(const std::vector & tAllAtoms, const std::vector & tAllHAtomIdx, const std::vector & tAllBonds, const std::vector & tAllAngles, const std::vector & tAllTorsions, const std::vector & tAllChirals, const std::vector & tAllPlanes, const std::map > & tAllRings, std::string tLibmolTabDir); // Input from files contains mainly atom id and chemical types, // bonds and connections, and perhaps chirals of atoms (e.g, mol/sdf file). // Angle and torsion angles formed from atoms will be re-found here, // so as planarity AllSystem(DictCifFile & tCifObj, std::string tLibmolTabDir); AllSystem(DictCifFile & tCifObj, std::string tLibmolTabDir, const double ubs, const double lbs, const double uas, const double las); AllSystem(Molecule & tMol, std::string tLibmolTabDir); AllSystem(SYBLMol2File & tMol2Obj, std::string tLibmolTabDir); // AllSystem(MolSdfFile & tSdfObj); // get the system after COD classification and search. AllSystem(const CodClassify & tProCodSys, std::string tLibmolTabDir); //Destructor ~AllSystem(); // System builder void AddAtoms(const std::vector & tAllAtoms); void AddAtom(const AtomDict & tAtom); void AddBonds(const std::vector & tAllBonds); void AddBond(const BondDict & tBond); void AddAngles(const std::vector & tAllAngles); void AddAngle(const AngleDict & tAngle); void AddTorsions(const std::vector & tAllTorsions); void AddTorsion(const TorsionDict & tTorsion); void AddMiniTorsions(const std::vector & tMiniTorsions); void AddChirals(const std::vector & tAllChirals); void AddChiral(const ChiralDict & tChiral); void AddPlanes(const std::vector & tAllPlanes); void AddPlane(const PlaneDict & tPlane); void AddRings(const std::map > & tAllRings); void AddRing(const RingDict & tRing); void AddPropComp(const ChemComp & tPropComp); void resetSystem(CodClassify & tCodSys); void resetSystem2(CodClassify & tCodSys); // Further setup angles, torsions, planes and chirals bool isOrgSys(); int atomPosition(ID tID); void setSysProps(); int getNumSpecAtomConnect(int i, ID tChemType); int getNumSpecAtomConnect(std::vector::iterator iA, ID tChemType); int getNumOxyConnect(std::vector::iterator iA); REAL getTotalOrderOneAtom(std::vector::iterator iA); // void setAtomsBondingAndChiralCenter(); void setAtomsCChemType(); void setAtomsCCP4Type(); const bool containMetal(); void setAtomsMetalType(); void setAtomsPartialCharges(); //Hydrogen distances related void setHDists(); void setHydroAtomConnect(); void addMissHydroAtoms(); // Angles related void setAllAngles(); void checkAngConstraints(); void checkSP2Constraints(std::vector tAngIdxs); void checkSP3Constraints(std::vector tAngIdxs); // These functions are torsion angles related void setOneTorsion(std::vector, REAL tValue, int tPeriod); void setTorsionIdxFromOneBond(int tIdx1, int tIdx2); void setPeptideTorsionIdxFromOneBond(int tIdx1, int tIdx2, std::map > tPepTorStdIds, std::vector & tChiTors, std::vector & tHhTors, std::vector & tCstTors); void setTorsionFromOneBond(int tIdx1, int tIdx2); void setTorsionFromOneBond(int tIdx1, int tIdx2, std::string tFlip); void SetOneSP1SP1Bond(int tIdx1, int tIdx2); void SetOneSP1SP2Bond(int tIdx1, int tIdx2); void SetOneSP1SP3Bond(int tIdx1, int tIdx2); void SetOneSP2SP2Bond(int tIdx1, int tIdx2); void SetOneSP2SP3Bond(int tIdx1, int tIdx2); void SetOneSP2SP3Bond(int tIdx1, int tIdx2, std::string tF); void SetOneSP3SP3Bond(int tIdx1, int tIdx2); void SetOneSP3SP3Bond(int tIdx1, int tIdx2, std::string tF); void SetOneSP3SP3Bond4H(int tIdx1, int tIdx2); bool checkSP3SP34H(int tIdx1, int tIdx2); void SetOneSP3OxyColumnBond(int tIdx1, int tIdx2, int