/* * File: CIFFile.h * Author: flong * * last updated on September 27, 2011, 12:51 AM */ #ifndef CIFFILE_H #define CIFFILE_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 LIBG_MODEL_H #include "libgmodel.h" #endif #ifndef SSBOND_H #include "ssbond.h" #endif #ifndef LIBG_LINK_H #include "libglink.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 ATOMSTREE_H #include "atomsTree.h" #endif #ifndef CRYSTINFO_H #include "crystInfo.h" #endif #ifndef PDBFILE_H #include "PDBFile.h" #endif /* #ifndef __MMDB_Manager__ #include "mmdb_manager.h" #endif #ifndef __MMDB_MMCIF__ #include #endif #ifndef __MMDB_IO__ #include #endif */ #ifndef CHEMPROPSET_H #include "chemPropSet.h" #endif #ifndef MOLECULE_H #include "molecule.h" #endif namespace LIBMOL { class Atom; class AtomDict; class Residue; class Chain; class Model; class Bond; class BondDict; class Angle; class AngleDict; class Torsion; class TorsionDict; class Chiral; class Ring; class RinDict; class CrystInfo; class Link; class PeriodicTable; class CCP4AtomType; class Molecule; struct DictCifHead { Name libName; ID monType; ID group; ID libVersion; Date libUpdate; DictCifHead():libName("?"),monType(""),group(""),libVersion("?"),libUpdate("?"){} }; /* struct ChemComp { ID id; Name code; // three-letter code Name name; Name group; // non-polymer, peptide or DNA etc. int numAtoms; int numH; ID level; ChemComp():id(NullString), code(NullString), name(NullString), group(NullString), numAtoms(0), numH(0), level(NullString) {} }; */ class GenCifFile : public File { public : // default constructor GenCifFile(); // copy constructor GenCifFile(Name tFname, std::ios_base::openmode tOpenMode); GenCifFile(Name tFname, std::string tParaFName, std::ios_base::openmode tOpenMode); GenCifFile(FileName tFname, std::ios_base::openmode tOpenMode); //GenCifFile(FileName tFname, // mmdb::io:: tOpenMode); // destructor virtual ~GenCifFile(); void setupSystem(); void setupSystem2(); void setupSystemCSD(); // special version CSD. disable most of // experiment parameters because they are // absent from the derived CSD cif files. void checkRFact(std::vector & tLines); void checkPowder(std::vector & tLines); void checkNeutronD(std::vector & tLines); void checkCalcAtoms(); bool checkOverAll(int tWorkMode); void setAllCrits(std::vector & tAllLines); void getPropsToMaps(std::vector >::iterator tOneBlockLines, std::map & tRowProps, std::map > > & tColProps, int & tIdx); void selectPropsToMaps(std::map & tRowProps, std::map > > & tColProps); void initAllCifKeys(); void getCifCrystInfo(std::vector >::iterator iBs); void getCifCrystInfo(std::map & tRowProps, std::map > > & tColProps); void getCifSymOps(std::vector >::iterator iBs); void getCifSymOps(std::map > & tOnePropGroup); void getCifAtomInfo(std::vector >::iterator iBs); void getCifAtomInfo2(std::vector >::iterator iBs); void getCifAtomInfo(std::map > & tOnePropGroup); void getAtomInfoFromLine(std::vector & tStrs, int tP1, int tP2, int tP3, int tP4, int tP5, int tPOcp, int tPCalc, int tPB); void getCifAtomOxiInfo(std::map > & tOnePropGroup); void getAtomOxiInfoFromLine(std::vector & tStrs, int tPosType, int tPosOxi); void setFlags(std::map & tL, std::string tS); // get information from different blocks in the dictionary cif file void getHeadInfo(std::vector tF); void getChemInfo(std::string tF); //a different argument // because symbol ' void getDataDescription(std::vector tF); // Atoms related void getAtomInfo(std::vector tF); void checkAtomElementID(); void checkNonHAtomOccp(); void setAtomsCCP4Type(); int atomPosition(ID tID); void setAtomsPartialCharges(); void getHAtomIdxs(); // Bonds related void getBondAndConnect(std::vector tF); void setHydroAtomConnect(); void setBondOrder(); void setSingleOrder(); void setBondOrderByCoords(); void setBondOrderByBondList(); void setBondOrderByChem(); void setBondOrderByType(); void addAtomSeriNumToBond(); void getAngleInfo(std::vector tF); // get angles based on bonds and set their initial values void setAllAngles(); void setAtomsCChemType(); void setAtomsMetalType(); void setAtomOxiType(); void addMissHydroAtoms(); void setAtomsVDWRadius(); short transOrder(std::string tO); void outSystem(); void outAtomBloc(); void outBondBloc(); void outAtomElems(Name