# pdbFile

- Structure
  pdbFile
    This structure is used to treat a pdb File.
    pdbFile pdb;
    pdb.PDB->ResidueSequenceNumber
    pdb.PDB->Coord.x
    pdb.PDB->Coord.y
- File
  - pdbFileRead (fpt, &pdb)
  - pdbFileWrite(fpt, &pdb)
- Check
  - pdbFileIsAtom
      if(pdbFileIsAtom(&pdb)) { }
  - pdbFileIsCA
      if(pdbFileIsCA(&pdb)) { }
  - pdbFileIsEndLine
      if(pdbFileIsEndLine(&pdb)) { }
  - pdbRecordisNearby : Adjacent Residue or not
      if(pdbRecordisNearby(&pdbRecord, &pdbRecord)) { }
  - pdbFileIsHelix
      if(pdbFileIsHelix(&pdb)) { }
  - pdbFileIsSheet
      if(pdbFileIsSheet(&pdb)) { }
  - pdbFileIsTurn
      if(pdbFileIsTurn(&pdb)) { }
  - pdbFileIsNegative
      if(pdbFileIsNegative(&pdb)) { }
  - pdbFileIsPositive
      if(pdbFileIsPositive(&pdb)) { }
  - pdbFileIsCharge
      if(pdbFileIsCharge(&pdb)) { }
- Check2
  - lpdbDistanceCheck : mode 0: Near 1: Far ; compare the distance between pdb->current with p v.s. distance
      if(lpdbDistanceCheck(&pdb, p, distance, mode)) {
  - lpdbDistanceNear
      if(lpdbDistanceNear(&pdb, p, distance, mode)) {
  - lpdbDistanceFar
      if(lpdbDistanceFar(&pdb, p, distance, mode)) {
- Get and Set

  Get

  - pdbFileCoordGet(&pdb, &x, &y, &z)
  - unsigned char pdbFileChainIdentifierGet(&pdb)
  - pdbFileResidueSequenceNumberGet(&pdb)
  - char* pdbFileResidueNameGet(&pdb,mode)

    Set

  - pdbFileCoordSet(&pdb, x, y, z)
  - pdbFileChainIdentifierSetAll(&pdb, c)
  - pdbFileChainIdentifierSet(&pdb, c)
  - pdbFileTemperatureFactorSet(&pdb, (double)temp)
- Seeking
  - pdbFileTop(&pdb)
  - pdbFileNext(&pdb)
  - pdbFileNextAtom(&pdb)
  - pdbFileNextCA(&pdb)
  - pdbFileNextProtein(&pdb)
  - pdbFileEnd(&pdb)
- New, append etc.
  - pdbFileNew(&pdb)
  - pdbFileAppend(&pdb)
  - pdbFileFree(&pdb)
- Print
  - pdbFilePrint(fpt, &pdb);
  - pdbFileRecordPrint(fpt, &pdb);
  - pdbFileRecordTablePrint(fpt, &pdb);
- Copy
  - pdbFileOneRecordCopy(&pdb, &src)
  - pdbFileCAOnlyCopyAll(&pdb, &src)
  - pdbFileCopyAll(&pdb, &src)
  - pdbFileOneProteinCopy(&pdb, &src, num)
  - pdbFileCAOnlyCopyAll(&pdb, &src)
- Translation and rotation
  - pdbTrans
  - pdbMatrixFileRead
  - pdbMatrixFileWrite
  - pdbMatrixFileFormat
- Transform
  - lpdb2mrc3d
      lpdb2mrc3d(&mrc, &pdb, &linfo, mode)

## Information from source codes

    ../src/lpdb2mrc2d.c:

    ../src/lpdb2mrc3d.c:

    ../src/lpdbCoord.c:

    ../src/lpdbCoordInfo.c:

    ../src/lpdbSelectedAtom.c:

    ../src/lpdbSurface.c:

    ../src/pdbFileRead.c:

    ../src/pdbFileWrite.c:

    ../src/pdbGet.c:

    ../src/pdbInfoGet.c:

    ../src/pdbRotation.c:

    ../src/pdbSecondaryStructure.c:

    ../src/pdbSet.c:

    ../src/pdbTrans.c:

    ../src/pdbUtil.c:

