/*
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 * Copyright 1991- The GROMACS Authors
 * and the project initiators Erik Lindahl, Berk Hess and David van der Spoel.
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 */
#ifndef GMX_TOPOLOGY_ATOMS_H
#define GMX_TOPOLOGY_ATOMS_H

#include <stdio.h>

#include <vector>

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

struct t_symtab;

/* The particle type */
enum class ParticleType : int
{
    Atom,
    Nucleus,
    Shell,
    Bond,
    VSite,
    Count
};

/* The particle type names */
const char* enumValueToString(ParticleType enumValue);

/* Enumerated type for pdb records. The other entries are ignored
 * when reading a pdb file
 */
enum class PdbRecordType : int
{
    Atom,
    Hetatm,
    Anisou,
    Cryst1,
    Compound,
    Model,
    EndModel,
    Ter,
    Header,
    Title,
    Remark,
    Conect,
    Count
};

const char* enumValueToString(PdbRecordType enumValue);

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       */
    ParticleType   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
{
    PdbRecordType 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;

//! Contains indices into group names for different groups.
using AtomGroupIndices = std::vector<int>;

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);

/*! \brief Compare information in the t_atoms data structure.
 *
 * \param[in] fp Pointer to file to write to.
 * \param[in] a1 Pointer to first data structure to compare.
 * \param[in] a2 Pointer to second data structure or nullptr.
 * \param[in] relativeTolerance Relative floating point comparison tolerance.
 * \param[in] absoluteTolerance Absolute floating point comparison tolerance.
 */
void compareAtoms(FILE* fp, const t_atoms* a1, const t_atoms* a2, real relativeTolerance, real absoluteTolerance);

/*! \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
