/*
 * This file is part of the GROMACS molecular simulation package.
 *
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 * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
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 */

struct t_atom {

%TypeHeaderCode
#include <gromacs/topology/atoms.h>
%End

    double         m; double q;        /* Mass and charge                      */
    double         mB; double 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 NOTSET              */
    char           *elem /NoSetter/;       /* Element name                         */
};

struct t_resinfo {

%TypeHeaderCode
#include <gromacs/topology/atoms.h>
%End

    char          **name {      /* Pointer to the residue name          */
    %GetCode
        sipPy = sipBuildResult(NULL, "s", *(sipCpp->name));
    %End
    %SetCode

    %End
    };
    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)   */
    %GetCode
        sipPy = sipBuildResult(NULL, "s", *(sipCpp->rtp));
    %End
    %SetCode

    %End
    };
};

struct t_pdbinfo {

%TypeHeaderCode
#include <gromacs/topology/atoms.h>
%End

    int      type;              /* PDB record name                      */
    int      atomnr;            /* PDB atom number                      */
    char     altloc;            /* Alternate location indicator         */
    char    *atomnm /NoSetter/; /* True atom name including leading spaces */
    double   occup;             /* Occupancy                            */
    double   bfac;              /* B-factor                             */
    bool bAnisotropic;          /* (an)isotropic switch                 */
    int     *uij {
    %GetCode
        sipPy = sipConvertToArray(sipCpp->uij, "i", 6, SIP_READ_ONLY);
    %End
    %SetCode

    %End
    };
};

struct t_grps {

%TypeHeaderCode
#include <gromacs/topology/atoms.h>
%End

    int   nr;                   /* Number of different groups           */
    int  *nm_ind {
    %GetCode
        sipPy = sipConvertToArray(sipCpp->nm_ind, "i", sipCpp->nr, SIP_READ_ONLY);
    %End
    %SetCode

    %End
    };
};

struct t_atoms {

%TypeHeaderCode
#include <gromacs/topology/atoms.h>
%End

    int            nr;          /* Nr of atoms                          */
    t_atom        *atom {
    %GetCode
        sipPy = sipConvertToTypedArray(sipCpp->atom, sipType_t_atom, NULL, sizeof(t_atom), sipCpp->nr, SIP_READ_ONLY);
    %End
    %SetCode

    %End
    };
                                /*[> 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;
    t_resinfo       *resinfo {
    %GetCode
        sipPy = sipConvertToTypedArray(sipCpp->resinfo, sipType_t_resinfo, NULL, sizeof(t_resinfo), sipCpp->nres, SIP_READ_ONLY);
    %End
    %SetCode

    %End
    };
    // FIXME: how many pdbinfo's are there?
    t_pdbinfo       *pdbinfo {
    %GetCode
        sipPy = sipConvertToTypedArray(sipCpp->pdbinfo, sipType_t_pdbinfo, NULL, sizeof(t_pdbinfo), sipCpp->nres, SIP_READ_ONLY);
    %End
    %SetCode

    %End
    };
};