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#ifndef GMX_GMXANA_GSTAT_H
#define GMX_GMXANA_GSTAT_H

#include <string>

#include "gromacs/commandline/pargs.h"
#include "gromacs/topology/index.h"

struct gmx_output_env_t;

/* must correspond with 'leg' g_chi.c:727 */
enum
{
    edPhi = 0,
    edPsi,
    edOmega,
    edChi1,
    edChi2,
    edChi3,
    edChi4,
    edChi5,
    edChi6,
    edMax
};

enum
{
    edPrintST = 0,
    edPrintRO
};

#define NONCHI 3
#define MAXCHI (edMax - NONCHI)
#define NROT 4 /* number of rotamers: 1=g(-), 2=t, 3=g(+), 0=other */

typedef struct
{
    int minCalpha, minC, H, N, C, O, Cn[MAXCHI + 3];
} t_dihatms; /* Cn[0]=N, Cn[1]=Ca, Cn[2]=Cb etc. */

struct t_dlist
{
    char        name[12];
    int         resnr;
    std::string residueName;
    int         j0[edMax]; /* Index in dih array (phi angle is first...) */
    t_dihatms   atm;
    int         b[edMax];
    int         ntr[edMax];
    real        S2[edMax];
    real        rot_occ[edMax][NROT];
};

typedef struct
{
    const char* name;    /* Description of the J coupling constant */
    real        A, B, C; /* Karplus coefficients */
    real        offset;  /* Offset for dihedral angle in histogram (e.g. -M_PI/3) */
    real        Jc;      /* Resulting Jcoupling */
    real        Jcsig;   /* Standard deviation in Jc */
} t_karplus;

void calc_distribution_props(int nh, const int histo[], real start, int nkkk, t_karplus kkk[], real* S2);
/* This routine takes a dihedral distribution and calculates
 * coupling constants and dihedral order parameters of it.
 *
 * nh      is the number of points
 * histo   is the array of datapoints which is assumed to span
 *         2 M_PI radians
 * start   is the starting angle of the histogram, this can be either 0
 *         or -M_PI
 * nkkk    is the number of karplus sets (multiple coupling constants may be
 *         derived from a single angle)
 * kkk     are the constants for calculating J coupling constants using a
 *         Karplus equation according to
 *
 *                  2
 *         J = A cos theta + B cos theta + C
 *
 *         where theta is phi - offset (phi is the angle in the histogram)
 * offset  is subtracted from phi before substitution in the Karplus
 *         equation
 * S2      is the resulting dihedral order parameter
 *
 */

void ana_dih_trans(const char*             fn_trans,
                   const char*             fn_histo,
                   real**                  dih,
                   int                     nframes,
                   int                     nangles,
                   const char*             grpname,
                   real*                   time,
                   bool                    bRb,
                   const gmx_output_env_t* oenv);
/*
 * Analyse dihedral transitions, by counting transitions per dihedral
 * and per frame. The total number of transitions is printed to
 * stderr, as well as the average time between transitions.
 *
 * is wrapper to low_ana_dih_trans, which also passes in and out the
     number of transitions per dihedral per residue. that uses struc dlist
     which is not external, so pp2shift.h must be included.

 * Dihedrals are supposed to be in either of three minima,
 * (trans, gauche+, gauche-)
 *
 * fn_trans  output file name for #transitions per timeframe
 * fn_histo  output file name for transition time histogram
 * dih       the actual dihedral angles
 * nframes   number of times frames
 * nangles   number of angles
 * grpname   a string for the header of plots
 * time      array (size nframes) of times of trajectory frames
 * bRb       determines whether the polymer convention is used
 *           (trans = 0)
 */

void low_ana_dih_trans(bool                    bTrans,
                       const char*             fn_trans,
                       bool                    bHisto,
                       const char*             fn_histo,
                       int                     maxchi,
                       real**                  dih,
                       gmx::ArrayRef<t_dlist>  dlist,
                       int                     nframes,
                       int                     nangles,
                       const char*             grpname,
                       int                     multiplicity[],
                       real*                   time,
                       bool                    bRb,
                       real                    core_frac,
                       const gmx_output_env_t* oenv);
/* as above but passes dlist so can copy occupancies into it, and multiplicity[]
 *  (1..nangles, corresp to dih[this][], so can have non-3 multiplicity of
 * rotamers. Also production of xvg output files is conditional
 * and the fractional width of each rotamer can be set ie for a 3 fold
 * dihedral with core_frac = 0.5 only the central 60 degrees is assigned
 * to each rotamer, the rest goes to rotamer zero */