## pdbFile.h

    #ifndef PDB_FILE_H
    #define PDB_FILE_H
    /*
    # %M% %Y% %I%
    # The latest update : %G% at %U%
    #
    #%Z% pdbFile.h ver %I%
    #%Z% Created by tacyas
    #%Z%
    #%Z% Usage : pdbFile.h
    #%Z% Attention
    #%Z%
    */
    #include
    #include "Matrix3D.h"
    #include "mrcImage.h"

    /* constant begin */
    #define PDB_FILE_RECORD_FULL_LENGTH (80)
    #define PDB_FILE_RECORD_START       (0)
    #define PDB_FILE_RECORD_LENGTH      (6)
    #define PDB_FILE_ATOM_NUMBER_START  (6)
    #define PDB_FILE_ATOM_NUMBER_LENGTH (5)
    #define PDB_FILE_ATOM_NAME_START    (12)
    #define PDB_FILE_ATOM_NAME_LENGTH   (4)
    #define PDB_FILE_LOCATION_START     (16)
    #define PDB_FILE_LOCATION_LENGTH    (1)
    #define PDB_FILE_RESIDUE_START      (17)
    #define PDB_FILE_RESIDUE_LENGTH     (3)
    #define PDB_FILE_CHAIN_IDENT_START  (21)
    #define PDB_FILE_CHAIN_IDENT_LENGTH (1)
    #define PDB_FILE_RESNUM_START       (22)
    #define PDB_FILE_RESNUM_LENGTH      (4)
    #define PDB_FILE_INSERTION_START    (26)
    #define PDB_FILE_INSERTION_LENGTH   (1)
    #define PDB_FILE_X_START            (30)
    #define PDB_FILE_X_LENGTH           (8)
    #define PDB_FILE_Y_START            (38)
    #define PDB_FILE_Y_LENGTH           (8)
    #define PDB_FILE_Z_START            (46)
    #define PDB_FILE_Z_LENGTH           (8)
    #define PDB_FILE_OCCUPANCY_START    (54)
    #define PDB_FILE_OCCUPANCY_LENGTH   (6)
    #define PDB_FILE_TEMPERATURE_START  (60)
    #define PDB_FILE_TEMPERATURE_LENGTH (6)
    #define PDB_FILE_FOOT_START         (67)
    #define PDB_FILE_FOOT_LENGTH        (3)
    #define PDB_FILE_FOOTNOTE_START     (70)
    #define PDB_FILE_FOOTNOTE_LENGTH    (10)
    #define MAX_RESIDUE_NUMBER          (20)
    #define RESIDUE_ONECHAR_MODE        (1)
    #define RESIDUE_THREECHAR_MODE      (3)
    #define pdbRecordAtom       ("ATOM  ")
    #define pdbRecordHeteroAtom ("HETATM")
    #define pdbRecordHelix      ("HELIX ")
    #define pdbRecordSheet      ("SHEET ")
    #define pdbRecordTurn       ("TURN  ")
    #define pdbRecordEnd        ("END   ")

    /* constant end */

    /* struct begin */
    typedef char  pdbFileParaTypeCharacter;
    typedef long  pdbFileParaTypeInteger;
    typedef float pdbFileParaTypeReal;

    typedef struct residueName {
      char residueName3[4];
      char residueName1[2];
    } residueName;

    typedef struct pdbCoord {
      pdbFileParaTypeReal x;
      pdbFileParaTypeReal y;
      pdbFileParaTypeReal z;
    } pdbCoord;

    typedef enum pdbSecondaryStructureHelixClass {
    	HelixClassRightHandedAlpha = 1,
    	HelixClassRightHandedOmega = 2,
    	HelixClassRightHandedPi    = 3,
    	HelixClassRightHandedGammda= 4,
    	HelixClassRightHanded310   = 5,
    	HelixClassLeftHandedAlpha  = 6,
    	HelixClassLeftHandedOmega  = 7,
    	HelixClassLeftHandedGammda = 9,
    	HelixClassPolyProline      = 10,
    } pdbSecondaryStructureHelixClass;

    typedef struct pdbSecondaryStructureHelix {
    	int  serNum;     	/* Serial Number */
    	char* helixID;   	/* HelixID : Three alpahnumeric characters */
    /* informtion for the initial residue */
    	char* initResName;/* Name of the initial residue : Three alpahnumeric characters */
    	char initChainID;  	/* Chain identifier */
    	int  initSeqNum;    /* Sequence number of the initial residue */
    	char initICode;
    /* informtion for the terminal residue */
    	char* endResName;/* Name of the initial residue : Three alpahnumeric characters */
    	char endChainID;  	/* Chain identifier */
    	int  endSeqNum;    /* Sequence number of the initial residue */
    	char endICode;

    	pdbSecondaryStructureHelixClass helixClass;
    	char* comment;
    	int  length;
    } pdbSecondaryStructureHelix;

    typedef struct pdbSecondaryStructureSheet {
    	int  strand; 		/* Strand number which starts 1 for eache strand wihtin a sheet and increases by one */
    	char* sheetID;    /* Sheet ID */
    	int  numStrands;    /* Number of strands in sheet */

