src/gromacs/gmxana/gstat.h

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  37 #ifndef GMX_GMXANA_GSTAT_H
  38 #define GMX_GMXANA_GSTAT_H
  39
  40 #include "gromacs/commandline/pargs.h"
  41 #include "gromacs/topology/index.h"
  42
  43 struct gmx_output_env_t;
  44 class ResidueType;
  45
  46 /* must correspond with 'leg' g_chi.c:727 */
  47 enum {
  48     edPhi = 0, edPsi, edOmega, edChi1, edChi2, edChi3, edChi4, edChi5, edChi6, edMax
  49 };
  50
  51 enum {
  52     edPrintST = 0, edPrintRO
  53 };
  54
  55 #define NHISTO 360
  56 #define NONCHI 3
  57 #define MAXCHI (edMax-NONCHI)
  58 #define NROT 4  /* number of rotamers: 1=g(-), 2=t, 3=g(+), 0=other */
  59
  60 typedef struct {
  61     int minCalpha, minC, H, N, C, O, Cn[MAXCHI+3];
  62 } t_dihatms; /* Cn[0]=N, Cn[1]=Ca, Cn[2]=Cb etc. */
  63
  64 typedef struct {
  65     char       name[12];
  66     int        resnr;
  67     int        index;     /* Index for amino acids (histograms) */
  68     int        j0[edMax]; /* Index in dih array (phi angle is first...) */
  69     t_dihatms  atm;
  70     int        b[edMax];
  71     int        ntr[edMax];
  72     real       S2[edMax];
  73     real       rot_occ[edMax][NROT];
  74
  75 } t_dlist;
  76
  77 typedef struct {
  78     const char *name;    /* Description of the J coupling constant */
  79     real        A, B, C; /* Karplus coefficients */
  80     real        offset;  /* Offset for dihedral angle in histogram (e.g. -M_PI/3) */
  81     real        Jc;      /* Resulting Jcoupling */
  82     real        Jcsig;   /* Standard deviation in Jc */
  83 } t_karplus;
  84
  85 void calc_distribution_props(int nh, const int histo[],
  86                              real start, int  nkkk, t_karplus kkk[],
  87                              real *S2);
  88 /* This routine takes a dihedral distribution and calculates
  89  * coupling constants and dihedral order parameters of it.
  90  *
  91  * nh      is the number of points
  92  * histo   is the array of datapoints which is assumed to span
  93  *         2 M_PI radians
  94  * start   is the starting angle of the histogram, this can be either 0
  95  *         or -M_PI
  96  * nkkk    is the number of karplus sets (multiple coupling constants may be
  97  *         derived from a single angle)
  98  * kkk     are the constants for calculating J coupling constants using a
  99  *         Karplus equation according to
 100  *
 101  *                  2
 102  *         J = A cos theta + B cos theta + C
 103  *
 104  *         where theta is phi - offset (phi is the angle in the histogram)
 105  * offset  is subtracted from phi before substitution in the Karplus
 106  *         equation
 107  * S2      is the resulting dihedral order parameter
 108  *
 109  */
 110
 111 void ana_dih_trans(const char *fn_trans, const char *fn_histo,
 112                    real **dih, int nframes, int nangles,
 113                    const char *grpname, real *time, gmx_bool bRb,
 114                    const gmx_output_env_t *oenv);
 115 /*
 116  * Analyse dihedral transitions, by counting transitions per dihedral
 117  * and per frame. The total number of transitions is printed to
 118  * stderr, as well as the average time between transitions.
 119  *
 120  * is wrapper to low_ana_dih_trans, which also passes in and out the
 121      number of transitions per dihedral per residue. that uses struc dlist
 122      which is not external, so pp2shift.h must be included.
 123
 124  * Dihedrals are supposed to be in either of three minima,
 125  * (trans, gauche+, gauche-)
 126  *
 127  * fn_trans  output file name for #transitions per timeframe
 128  * fn_histo  output file name for transition time histogram
 129  * dih       the actual dihedral angles
 130  * nframes   number of times frames
 131  * nangles   number of angles
 132  * grpname   a string for the header of plots
 133  * time      array (size nframes) of times of trajectory frames
 134  * bRb       determines whether the polymer convention is used
 135  *           (trans = 0)
 136  */
 137
 138 void low_ana_dih_trans(gmx_bool bTrans, const char *fn_trans,
 139                        gmx_bool bHisto, const char *fn_histo, int maxchi,
 140                        real **dih, int nlist, t_dlist dlist[],
 141                        int nframes, int nangles, const char *grpname,
 142                        int multiplicity[], real *time, gmx_bool bRb,
 143                        real core_frac, const gmx_output_env_t *oenv);
 144 /* as above but passes dlist so can copy occupancies into it, and multiplicity[]
 145  *  (1..nangles, corresp to dih[this][], so can have non-3 multiplicity of
 146  * rotamers. Also production of xvg output files is conditional
 147  * and the fractional width of each rotamer can be set ie for a 3 fold
 148  * dihedral with core_frac = 0.5 only the central 60 degrees is assigned
 149  * to each rotamer, the rest goes to rotamer zero */
 150
 151
 152
 153 void read_ang_dih(const char *trj_fn,
 154                   gmx_bool bAngles, gmx_bool bSaveAll, gmx_bool bRb, gmx_bool bPBC,
 155                   int maxangstat, int angstat[],
 156                   int *nframes, real **time,
 157                   int isize, int index[],
 158                   real **trans_frac,
 159                   real **aver_angle,
 160                   real *dih[],
 161                   const gmx_output_env_t *oenv);
 162 /*
 163  * Read a trajectory and calculate angles and dihedrals.
