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#ifndef GMX_TOPOLOGY_ATOMS_H
#define GMX_TOPOLOGY_ATOMS_H

#include <stdio.h>

#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/real.h"
#include "gromacs/utility/unique_cptr.h"

struct t_symtab;

/* The particle type */
enum {
    eptAtom, eptNucleus, eptShell, eptBond, eptVSite, eptNR
};

/* The particle type names */
extern const char *ptype_str[eptNR+1];

/* Enumerated type for pdb records. The other entries are ignored
 * when reading a pdb file
 */
enum PDB_record {
    epdbATOM,   epdbHETATM, epdbANISOU, epdbCRYST1, epdbCOMPND,
    epdbMODEL,  epdbENDMDL, epdbTER,    epdbHEADER, epdbTITLE, epdbREMARK,
    epdbCONECT, epdbNR
};

typedef struct t_atom
{
    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            resind;      /* Index into resinfo (in t_atoms)      */
    int            atomnumber;  /* Atomic Number or 0                   */
    char           elem[4];     /* Element name                         */
} t_atom;

typedef struct t_resinfo
{
    char          **name;       /* Pointer to the residue name          */
    int             nr;         /* Residue number                       */
    unsigned char   ic;         /* Code for insertion of residues       */
    int             chainnum;   /* Iincremented at TER or new chain id  */
    char            chainid;    /* Chain identifier written/read to pdb */
    char          **rtp;        /* rtp building block name (optional)   */
} t_resinfo;

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

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

typedef struct t_atoms
{
    int          nr;            /* Nr of atoms                          */
    t_atom      *atom;          /* Array of atoms (dim: nr)             */
                                /* The following entries will not       */
                                /* always 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;          /* The number of resinfo entries        */
    t_resinfo   *resinfo;       /* Array of residue names and numbers   */
    t_pdbinfo   *pdbinfo;       /* PDB Information, such as aniso. Bfac */

    /* Flags that tell if properties are set for all nr atoms.
     * For B-state parameters, both haveBState and the mass/charge/type
     * flag should be TRUE.
     */
    gmx_bool     haveMass;      /* Mass available                       */
    gmx_bool     haveCharge;    /* Charge available                     */
    gmx_bool     haveType;      /* Atom type available                  */
    gmx_bool     haveBState;    /* B-state parameters available         */
    gmx_bool     havePdbInfo;   /* pdbinfo available                    */
} t_atoms;

typedef struct t_atomtypes
{
    int           nr;           /* number of atomtypes                          */
    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))

void init_atom(t_atoms *at);
void init_atomtypes(t_atomtypes *at);
void done_atom(t_atoms *at);
void done_and_delete_atoms(t_atoms *atoms);
void done_atomtypes(t_atomtypes *at);

void init_t_atoms(t_atoms *atoms, int natoms, gmx_bool bPdbinfo);
/* allocate memory for the arrays, set nr to natoms and nres to 0
 * set pdbinfo to NULL or allocate memory for it */

void gmx_pdbinfo_init_default(t_pdbinfo *pdbinfo);

t_atoms *copy_t_atoms(const t_atoms *src);
/* copy an atoms struct from src to a new one */

void add_t_atoms(t_atoms *atoms, int natom_extra, int nres_extra);
/* allocate extra space for more atoms and or residues */

void t_atoms_set_resinfo(t_atoms *atoms, int atom_ind, struct t_symtab *symtab,
                         const char *resname, int resnr, unsigned char ic,
                         int chainnum, char chainid);
/* Set the residue name, number, insertion code and chain identifier
 * of atom index atom_ind.
 */

void pr_atoms(FILE *fp, int indent, const char *title, const t_atoms *atoms,
              gmx_bool bShownumbers);
void pr_atomtypes(FILE *fp, int indent, const char *title,
                  const t_atomtypes *atomtypes, gmx_bool bShowNumbers);

void cmp_atoms(FILE *fp, const t_atoms *a1, const t_atoms *a2, real ftol, real abstol);

/*! \brief Set mass for each atom using the atom and residue names using a database
 *
 * If atoms->haveMass = TRUE does nothing.
 * If printMissingMasss = TRUE, prints details for first 10 missing masses
 * to stderr.
 */
void atomsSetMassesBasedOnNames(t_atoms *atoms, gmx_bool printMissingMasses);

//! Deleter for t_atoms, needed until it has a proper destructor.
using AtomsDataPtr = gmx::unique_cptr<t_atoms, done_and_delete_atoms>;


#endif
