/*  _______________________________________________________________________
 *
 *                        RDPARM/PTRAJ: APR 2000
 *  _______________________________________________________________________
 *
 *  $Header: /thr/gamow/cvsroot/amber7/src/ptraj/ptraj.h,v 1.10 2000/05/10 21:52:01 cheatham Exp $
 *
 *  Revision: $Revision: 1.10 $
 *  Date: $Date: 2000/05/10 21:52:01 $
 *  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 main header file for the ptraj and rdparm code.            
 *
 *   NOTE: All of the prototypes and structure definitions reside in 
 *   individual files based on the name of the source code file.     
 *   Despite this logical separation, all the individual include     
 *   files are included indirectly and automatically by including    
 *   this single include file.  To separate local and global definitions
 *   within the header files, environment variables are set in each of 
 *   the header files (#define X_MODULE where X is the name of the source 
 *   file) to differentiate local information needed for the source file
 *   and globabally accessible (and prototyped) definitions.
 */
                                                                   
#include "constants.h"
#include "ptraj_local.h"
#include "utility.h"
#include "pdb/pdb.h"
#include "dispatch.h"
#include "actions.h"
#include "analyze.h"
#include "rdparm.h"
#include "io.h"
#include "help.h"
#include "vector.h"
#include "trajectory.h"
#include "torsion.h"
#include "rms.h"
#include "display.h"
#include "interface.h"
#include "experimental.h"


/*
 *   MACHINE DEPENDENCY
 *
 *   Although most of this code is written in C, FORTRAN routines may
 *   also be called although none currently is anymore...  
 *   Various systems handle calling FORTRAN routines from C differently.
 *   We can overcome this the use of the C preprocess (CPP).  Most systems 
 *   call FORTRAN function "foobar" from C via the "foobar_()" call.
 *   Exceptions:
 *     HPUX       -- no appended underscore (i.e. "foobar()")
 *     UNICOS     -- no appended underscore, all capitals! (i.e. "FOOBAR()")
 */


/*
 * CRAY special case to avoid expf call...
 */
#ifdef CRAY
#define expf exp
#endif


/*
 *  GLOBAL DEFINES and ENUMERATED TYPES local to ptraj.c
 */

#ifdef PTRAJ_MODULE


ptrajState *ptrajCurrentStatePointer = NULL;  
  /*
   *  this holds the current state which may evolve as actions are setup.
   *  Each action has a local copy (setup as the action is initialized...
   */

stackType *transformFileStack = NULL;
coordinateInfo *outInfo = NULL;
stackType *transformReferenceStack = NULL;
coordinateInfo *referenceInfo = NULL;
stackType *transformActionStack = NULL;
stackType *transformAnalyzeStack = NULL;
stackType *vectorStack = NULL;
stackType *scalarStack = NULL;
stackType *hbondStack = NULL;

int prnlev = 0;

#else

extern stackType *vectorStack;
extern stackType *scalarStack;
extern stackType *hbondStack;
extern coordinateInfo *outInfo;
extern stackType *transformReferenceStack;
extern coordinateInfo *referenceInfo;
extern int prnlev;

#endif /* ifdef PTRAJ_MODULE */


/*
 *   FUNCTION PROTOTYPES
 *
 *   The following functions are defined in ptraj.c and are externally
 *   accessible.  In order to hide this prototyping/referencing from the 
 *   ptraj.c source (which like the other source files includes 
 *   this header file) the C preprocessor (CPP) token "PTRAJ_MODULE" is 
 *   defined at the top of the ptraj.c source to prevent inclusion...  
 *   This general strategy has been used throughout the source
 *   where the defined CPP token is equivalent to the capitalized 
 *   file name without the ".c" appended with "_MODULE"
 */

#ifndef PTRAJ_MODULE
#  ifdef __STDC__

extern void ptraj(char *);
extern void checkCoordinatesWrap(char *);
extern int *processAtomMask(char *, ptrajState *);
extern void checkAtomMask(char *);
extern int *returnAtomMask(char *);
extern void atomMaskIsActive(int *, ptrajState *, int *, int *);
extern ptrajState **ptrajCurrentState();
extern void ptrajSetup(stackType *, int);
extern void ptrajSetupAnalyze(stackType *, int);
extern void ptrajSetupIO(stackType *, int);
extern void ptrajInitializeState(ptrajState **, char *);
extern int  atomToResidue(int, int, int *);
extern int  atomToSolventMolecule(int, int, int *, int *);
extern int  atomToMolecule(int, int, int *);
extern void modifyStateByMask(ptrajState **, ptrajState **, int *, int);
extern scalarInfo *scalarStackGetName(stackType **, char *);
extern transformHBondInfo *hbondInfoStackGetName(stackType **, char *);
extern void boxToRecip(double box[6], double ucell[9], double recip[9]);
extern double calculateDistance2(int, int, double *, double *, double *,
				 double *, double *, double *, double);
extern double calculateMinImagedDistance2(double *, double *, double *, 
					  double, double, double, double, double, double,
					  int *, int *, int *);

#  else

extern void ptraj();
extern void checkCoordinatesWrap();
extern int *processAtomMask();
extern void checkAtomMask();
extern int *returnAtomMask();
extern void atomMaskIsActive();
extern ptrajState **ptrajCurrentState();
extern void ptrajSetup();
extern void ptrajSetupAnalyze();
extern void ptrajSetupIO();
extern void ptrajInitializeState();
extern int  atomToResidue();
extern int  atomToSolventMolecule();
extern int  atomToMolecule();
extern void modifyStateByMask();
extern scalarInfo *scalarStackGetName();
extern transformHBondInfo *hbondInfoStackGetName();
extern void boxToRecip();
extern double calculateDistance2();
extern double calculateMinImagedDistance2();

#  endif

#endif /* PTRAJ_MODULE */