    /* initial residue */
    	char* initResName;/* Name of the initial residue : Three alpahnumeric characters */
    	char initChainID;  	/* Chain identifier */
    	int  initSeqNum;    /* Sequence number of the initial residue */
    	char initICode;

    /* informtion for the terminal residue */
    	char* endResName;/* Name of the initial residue : Three alpahnumeric characters */
    	char endChainID;  	/* Chain identifier */
    	int  endSeqNum;    /* Sequence number of the initial residue */
    	char endICode;

    	int sense;  /* 0: first strand, 1: parallel, -1: anti-paralle */

    	char* curAtom; /* Registration. Atom name in current strand */
    	char* curResName; /* Registration. Residue name in current strand */
    	char curChainID; /* Registration. Chain ID in current strand */
    	int  curResSeq;  /* Registration. Res sequence in current strand */
    	char curICode;  /* Registration. Insertion code in current strand */

    	char* prevAtom; /* Registration. Atom name in current strand */
    	char* prevResName; /* Registration. Residue name in current strand */
    	char prevChainID; /* Registration. Chain ID in current strand */
    	int prevResSeq;  /* Registration. Res sequence in current strand */
    	char prevICode;  /* Registration. Insertion code in current strand */
    }pdbSecondaryStructureSheet;

    typedef struct pdbSecondaryStructureTurn {
    	int  serNum;     	/* Serial Number */
    	char* turnID;   	/* Turn ID : Three alpahnumeric characters */
    /* informtion for the initial residue */
    	char* initResName;/* Name of the initial residue : Three alpahnumeric characters */
    	char initChainID;  	/* Chain identifier */
    	int  initSeqNum;    /* Sequence number of the initial residue */
    	char initICode;
    /* informtion for the terminal residue */
    	char* endResName;/* Name of the initial residue : Three alpahnumeric characters */
    	char endChainID;  	/* Chain identifier */
    	int  endSeqNum;    /* Sequence number of the initial residue */
    	char endICode;

    	char* comment;
    }pdbSecondaryStructureTurn;

    typedef struct pdbSecondaryStructureNo {
    	int   serNum;     	/* Serial Number */
    	char* noID;   	    /* Turn ID : Three alpahnumeric characters */
    /* informtion for the initial residue */
    	char* initResName;/* Name of the initial residue : Three alpahnumeric characters */
    	char initChainID;  	/* Chain identifier */
    	int  initSeqNum;    /* Sequence number of the initial residue */
    	char initICode;
    /* informtion for the terminal residue */
    	char* endResName;/* Name of the initial residue : Three alpahnumeric characters */
    	char endChainID;  	/* Chain identifier */
    	int  endSeqNum;    /* Sequence number of the initial residue */
    	char endICode;

    	char* comment;
    }pdbSecondaryStructureNo;

    typedef enum pdbFileSecondaryStructureMode {
    	pdbFileSecondaryStructureModeNo    = 0,
    	pdbFileSecondaryStructureModeHelix = 1,
    	pdbFileSecondaryStructureModeSheet = 2,
    	pdbFileSecondaryStructureModeTurn  = 3
    } pdbFileSecondaryStructureMode;

    typedef struct pdbFileSecondaryStructureRecord pdbFileSecondaryStructureRecord;
    struct pdbFileSecondaryStructureRecord {
    	pdbFileSecondaryStructureMode mode;
    	pdbSecondaryStructureHelix*   helix;
    	pdbSecondaryStructureSheet*   sheet;
    	pdbSecondaryStructureTurn*    turn;
    	pdbSecondaryStructureNo*      no;

    	pdbFileSecondaryStructureRecord* prev;
    	pdbFileSecondaryStructureRecord* next;
    };

    typedef struct pdbFileSecondaryStructure {
    	int nSecondaryStructure;
    	pdbFileSecondaryStructureRecord* top;
    	pdbFileSecondaryStructureRecord* SecondaryStructure;
    } pdbFileSecondaryStructure;

    typedef struct pdbRecord pdbRecord;

    struct pdbRecord {
      pdbFileParaTypeCharacter FullRecord[PDB_FILE_RECORD_FULL_LENGTH+1];

      pdbFileParaTypeCharacter Record[PDB_FILE_RECORD_LENGTH+1];

