/*
 * $Id: atoms.h,v 1.24 2008/08/05 14:41:51 hess Exp $
 * 
 *                This source code is part of
 * 
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 *          GROningen MAchine for Chemical Simulations
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 * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
 * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
 * Copyright (c) 2001-2004, The GROMACS development team,
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 */
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif

enum {
  eptAtom, eptNucleus, eptShell, eptBond, eptVSite, eptNR
};
/* The particle type */
 
typedef struct {
  real 		m,q;		/* Mass and charge			*/
  real 		mB,qB;		/* Mass and charge for Free Energy calc */
  unsigned short type;		/* Atom type				*/
  unsigned short typeB;		/* Atom type for Free Energy calc	*/
  int           ptype;		/* Particle type			*/
  int 		resnr;		/* Residue number			*/
  int           atomnumber;     /* Atomic Number or NOTSET              */
  unsigned char chain;          /* chain identifier                     */
} t_atom;

typedef struct {
  int  type;                    /* PDB record name                      */
  int  atomnr;                  /* PDB atom number                      */
  char altloc;                  /* Alternate location indicator         */
  char atomnm[6];               /* True atom name including spaces      */
  char pdbresnr[6];             /* PDB res number                       */
  real occup;                   /* Occupancy                            */
  real bfac;                    /* B-factor                             */
  bool bAnisotropic;            /* (an)isotropic switch                 */
  int  uij[6];                  /* Anisotropic B-factor                 */
} t_pdbinfo;

typedef struct {
  int  nr;			/* Number of different groups		*/
  int  *nm_ind;                 /* Index in the group names             */
} t_grps;

typedef struct {
  int           nr;             /* Nr of atoms                          */
  t_atom	*atom;		/* Array of atoms (dim: nr)		*/
				/* The following entries will not 	*/
				/* allways be used (nres==0)	 	*/
  char		***atomname;	/* Array of pointers to atom name	*/
				/* use: (*(atomname[i]))		*/
  char		***atomtype;	/* Array of pointers to atom types	*/
				/* use: (*(atomtype[i]))		*/
  char		***atomtypeB;	/* Array of pointers to B atom types	*/
				/* use: (*(atomtypeB[i]))		*/
  int		nres;		/* Nr of residue names			*/
  char		***resname; 	/* Array of pointers to residue names 	*/
				/* use: (*(resname[i]))	       	*/
  t_pdbinfo     *pdbinfo;       /* PDB Information, such as aniso. Bfac */
} t_atoms;

typedef struct {
  int           nr;              /* number of atomtypes                     */
  real         *radius;         /* GBSA radius for each atomtype        */
  real         *vol;            /* GBSA efective volume for each atomtype   */
  real         *surftens;       /* implicit solvent surftens for each atomtype */
  int          *atomnumber;     /* Atomic number, used for QM/MM */
} t_atomtypes;


#define PERTURBED(a) (((a).mB != (a).m) || ((a).qB != (a).q) || ((a).typeB != (a).type))