tUserOutRoot); void outCrystInfo(Name tUserOutRoot); /* The core member functions are that 1. From a group of atoms, build a connection (or neighbor) list for * each atom. (neighbAtoms in Atom class fulfill partly this purpose * because COD-class codes include ring symbols, which need to be * sorted out) * 2. Based on the connection lists, setup a COD-class code for each * atom. * 3. Search COD using corresponding COD-class codes of atoms to find * new bond values. * 4. The same applies for bond-angles, torsion-angles, chiral volumes * 5. Output new CIF and restraint files */ void ringDetecting(); void checkOnePathSec(std::vector & seenAtoms, std::map & seenIDs, AtomDict & curAto, int iMax, std::vector::iterator iAto); //a recursive function void checkOnePathSec(AtomDict & curAto, int iMax, std::vector::iterator iOriAto, int SeriNumPreAto, int curLev, std::map & seenAtomIDs, std::map & atomIDsInPath); void setAtomCodClassName(AtomDict &tAtom, AtomDict &tOriAtom, int tLev); void outRingSec(AtomDict & tAtom); std::string outRingSecStr(AtomDict &tAtom); // 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 CodAtomClassify(int dLev); void getAnglesFromPDB(ID tFName); void outRestraintCif(FileName tFName, ID tMonoRootName); void outPDB(FileName tFName, ID tMonoRootName); void reOrdErrMsg(); int curBlockLine; bool lErr; std::vector allCryst; std::map > allCifKeys; std::map existCifKeys; std::map > hasProps; DictCifHead dictCifHead; ChemComp propComp; std::map dataDesc; std::vector allAtoms; std::vector allHAtomIdx; std::vector allBonds; std::vector allAngles; std::map > > allAnglesIdxs; std::map DefaultCoordGeos; std::map > DefaultCoordGeos2; std::vector allTorsions; std::vector allChirals; std::vector allPlanes; std::map > allRings; std::vector allRingsV; // std::vector allRings; std::vector allHydroAtoms; std::map typeChargeMap; std::vector MetalTable; std::vector errMsg; std::ofstream outFile; std::ifstream inFile; bool hasCoords; bool hasH; bool hasMetal; bool symmOprOK; bool notPowder; bool notNeuD; bool resolOK; bool RFactorOK; bool colidOK; // check before molecule generated bool hasOcpLab; bool hasHeavyCalcAtoms; bool nonCheck; bool checkR; bool checkResol; REAL allR; REAL gtR; REAL obsR; REAL allWR; REAL gtWR; REAL refWR; REAL resol; REAL RTHRESHOLD_U; // replacement RTHRESHOLD // defined in constants.h REAL RESOLTHRESHOLD_U; // replacement RESOLTHRESHOLD // defined in constants.h private: int itsCurAtomSeriNum; AtomDict * itsCurAtom; std::string itsCurBlock; std::map > itsDataBlockMap; CrystInfo * itsCurCryst; }; class DictCifFile : public File { public : // default constructor DictCifFile(); // copy constructor DictCifFile(Name tFname, std::ios_base::openmode tOpenMode); DictCifFile(FileName tFname, std::ios_base::openmode tOpenMode); // The following constructor is based on mmdb lib //DictCifFile(FileName tFname); // For transfering information from PDB to CIF DictCifFile(FileName tCifName, FileName tPdbName); // destructor virtual ~DictCifFile(); void setupSystem(); void setupSystem3Secs(std::ifstream & tInCif); void initCifKeys(); void checkBloc(std::map & tL, std::vector tF); void setFlags(std::map & tL, std::string tS); // get information from different blocks in the dictionary cif file void getHeadInfo(std::vector tF); void getChemInfo(std::string tF); //a different argument // because symbol ' void getDataDescription(std::vector tF); // Atoms related void getAtomInfo(std::vector tF); void setAtomsCCP4Type(); int atomPosition(ID tID); void setAtomsPartialCharges(); // Bonds related void getBondAndConnect(std::vector tF); void setHydroAtomConnect(); void setBondOrder(); void setSingleOrder(); void setBondOrderByCoords(); void setBondOrderByBondList(); void setBondOrderByChem(); void setBondOrderByType(); void addAtomSeriNumToBond(); void getAngleInfo(std::vector tF); // get angles based on bonds and set their initial values void setAllAngles(); // This function read torsion angles from a cif file(not used) void setOneTorsion(std::vector, REAL tValue, int tPeriod); void setTorsionIdxFromOneBond(int tIdx1, int tIdx2); void setTorsionFromOneBond(int tIdx1, int tIdx2); void setTorsionFromOneBond(int tIdx1, int tIdx2, std::string tFlip); 