    /* ATOM and HETATM Record */
      pdbFileParaTypeInteger   AtomSerialNumber;
      pdbFileParaTypeCharacter AtomName[PDB_FILE_ATOM_NAME_LENGTH+1];
      pdbFileParaTypeCharacter LocationIndicator;
      pdbFileParaTypeCharacter ResidueName[PDB_FILE_RESIDUE_LENGTH+1];
      pdbFileParaTypeCharacter ChainIdentifier;
      pdbFileParaTypeInteger   ResidueSequenceNumber;
      pdbFileParaTypeCharacter InsertionCode;
      pdbCoord                 Coord;
      pdbFileParaTypeReal      Occupancy;
      pdbFileParaTypeReal      TemperatureFactor;
      pdbFileParaTypeInteger   FootnoteNumber;
      pdbFileParaTypeCharacter Footnote[PDB_FILE_FOOTNOTE_LENGTH+1];

      pdbRecord*               prev;
      pdbRecord*               next;

    };

    typedef struct pdbFile {
      pdbRecord* top;
      pdbRecord* PDB;
      pdbFileParaTypeInteger nAtom;
      pdbFileSecondaryStructure second;
    } pdbFile;
    /* struct end */

    #ifdef __cplusplus
    extern "C" {
    #endif

    /* prototype begin */
    /* in pdbFileRead.c */
    extern void pdbFileRead(FILE* fpt, pdbFile* pdb);
    /* in pdbFileWrite.c */
    extern void pdbFileWrite(FILE* fpt, pdbFile* pdb);
    extern void pdbFileWriteCoord(FILE* fpt, pdbFile* pdb);
    /*werewolf presents*/
    extern void pdbFileTableWrite(FILE* fpt, pdbFile* pdb);
    extern void pdbFileWriteSecondaryStructure(FILE* fpt, pdbFileSecondaryStructure* second);

    extern void pdbMatrixFileFormat(FILE* fpt);
    extern void pdbMatrixFileRead(FILE* fpt, Matrix3D Matrix);
    extern void pdbMatrixFileWrite(FILE* fpt, Matrix3D Matrix);

    extern void pdbTrans(pdbFile* pdb, Matrix3D Matrix);
    //extern void pdbTransCuda(pdbFile* pdb, Matrix3D Matrix);
    extern void pdbTransCuda(float* hv, int n, Matrix3D Matrix);

    extern void pdbFileResidueSequenceNumberIncrementAll(pdbFile* pdb, int n);
    extern void pdbFileResidueSequenceNumberIncrement(pdbFile* pdb, int n);

    extern void pdbFileChainIdentifierSetAll(pdbFile* pdb, unsigned char c);
    extern void pdbFileChainIdentifierSet(pdbFile* pdb, unsigned char c);
    extern unsigned char pdbFileChainIdentifierGet(pdbFile* pdb);

    extern pdbFileParaTypeReal pdbFileTemperatureFactorGet(pdbFile* pdb);
    extern void pdbFileTemperatureFactorSet(pdbFile* pdb, double temp);

    extern pdbFileParaTypeReal pdbFileOccupancyGet(pdbFile* pdb);
    extern void pdbFileOccupancySet(pdbFile* pdb, double temp);

    extern long pdbFileCoordSet(pdbFile* pdb, pdbFileParaTypeReal x, pdbFileParaTypeReal y, pdbFileParaTypeReal z);

    extern long pdbFileCoordGet(pdbFile* pdb, pdbFileParaTypeReal* x, pdbFileParaTypeReal* y, pdbFileParaTypeReal* z);
    extern long pdbFileResidueSequenceNumberGet(pdbFile* pdb);
    extern char* pdbFileResidueNameGet(pdbFile* pdb,int mode);

