/*  _______________________________________________________________________
 *
 *                        RDPARM/PTRAJ: APR 2000
 *  _______________________________________________________________________
 *
 *  $Header: /thr/gamow/cvsroot/amber7/src/ptraj/ptraj_local.h,v 1.7 2000/05/10 21:52:01 cheatham Exp $
 *
 *  Revision: $Revision: 1.7 $
 *  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)
 *  _______________________________________________________________________
 */



/* The parameter file assumes the atom, residue, symbol, etc. names to be *
 * four characters (we will store them as strings, requiring a newline,   *
 * hence the size is 5).                                                  */
#define NAME_SIZE 5
#define NAME_DEFAULT "    "
typedef char Name[NAME_SIZE];



/*
 *  state information necessary for the transformation routines
 */
typedef struct _ptrajState { 
  double box[6];             /* box lengths and angles */
  double *masses;            /* atom masses */
  double *charges;           /* atom charges */
  int atoms;                 /* number of atoms */
  int residues;              /* number of residues */
  int *ipres;                /* atoms in each residue */
  int IFBOX;                 /* is there box information? */
  int boxfixed[6];           /* equal to 1 if this box coordinate is fixed */
  int molecules;             /* total number of molecules */
  int *moleculeInfo;         /* number of atoms in each molecule */
  int *solventMask;          /* atoms in the solvent */
  int solventMolecules;      /* number of solvent molecules */
  int *solventMoleculeStart; /* pointer into solventMask for first atom of each solvent */
  int *solventMoleculeStop;  /* pointer into solventMask for last atom of each solvent */
  int solventAtoms;          /* number of solvent atoms */
  Name *atomName;            /* atom names */
  Name *residueName;         /* residue names */
  int maxFrames;             /* number of useful frames in 1 pass of trajin's */
} ptrajState;

#define INITIALIZE_ptrajState( _p_ ) \
  _p_->box[0] = 0.0; _p_->box[1] = 0.0; _p_->box[2] = 0.0; \
  _p_->box[3] = 90.0; _p_->box[4] = 90.0; _p_->box[5] = 90.0; \
  _p_->masses = NULL; \
  _p_->charges = NULL; \
  _p_->atoms = 0; \
  _p_->residues = 0; \
  _p_->ipres = NULL; \
  _p_->IFBOX = 0; \
  _p_->boxfixed[0] = 0; _p_->boxfixed[1] = 0; _p_->boxfixed[2] = 0; \
  _p_->boxfixed[3] = 0; _p_->boxfixed[4] = 0; _p_->boxfixed[5] = 0; \
  _p_->molecules = 0; \
  _p_->moleculeInfo = NULL; \
  _p_->solventMask = NULL; \
  _p_->solventMolecules = 0; \
  _p_->solventMoleculeStart = NULL; \
  _p_->solventMoleculeStop = NULL; \
  _p_->solventAtoms = 0; \
  _p_->atomName = NULL; \
  _p_->residueName = NULL; \
  _p_->maxFrames = 0

  

/*
 *  structures used in the processing of the atom specification
 */

enum _parseOperators { 
  PARSE_NOOP,
  PARSE_CONTINUATION,
  PARSE_ATOM,
  PARSE_RESIDUE
};

typedef struct _parseEntry {
  char *token;
  int operator;
  int isnumber;
} parseEntry;


typedef enum _ptrajMode { PTRAJ_NOOP,   PTRAJ_ACTION, PTRAJ_SETUP, 
			  PTRAJ_STATUS, PTRAJ_PRINT,  PTRAJ_CLEANUP }
ptrajMode;