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 setAllTorsionsInOneRing(std::vector & tBondIdx, RingDict & tR); // This function get torsion angles from a set of bonds // not using the following one void getTorsionFromBonds(std::vector & tBonds); // Chiral-related void getChiralInfo(std::vector tF); // void setAtomsBondingAndChiralCenter(); // using standalone one void setAllChirals(); void setDefaultCoordGeos(); // user's definition of metal coordination geometries void getMetalCNGeo(std::vector tF); void setAtomsCChemType(); void setAtomsMetalType(); void addMissHydroAtoms(); void setAtomsVDWRadius(); short transOrder(std::string tO); void outSystem(); void outAtomBloc(); void outBondBloc(); void transCoordsPdbToCif(DictPDBFile & tPdbObj); /* The core member functions are that 1. From a group of atoms, build a connection (or neighbor) list for * each atom. (neighbAtoms in Atom class fulfill partly this purpose * because COD-class codes include ring symbols, which need to be * sorted out) * 2. Based on the connection lists, setup a COD-class code for each * atom. * 3. Search COD using corresponding COD-class codes of atoms to find * new bond values. * 4. The same applies for bond-angles, torsion-angles, chiral volumes * 5. Output new CIF and restraint files */ void ringDetecting(); void checkOnePathSec(std::vector & seenAtoms, std::map & seenIDs, AtomDict & curAto, int iMax, std::vector::iterator iAto); //a recursive function void checkOnePathSec(AtomDict & curAto, int iMax, std::vector::iterator iOriAto, int SeriNumPreAto, int curLev, std::map & seenAtomIDs, std::map & atomIDsInPath); void setAtomCodClassName(AtomDict &tAtom, AtomDict &tOriAtom, int tLev); void outRingSec(AtomDict & tAtom); std::string outRingSecStr(AtomDict &tAtom); // 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 CodAtomClassify(int dLev); void getAnglesFromPDB(ID tFName); void outRestraintCif(FileName tFName, ID tMonoRootName); void outPDB(FileName tFName, ID tMonoRootName); int curBlockLine; bool isPeptide; bool isDRna; std::map > allCifKeys; std::map > hasProps; DictCifHead dictCifHead; ChemComp propComp; std::map dataDesc; std::vector allAtoms; std::vector allHAtomIdx; std::vector allBonds; std::vector allAngles; std::map > > allAnglesIdxs; std::map DefaultCoordGeos; std::map > DefaultCoordGeos2; std::vector allTorsions; std::vector allChirals; std::vector allPlanes; std::map > allRings; std::vector allRingsV; // std::vector allRings; std::vector allHydroAtoms; std::vector MetalTable; std::ofstream outFile; std::ifstream inFile; // For File transfer std::map > allUnchangedBlocks; bool hasConnect; bool hasCoords; bool hasH; bool hasCCP4Type; private: int itsCurAtomSeriNum; AtomDict * itsCurAtom; int itsCurBondSeriNum; BondDict * itsCurBond; int itsCurAngleSeriNum; AngleDict * itsCurAngle; int itsCurTorsionSeriNum; TorsionDict * itsCurTorsion; int itsCurChiralSeriNum; ChiralDict * itsCurChiral; }; extern void outMMCif(FileName tFName, ID tMonoRootName, ChemComp & tPropComp, std::vector& tAtoms, // std::vector & tHydroAtoms, std::vector& tBonds, std::vector& tAngs, std::vector& tTorsions, std::vector & tRings, std::vector& tPlas, std::vector& tChs, const double tUBS, const double tLBS, const double tUAS, const double tLAS, std::map > > & tHDistMap); extern void outMMCif2(FileName tFName, ID tMonoRootName, ChemComp & tPropComp, std::vector& tAtoms, // std::vector & tHydroAtoms, std::vector& tBonds, std::vector& tAngs, std::vector& tTorsions, std::vector & tRings, std::vector& tPlas, std::vector& tChs); extern void outMMCif3(FileName tFName, ID tMonoRootName, std::vector& tAtoms, std::vector& tBonds, std::vector & tRings); extern void outMMCifFromOneMol(FileName tFName, ID tMonoRootName, Molecule & tMol); extern int getHAtomNum(std::vector& tAtoms); extern void outHAtomIds(FileName tFName); extern void outMMCif3Secs(FileName tFName, ID tMonoRootName, std::vector & tAtoms, std::map > & tUnChangedEntries); extern void outAtomTypesAndConnections(FileName tFName, ID tMonoRootName, std::vector& tAtoms, std::vector& tBonds, std::vector & tRings); extern void outMetalAtomInfo(FileName tFName, GenCifFile & tCifObj); extern void outSelectedAtomInfo(FileName tFName, std::vector & tIds); } #endif /* CIFFILE_H */