/*  _______________________________________________________________________
 *
 *                        RDPARM/PTRAJ: APR 2000
 *  _______________________________________________________________________
 *
 *  $Header: /thr/gamow/cvsroot/amber7/src/ptraj/analyze.h,v 1.2 2000/05/10 21:51:59 cheatham Exp $
 *
 *  Revision: $Revision: 1.2 $
 *  Date: $Date: 2000/05/10 21:51:59 $
 *  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)
 *  _______________________________________________________________________
 */


/*
 *  This is the header file for analyze.c which contains the basic structures
 *  necessary for analyzing data acculated by the various actions in ptraj()
 *
 * (1) EXTERNALLY VISIBLE DEFINITIONS
 * (2) GLOBAL VARIABLES
 * (3) EXTERNALLY VISIBLE FUNCTION PROTOTYPES
 * (4) LOCAL STRUCTURES
 */


/*
 * (1) EXTERNALLY VISIBLE DEFINITIONS
 */


  /*
   *  ANALYZE INFORMATION
   */

typedef enum _analyzeType { 
  ANALYZE_NOOP, 
  ANALYZE_CORRELATIONCOEFFICIENT,
  ANALYZE_HBOND,
  ANALYZE_SET,
  ANALYZE_STATISTICS,
  ANALYZE_TEST
} analyzeType;


#  ifdef __STDC__
typedef int (*analyzeFunction)(void *, stackType *, int);
#  else
typedef int (*analyzeFunction)();
#  endif

typedef struct _analyzeInformation { 
  analyzeFunction fxn; 
  analyzeType type;
  int iarg1;
  int iarg2;
  int iarg3;
  int iarg4;
  double darg1;
  double darg2;
  double darg3;
  double darg4;
  void *carg1;
  void *carg2;
  void *carg3;
  void *carg4;
} analyzeInformation;

#define INITIALIZE_analyzeInformation(_p_) \
  _p_->fxn = NULL;            \
  _p_->type = ANALYZE_NOOP;   \
  _p_->iarg1 = 0;             \
  _p_->iarg2 = 0;             \
  _p_->iarg3 = 0;             \
  _p_->iarg4 = 0;             \
  _p_->darg1 = 0.0;           \
  _p_->darg2 = 0.0;           \
  _p_->darg3 = 0.0;           \
  _p_->darg4 = 0.0;           \
  _p_->carg1 = NULL;          \
  _p_->carg2 = NULL;          \
  _p_->carg3 = NULL;          \
  _p_->carg4 = NULL


  /*
   *  Information for the stackStack, i.e. saving various 
   *  scalar values for later processing
   */

typedef enum _scalarMode { SCALAR_NULL, 
			   SCALAR_DISTANCE, 
			   SCALAR_ANGLE, 
			   SCALAR_TORSION,
			   SCALAR_PUCKER,
			   SCALAR_RMS
} scalarMode;

typedef struct _scalarInfo {
  char *name;
  char *filename;
  scalarMode mode;
  int atom1, atom2, atom3, atom4, atom5;
  int *mask1, *mask2, *mask3, *mask4, *mask5;
  int totalFrames;
  int frame;
  double *value;
  void *results;
} scalarInfo;


#define INITIALIZE_scalarInfo(_p_) \
  _p_->name      = NULL; \
  _p_->filename  = NULL; \
  _p_->mode      = SCALAR_NULL; \
  _p_->atom1 = -1; _p_->atom2 = -1; _p_->atom3 = -1; _p_->atom4 = -1; _p_->atom5 = -1; \
  _p_->mask1=NULL; _p_->mask2=NULL; _p_->mask3=NULL; _p_->mask4=NULL; _p_->mask5=NULL; \
  _p_->totalFrames = 0;  \
  _p_->frame     = 0;    \
  _p_->value     = NULL; \
  _p_->results   = NULL



/*
 * (2) GLOBAL VARIABLES
 */




/*
 * (3) EXTERNALLY VISIBLE FUNCTION PROTOTYPES
 */


#ifndef ANALYZE_MODULE


#  ifdef __STDC__

extern int analyzeTest(analyzeInformation *, stackType *, int);
extern int analyzeCorrelationCoefficient(analyzeInformation *, stackType *, int);
extern int analyzeHBond(analyzeInformation *, stackType *, int);
extern int analyzeSet(analyzeInformation *, stackType *, int);
extern int analyzeStatistics(analyzeInformation *, stackType *, int);
extern int analyzeTest(analyzeInformation *, stackType *, int);

#  else  /* __STDC__ */

extern int analyzeTest();
extern int analyzeCorrelationCoefficient();
extern int analyzeHBond();
extern int analyzeSet();
extern int analyzeStatistics();
extern int analyzeTest();

#  endif /* __STDC__ */


#endif /* ANALYZE_MODULE */



/*
 * (4) LOCAL STRUCTURES
 */

typedef enum _unaryOperator { UNARY_NOOP,     UNARY_NORMALIZE, 
			      UNARY_COSINE,   UNARY_SINE,
			      UNARY_ARCCOS,   UNARY_ARCSIN,
			      UNARY_SHIFT 
} unaryOperator;

typedef enum _binaryOperator { BINARY_NOOP,   BINARY_PLUS,
			       BINARY_MINUS,  BINARY_TIMES,
			       BINARY_DIVIDE
} binaryOperator;



typedef struct _correlationCoefficientResults {
  int N;
  double average;
  double a2;
  double stddev;
  double coeff;
  double a;
  double b;
  double significance;
} correlationCoefficientResults;

#define INITIALIZE_correlationCoefficientResults(_p_) \
  _p_->N = 0; \
  _p_->average = 0.0; \
  _p_->a2 = 0.0; \
  _p_->stddev = 0.0; \
  _p_->coeff = 0.0; \
  _p_->a = 0.0; \
  _p_->b = 0.0; \
  _p_->significance = 0.0