 164  *
 165  * trj_fn      file name of trajectory
 166  * bAngles     do we have to read angles or dihedrals
 167  * bSaveAll    do we have to store all in the dih array
 168  * bRb         do we have Ryckaert-Bellemans dihedrals (trans = 0)
 169  * bPBC        compute angles module 2 Pi
 170  * maxangstat  number of entries in distribution array
 171  * angstat     angle distribution
 172  * *nframes    number of frames read
 173  * time        simulation time at each time frame
 174  * isize       number of entries in the index, when angles 3*number of angles
 175  *             else 4*number of angles
 176  * index       atom numbers that define the angles or dihedrals
 177  *             (i,j,k) resp (i,j,k,l)
 178  * trans_frac  number of dihedrals in trans
 179  * aver_angle  average angle at each time frame
 180  * dih         all angles at each time frame
 181  */
 182
 183 void make_histo(FILE *log,
 184                 int ndata, real data[], int npoints, int histo[],
 185                 real minx, real maxx);
 186 /*
 187  * Make a histogram from data. The min and max of the data array can
 188  * be determined (if minx == 0 and maxx == 0)
 189  * and the index in the histogram is computed from
 190  * ind = npoints/(max(data) - min(data))
 191  *
 192  * log       write error output to this file
 193  * ndata     number of points in data
 194  * data      data points
 195  * npoints   number of points in histogram
 196  * histo     histogram array. This is NOT set to zero, to allow you
 197  *           to add multiple histograms
 198  * minx      start of the histogram
 199  * maxx      end of the histogram
 200  *           if both are 0, these values are computed by the routine itself
 201  */
 202
 203 void normalize_histo(int npoints, const int histo[], real dx, real normhisto[]);
 204 /*
 205  * Normalize a histogram so that the integral over the histo is 1
 206  *
 207  * npoints    number of points in the histo array
 208  * histo      input histogram
 209  * dx         distance between points on the X-axis
 210  * normhisto  normalized output histogram
 211  */
 212
 213 /* Routines from pp2shift (anadih.c etc.) */
 214
 215 void do_pp2shifts(FILE *fp, int nframes,
 216                   int nlist, t_dlist dlist[], real **dih);
 217
 218 gmx_bool has_dihedral(int Dih, t_dlist *dl);
 219
 220 t_dlist *mk_dlist(FILE *log,
 221                   const t_atoms *atoms, int *nlist,
 222                   gmx_bool bPhi, gmx_bool bPsi, gmx_bool bChi, gmx_bool bHChi,
 223                   int maxchi, int r0, ResidueType *rt);
 224
 225 void pr_dlist(FILE *fp, int nl, t_dlist dl[], real dt,  int printtype,
 226               gmx_bool bPhi, gmx_bool bPsi, gmx_bool bChi, gmx_bool bOmega, int maxchi);
 227
 228 int pr_trans(FILE *fp, int nl, t_dlist dl[], real dt, int Xi);
 229
 230 void mk_chi_lookup (int **lookup, int maxchi,
 231                     int nlist, t_dlist dlist[]);
 232
 233 void mk_multiplicity_lookup (int *multiplicity, int maxchi,
 234                              int nlist, t_dlist dlist[], int nangle);
 235
 236 void get_chi_product_traj (real **dih, int nframes,
 237                            int nlist, int maxchi, t_dlist dlist[],
 238                            real time[], int **lookup, int *multiplicity,
 239                            gmx_bool bRb, gmx_bool bNormalize,
 240                            real core_frac, gmx_bool bAll, const char *fnall,
 241                            const gmx_output_env_t *oenv);
 242
 243 void print_one (const gmx_output_env_t *oenv, const char *base,
 244                 const char *name,
 245                 const char *title, const char *ylabel, int nf,
 246                 real time[], real data[]);
 247
 248 /* Routines from g_hbond */
 249 void analyse_corr(int n, real t[], real ct[], real nt[], real kt[],
 250                   real sigma_ct[], real sigma_nt[], real sigma_kt[],
 251                   real fit_start, real temp);
 252
 253 void compute_derivative(int nn, const real x[], const real y[], real dydx[]);
 254
 255 #endif