/* * File: PDBFile.h * Author: flong * * Created on August 31, 2011, 11:44 AM */ #ifndef PDBFILE_H #define PDBFILE_H #ifndef KERNEL_H #include "kernel.h" #endif #ifndef PDBHEADERSEC_H #include "PDBHeaderSec.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 RESIDUE_H #include "residue.h" #endif #ifndef CHAIN_H #include "chain.h" #endif #ifndef LIBG_MODEL_H #include "libgmodel.h" #endif #ifndef BOND_H #include "bond.h" #endif #ifndef ANGLE_H #include "angle.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 MONOMERLIB_H #include "MonomerLib.h" #endif #ifndef CRYSTINFO_H #include "crystInfo.h" #endif namespace LIBMOL { class Atom; class AtomDict; class Residue; class ModRes; class Chain; class Model; class Helix; class Sheet; class Strand; class Turn; class SSBond; class Link; class CrystInfo; enum PDBRecordType { UnknownType = 0, AnisouType, AtomType, AuthorType, CaveatType, CispepType, CompndType, ConectType, Cryst1Type, DbRefType, DbRef1Type, DbRef2Type, EndType, EndMdlType, ExpDtaType, ForMulType, FtNoteType, HeadType, HelixType, HetType, HetatmType, HetNamType, HetSynType, HydBndType, JrnlType, keywdsType, LinkType, MasterType, ModelType, ModResType, MTRIX1Type, MTRIX2Type, MTRIX3Type, ObslteType, ORIGX1Type, ORIGX2Type, ORIGX3Type, RemarkType, RevDatType, SCALE1Type, SCALE2Type, SCALE3Type, SeqAdvType, SeqResType, SheetType, SigAtmType, SigUijType, SiteType, SltBrgType, SourceType, SprsdeType, SsBondType, TerType, TitleType, TurnType, TVectType }; class PDBFile : public File { public : // default constructor PDBFile(); // copy constructor PDBFile(Name tFname, std::ios_base::openmode tOpenMode); PDBFile(FileName tFname, std::ios_base::openmode tOpenMode); // destructor virtual ~PDBFile(); std::vector PDBRecordHeader; void setPDBRecordHeader(); // structure that stores the records in the coordinate section. // Maybe using class Atom directly is simple enough struct PDBAtom { Name recordName; SeriNumber seriNum; std::string name; std::string altLoc; // alternate location indicator std::string resName; // amino acid abbreviation for an atom ID atomID; // atom role name. See PDB convention ID chainID; // the chain ID for an atom SeriNumber segNum; // segment serial number std::string insCode; // Code for insertion of residues std::string elementType; // the element type of an atom std::string itsSegID; // segment identifier }; // Extract information from a PDB file // Read line by line from a PDB file and // and get all information needed from it void setupSystem(); // Get a record type from the first 6 letters in a PDB line int getRecordType(ALine tLine); /* The following member functions get different information from different type of record-lines */ bool extractTitleInfo(ALine tLine); // Primary Structure Section bool extractSEQRESInfo(ALine tLine); // get chains bool extractMODRESInfo(ALine tLine); // Secondary Structure Section bool extractHelixInfo(ALine tLine); bool extractSheetInfo(ALine tLine); // Connectivity Annotation Section bool extractSSBondInfo(ALine tLine); bool extractLinkInfo(ALine tLine); // Crystallographic and Coordinate Transformation Section bool extractCryst1Info(ALine tLine); bool extractOrigXNInfo(ALine tLine); bool extractScaleNInfo(ALine tLine); bool extractMatrixNInfo(ALine tLine); // Coordinate Section void initOneModel(); void initOneModel(ALine tLine); bool extractAtomInfo(ALine tLine); bool extractAtomInfo(Atom & tAtom, Residue & tResidue, Chain & tChain, ALine tLine); bool extractAnisouInfo(ALine tLine); bool extractTerInfo(ALine tLine); bool extractHetatmInfo(ALine tLine); bool extractEndMdlInfo(ALine tLine); bool extractConnectInfo(ALine tLine); bool extractBookeepInfo(ALine tLine); // access some general information ID getPDBID() const; Date getDepositedDate() const; std::string getDesciption(); ObsoleteInfo getObsoleteInfo(); std::vector getModelList(); void setModelList(); void setResidueGroupType(FileName tF); // output a structure to a PDB file void writeTitleSection(); void writePrimaryStructureSection(); void writeHeterogenSection(); void writeSecondaryStructureSection(); void writeConnectivityAnnotationSection(); void writeMiscellaneousFeaturesSection(); void writeCrystallographicSection(); void writeCoordinateSection(); void writeConnectivitySection(); void writeBookKeepingSection(); // related bonds, bond angle, torsion angles, residues, chain. models std::vector allModels; std::vector allChains; std::vector allModRes; std::vector allAtomList; std::vector allHetAtmList; std::vector allSSBonds; std::vector allLinks; std::vector allHelices; std::vector allSheets; HeadSec allHeaderInfo; std::ofstream outFile; std::ifstream inFile; private : PDBRecordType itsTempRecordType; Model * itsCurrentModel; Atom * itsCurrentAtom; bool itsCurrentAltLoc; Atom * itsCurrentHetAtm; Residue * itsCurrentResidue; ModRes * itsCurrentModRes; Chain * itsCurrentChain; Helix * itsCurrentHelix; Sheet * itsCurrentSheet; SSBond * itsCurrentSSBond; CrystInfo * itsCrystInfo; }; // A simple version of PDB processor, extract only atom information // in particular, atomic coordinates class DictPDBFile { public : // default constructor DictPDBFile(); // copy constructor DictPDBFile(Name tFname, std::ios_base::openmode tOpenMode); inline ~DictPDBFile() { } // Extract information from a PDB file // Read line by line from a PDB file and // and get all information needed from it void setupSystem(); // atoms only std::map > allHetAtmList; std::ifstream inFile; }; void extern outPDB(FileName tFName, ID tMonoRootName, std::vector& tAtoms, int tMode); } #endif /* PDBFILE_H */