tPer, REAL tIniValue); void SetOneSP3OxyColumnBond(int tIdx1, int tIdx2, int tPer, REAL tIniValue, std::string tF); void setAllTorsions(); void setAllTorsions2(); void setPeptideTorsions(); void setAllTorsionsInOneRing(std::vector & tBondIdx, RingDict & tR); void checkSugarRings(); void checkOneRingSugar(std::vector::iterator tRing); std::string getRStr(std::map > & tOCAtms, std::vector::iterator tRing); void setSugarRingTors(); void setSugarRingTorsExtIds( std::vector::iterator tRing); void expandTorsSet(const std::vector & tTorsSet); /* Torsion related void setAllTorsions(); void getTorsionFromBonds(std::vector & tBonds); void setTorsionIdxFromOneBond(int tIdx1, int tIdx2); void setTorsionFromOneBond(int tIdx1, int tIdx2); void SetOneSP2SP2Bond(int tIdx1, int tIdx2); void SetOneSP2SP3Bond(int tIdx1, int tIdx2); void SetOneSP3SP3Bond(int tIdx1, int tIdx2); void SetOneSP3OxyColumnBond(int tIdx1, int tIdx2, int tPer, REAL tIniValue); void setOneTorsion(std::vector, REAL tValue, int tPeriod); */ void ringDetecting(); void checkOnePathSec(AtomDict & curAto, int iMax, std::vector::iterator iOriAto, int SeriNumPreAto, int curLev, std::map & seenAtomIDs, std::map & atomIDsInPath); void outRingSec(AtomDict & tAtom); std::string outRingSecStr(AtomDict &tAtom); // Chiral-related void chiralExch(); // Plane related void detectPlaneGroups(); void groupOrgAtomsToPlanes(); void setSmallestPLs(std::vector & tSPls); void mergeLargePLGroups(std::vector & tSmaPls); bool isInSameRing(PlaneDict & tP1, PlaneDict & tP2); bool furtherM(std::vector &tV1, std::vector &tV2); void doubleCheckM(); // COD database related void setAtomCodClassName(AtomDict &tAtom, AtomDict &tOriAtom, int tLev); void CodAtomClassify(int dLev); // metal-related void setDefaultCoordGeos(); void getMetaLConn(FileName tMCFileName); // COD applications void setupAllTargetValuesFromCOD(ID tOutName, ID tMonoName, ID tLibmolTabDir); void setupAllTargetValuesFromCOD2(ID tOutName, ID tMonoName, ID tLibmolTabDir); // Other applications //void SetupCoords(); //void RingFusion(); //void SetupSpanTree(); void GeoOpt(); // output restraints in cif format void OutputRestraintCif(FileName tCifName); // output atomic coordinates in a file of PDB format // member variables bool hasCoords; bool hasCCP4Type; bool usingInChiral; bool isPeptide; bool withSugar; bool lMdPls; std::string libmolTabDir; double upperBondSig; double lowBondSig; double upperAngleSig; double lowAngleSig; ChemComp propComp; std::vector allAtoms; std::vector allHAtomIdx; //repeated ones std::vector allHydroAtoms; std::vector allBonds; std::vector allAngles; std::map > > allAnglesIdxs; std::vector allTorsions; std::vector miniTorsions; std::vector > allTorsionSets; std::vector allChirals; std::vector allPlanes; std::map > allRings; std::vector allRingsV; std::vector MetalTable; std::map DefaultCoordGeos; std::map > DefaultCoordGeos2; std::vector allDummyAtoms; std::map > > HydrDistTable; std::map > metalConn; private: bool itsContainMetal; int itsCurAngleSeriNum; AngleDict * itsCurAngle; int itsCurTorsionSeriNum; TorsionDict * itsCurTorsion; int itsCurChiralSeriNum; ChiralDict * itsCurChiral; }; void setSubSys(std::vector tDoneSet, std::vector & tAtoms, std::vector & tBonds, std::vector & tAngles, std::vector & tTorsions, std::map > & tRings, std::vector & tPlas, std::vector & tChs, AllSystem & tSubSys); void extern optSubsys(AllSystem & tSubSys); void extern outCodAndCcp4AtomTypes(FileName tFName, std::vector & tAtoms); void extern outProElecDistances(FileName tFName, AllSystem & tMonomer); } #endif /* ALLSYSTEM_H */