void read_ang_dih(const char*             trj_fn,
                  bool                    bAngles,
                  bool                    bSaveAll,
                  bool                    bRb,
                  bool                    bPBC,
                  int                     maxangstat,
                  int                     angstat[],
                  int*                    nframes,
                  real**                  time,
                  int                     isize,
                  int                     index[],
                  real**                  trans_frac,
                  real**                  aver_angle,
                  real*                   dih[],
                  const gmx_output_env_t* oenv);
/*
 * Read a trajectory and calculate angles and dihedrals.
 *
 * trj_fn      file name of trajectory
 * bAngles     do we have to read angles or dihedrals
 * bSaveAll    do we have to store all in the dih array
 * bRb         do we have Ryckaert-Bellemans dihedrals (trans = 0)
 * bPBC        compute angles module 2 Pi
 * maxangstat  number of entries in distribution array
 * angstat     angle distribution
 * *nframes    number of frames read
 * time        simulation time at each time frame
 * isize       number of entries in the index, when angles 3*number of angles
 *             else 4*number of angles
 * index       atom numbers that define the angles or dihedrals
 *             (i,j,k) resp (i,j,k,l)
 * trans_frac  number of dihedrals in trans
 * aver_angle  average angle at each time frame
 * dih         all angles at each time frame
 */

void make_histo(FILE* log, int ndata, real data[], int npoints, int histo[], real minx, real maxx);
/*
 * Make a histogram from data. The min and max of the data array can
 * be determined (if minx == 0 and maxx == 0)
 * and the index in the histogram is computed from
 * ind = npoints/(max(data) - min(data))
 *
 * log       write error output to this file
 * ndata     number of points in data
 * data      data points
 * npoints   number of points in histogram
 * histo     histogram array. This is NOT set to zero, to allow you
 *           to add multiple histograms
 * minx      start of the histogram
 * maxx      end of the histogram
 *           if both are 0, these values are computed by the routine itself
 */

void normalize_histo(gmx::ArrayRef<const int> histo, real dx, gmx::ArrayRef<real> normhisto);
/*
 * Normalize a histogram so that the integral over the histo is 1
 *
 * histo      input histogram
 * dx         distance between points on the X-axis
 * normhisto  normalized output histogram
 */

/* Routines from pp2shift (anadih.c etc.) */

void do_pp2shifts(FILE* fp, int nframes, gmx::ArrayRef<const t_dlist> dlist, real** dih);

bool has_dihedral(int Dih, const t_dlist& dlist);

/*! \brief Describe the dihedrals in the residues of the \c atoms
 * structure
 *
 * Return a vector with a t_dlist entry for each residue in \c
 * atoms. The entry for a residue contains its name, its index within
 * the residues, and a mapping from chemical peptide atom names to
 * atom indices based on the atom names. Many fields of t_dlist are
 * not yet filled. */
std::vector<t_dlist>
mk_dlist(FILE* log, const t_atoms* atoms, bool bPhi, bool bPsi, bool bChi, bool bHChi, int maxchi, int r0);

void pr_dlist(FILE*                        fp,
              gmx::ArrayRef<const t_dlist> dlist,
              real                         dt,
              int                          printtype,
              bool                         bPhi,
              bool                         bPsi,
              bool                         bChi,
              bool                         bOmega,
              int                          maxchi);

void mk_chi_lookup(int** lookup, int maxchi, gmx::ArrayRef<const t_dlist> dlist);

void mk_multiplicity_lookup(int* multiplicity, int maxchi, gmx::ArrayRef<const t_dlist> dlist, int nangle);

void get_chi_product_traj(real**                       dih,
                          int                          nframes,
                          int                          maxchi,
                          gmx::ArrayRef<const t_dlist> dlist,
                          real                         time[],
                          int**                        lookup,
                          int*                         multiplicity,
                          bool                         bRb,
                          bool                         bNormalize,
                          real                         core_frac,
                          bool                         bAll,
                          const char*                  fnall,
                          const gmx_output_env_t*      oenv);

void print_one(const gmx_output_env_t* oenv,
               const char*             base,
               const char*             name,
               const char*             title,
               const char*             ylabel,
               int                     nf,
               real                    time[],
               real                    data[]);

/* Routines from g_hbond */
void analyse_corr(int  n,
                  real t[],
                  real ct[],
                  real nt[],
                  real kt[],
                  real sigma_ct[],
                  real sigma_nt[],
                  real sigma_kt[],
                  real fit_start,
                  real temp);

void compute_derivative(int nn, const real x[], const real y[], real dydx[]);

#endif
