/*  _______________________________________________________________________
 *
 *                        RDPARM/PTRAJ: APR 2000
 *  _______________________________________________________________________
 *
 *  $Header: /thr/gamow/cvsroot/amber7/src/ptraj/trajectory.h,v 1.5 2000/05/10 21:52:02 cheatham Exp $
 *
 *  Revision: $Revision: 1.5 $
 *  Date: $Date: 2000/05/10 21:52:02 $
 *  Last checked in by $Author: cheatham $
 *
 *  This source is now archived under CVS at Scripps in the amber7 tree.
 *
 *  NOTE: this is a beta, pre-release version, is under constant development,
 *  probably contains some bugs and is under constant revision; therefore
 *  take care.  Please report bugs (and fixes!) to cheatham@chpc.utah.edu or 
 *  cheatham@cgl.ucsf.edu
 *
 *  Do not distribute this code without explicit permission.
 *  Do not incorporate into other codes without explicit permission.
 *
 *  Current contact information:
 *
 *     Thomas Cheatham, III
 *     2000 East, 30 South, Skaggs Hall 201
 *     Department of Medicinal Chemistry
 *     University of Utah
 *     Salt Lake City, UT 84112-5820
 *     cheatham@chpc.utah.edu
 *     (801) 587-9653
 *     FAX: (801) 585-5366
 *
 *  Other contributors:
 *
 *    David Case (Scripps)
 *    Michael Crowley (Scripps)
 *    Jed Pitera (UCSF)
 *    Vickie Tsui (Scripps)
 *  _______________________________________________________________________
 */


/*
 *  header file for trajectory.c
 */




   /*
    *  possible coordinate types
    */
typedef enum _coordType { 
  COORD_UNKNOWN,
  COORD_AMBER_TRAJECTORY,
  COORD_AMBER_RESTART,
  COORD_PDB,
  COORD_BINPOS,
  COORD_CHARMM_TRAJECTORY
} coordType;

/*
 *  information relating to a coordinate file
 */
typedef struct _coordinateInfo {
  FILE *file;
  char *filename;
  int start;
  int stop;
  int offset;
  int isBox;
  int isVelocity;
  int option1;
  int option2;
  int *mask;
  double *x;
  double *y;
  double *z;
  void *info;
  coordType type;
} coordinateInfo;

#define INITIALIZE_coordinateInfo(_p_) \
  _p_->file = NULL; \
  _p_->filename = NULL; \
  _p_->start = 1; \
  _p_->stop = -1; \
  _p_->offset = 1; \
  _p_->isBox = 0; \
  _p_->isVelocity = 0; \
  _p_->option1 = 0; \
  _p_->option2 = 0; \
  _p_->mask = NULL; \
  _p_->x = NULL; \
  _p_->y = NULL; \
  _p_->z = NULL; \
  _p_->info = NULL; \
  _p_->type = COORD_UNKNOWN


   /*
    *  union structures for binary I/O, i.e. read in as bytes which can be 
    *  interpreted as float or integer
    */
typedef union _byte {
  char   c[4];
  int    i;
  float  f;
} byte;


typedef union _bytebyte {
  char   c[8];
  double d;
} bytebyte;


typedef struct _charmmTrajectoryInfo {
  int byteorder;         /* endian-ness, 1:LITTLE or [3][2][1][0]; 0:BIG or [0][1][2][3] */
  byte magic;            /* the magic header, should be "CORD" */
  int icntrl[20];        /* the control variables */
  int ntitle;            /* the number of title lines */
  stackType *titleStack; /* a stack for the title */
  int natrec;            /* the number of written atom records */
  int nfreat;            /* the number of free atoms */
  int *freeat;           /* a list of the free atoms */
  double xtlabc[6];      /* the crystal information in XTLABC form */
  double *fixedx;        /* fixed atom coords */
  double *fixedy;        /* fixed atom coords */
  double *fixedz;        /* fixed atom coords */
} charmmTrajectoryInfo;

#define INITIALIZE_charmmTrajectoryInfo( _p_ ) \
  _p_->byteorder = 0; \
  _p_->magic.i = 0; \
  _p_->titleStack = NULL; \
  _p_->natrec = 0; \
  _p_->nfreat = 0; \
  _p_->freeat = NULL; \
  _p_->fixedx = NULL; \
  _p_->fixedy = NULL; \
  _p_->fixedz = NULL





#ifndef TRAJECTORY_MODULE
#  ifdef __STDC__

extern Restart * readAmberRestart(int, char *, FILE *);
extern int getCoordinatesFromRestart(FILE *, double *, double *, double *,
                                    double *, double *, double *,
				     double *, double *, double *);
extern int getCoordinatesFromPdb(pdb_record *, double *, double *, double *);
extern void dumpAmberRestart(FILE *, int, double *, double *, double *, 
			     double *, double *, double *, double *);
extern void writeAmberRestart(Restart *, char *, FILE *);
extern int loadPdb(FILE *, pdb_record **);
extern void savePdb(FILE *, pdb_record *);
extern pdb_record *parmToPdb(Parm *, int *);
extern pdb_record *ptrajStateToPdb(ptrajState *, int *, int);
extern void putCoordinatesInPdb(pdb_record *, int, 
				double *, double *, double *);
extern int readAmberTrajectory(FILE *, int, double *, double *, double *, 
			       double *, int, int);
extern void dumpAmberTrajectory(FILE *, int, double *, double *, double *, double *);
extern void writebinpos(FILE *, int, double *, double *, double *);
extern int openbinpos();
extern int readbinpos(FILE *, int *, float *, int *);
extern int readCharmmTrajectory(FILE *, charmmTrajectoryInfo **, 
				double *, double *, double *, double *, int);
extern void dumpCharmmTrajectory(FILE *, charmmTrajectoryInfo *, int, 
				 double *, double *, double *, double *, int);
extern void printString(void *);
#  else

extern Restart * readAmberRestart();
extern int getCoordinatesFromRestart();
extern int getCoordinatesFromPdb();
extern void dumpAmberRestart();
extern void writeAmberRestart();
extern int loadPdb();
extern void savePdb();
extern pdb_record *parmToPdb();
extern pdb_record *ptrajStateToPdb();
extern putCoordinatesInPdb();
extern int readAmberTrajectory();
extern void dumpAmberTrajectory();
extern void writebinpos();
extern int openbinpos();
extern int readbinpos();
extern int readCharmmTrajectory();
extern void dumpCharmmTrajectory();
extern void printString();
#  endif
#endif