    extern pdbRecord* pdbFileTop(pdbFile* pdb);
    extern pdbRecord* pdbFileTopPointer(pdbFile* pdb);
    extern pdbRecord* pdbFileNext(pdbFile* pdb);
    extern pdbRecord* pdbFileNextAtom(pdbFile* pdb);
    extern pdbRecord* pdbFileNextCA(pdbFile* pdb);
    extern pdbRecord* pdbFilePrev(pdbFile* pdb);
    extern pdbRecord* pdbFilePrevAtom(pdbFile* pdb);
    extern pdbRecord* pdbFilePrevCA(pdbFile* pdb);
    extern long pdbFileEnd(pdbFile* pdb);
    extern long pdbFileGoToEnd(pdbFile* pdb);
    extern long pdbFileIsEndLine(pdbFile* pdb);
    extern long pdbFileIsAtom(pdbFile* pdb);
    extern long pdbRecordIsNearby(pdbRecord record1,pdbRecord record2);
    extern long pdbFileIsCA(pdbFile* pdb);
    extern long pdbFileIsNegative(pdbFile* pdb);
    extern long pdbFileIsPositive(pdbFile* pdb);
    extern long pdbFileIsCharge(pdbFile* pdb);
    extern long pdbFileIsSecondaryStructure(pdbFile* pdb);
    extern long pdbFileIsHelix(pdbFile* pdb);
    extern long pdbFileIsSheet(pdbFile* pdb);
    extern long pdbFileIsTurn(pdbFile* pdb);
    extern pdbRecord* pdbFileNew(pdbFile* pdb);
    extern pdbRecord* pdbFileAppend(pdbFile* pdb);
    extern pdbRecord* pdbFileFree(pdbFile* pdb);
    extern pdbRecord* pdbFileRecordPrint(FILE* fpt, pdbFile* pdb);

    extern pdbFileParaTypeInteger pdbZValueGet(pdbFile* pdb);
    /*werewolf presented*/
    extern pdbRecord* pdbFileRecordTablePrint(FILE* fpt, pdbFile* pdb);

    extern pdbFileSecondaryStructureRecord* pdbFileSecondaryStructureRecordPrint(FILE* fpt, pdbFileSecondaryStructureRecord* second);
    extern pdbRecord* pdbFileCAOnlyCopy(pdbFile* pdb, pdbFile* src);
    extern void pdbFileCAOnlyCopyAll(pdbFile* pdb, pdbFile* src);
    extern void pdbFileCopyAll(pdbFile* dst, pdbFile* src);
    extern void pdbFileAppendAll(pdbFile* dst, pdbFile* src);
    extern pdbRecord* pdbFileOneRecordCopy(pdbFile* dst, pdbFile* src);
    extern void pdbFileOneProteinCopy(pdbFile* dst, pdbFile* src, long num);

    extern void pdbRotationFollowingEulerAngle(pdbFile* pdb, char Mode[4], pdbFileParaTypeReal rot1, pdbFileParaTypeReal rot2, pdbFileParaTypeReal rot3);
    extern void pdbRotationFollowingEulerAngleInverse(pdbFile* pdb, char Mode[4], pdbFileParaTypeReal rot1, pdbFileParaTypeReal rot2, pdbFileParaTypeReal rot3);
    extern void pdbRotationXYZ(pdbFile* pdb, pdbFileParaTypeReal rotx, pdbFileParaTypeReal roty, pdbFileParaTypeReal rotz);
    extern void pdbRotationZYX(pdbFile* pdb, pdbFileParaTypeReal rotx, pdbFileParaTypeReal roty, pdbFileParaTypeReal rotz);
    extern void pdbRotationZXY(pdbFile* pdb, pdbFileParaTypeReal rotx, pdbFileParaTypeReal roty, pdbFileParaTypeReal rotz);
    extern void pdbRotationYXZ(pdbFile* pdb, pdbFileParaTypeReal rotx, pdbFileParaTypeReal roty, pdbFileParaTypeReal rotz);

    extern int pdbSecondaryStructureSetFromPDB(pdbFile* pdb, pdbFileSecondaryStructure* second);
    extern int pdbNoSecondaryStructureSetFromPDB(pdbFile* pdb, pdbFileSecondaryStructure* second);
    extern int pdbSecondaryStructureAppend(pdbFileSecondaryStructure* second);
    extern pdbFileSecondaryStructureMode pdbFileWithSecondaryStructure(pdbFile* pdb, pdbFileSecondaryStructure* second);

    /* prototype end */

    #ifdef __cplusplus
    }
    #endif
    #endif /* PDB_FILE_H */