src/gromacs/gmxana/pp2shift.c

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  37 #ifdef HAVE_CONFIG_H
  38 #include <config.h>
  39 #endif
  40
  41 #include <stdlib.h>
  42 #include <math.h>
  43 #include "typedefs.h"
  44 #include "gromacs/utility/futil.h"
  45 #include "macros.h"
  46 #include "gromacs/math/units.h"
  47 #include "gromacs/utility/smalloc.h"
  48 #include "gstat.h"
  49 #include "gromacs/fileio/matio.h"
  50 #include "copyrite.h"
  51 #include "gromacs/utility/fatalerror.h"
  52
  53 typedef struct {
  54     int    nx, ny;
  55     real   dx, dy;
  56     real **data;
  57 } t_shiftdata;
  58
  59 static real interpolate(real phi, real psi, t_shiftdata *sd)
  60 {
  61     int  iphi, ipsi, iphi1, ipsi1;
  62     real fphi, fpsi, wx0, wx1, wy0, wy1;
  63
  64     /*phi  += M_PI;
  65        if (phi > 2*M_PI) phi -= 2*M_PI;
  66        psi  += M_PI;
  67        if (psi > 2*M_PI) psi -= 2*M_PI;
  68      */
  69     while (phi < 0)
  70     {
  71         phi += 2*M_PI;
  72     }
  73     while (psi < 0)
  74     {
  75         psi += 2*M_PI;
  76     }
  77     phi    = 2*M_PI-phi;
  78
  79     fphi  = phi*sd->dx;
  80     fpsi  = psi*sd->dy;
  81
  82     iphi  = (int)fphi;
  83     ipsi  = (int)fpsi;
  84     fphi -= iphi; /* Fraction (offset from gridpoint) */
  85     fpsi -= ipsi;
  86
  87     wx0   = 1.0-fphi;
  88     wx1   = fphi;
  89     wy0   = 1.0-fpsi;
  90     wy1   = fpsi;
  91     iphi  = iphi % sd->nx;
  92     ipsi  = ipsi % sd->ny;
  93     iphi1 = (iphi+1) % sd->nx;
  94     ipsi1 = (ipsi+1) % sd->ny;
  95
  96     return (sd->data[iphi]  [ipsi]  * wx0*wy0 +
  97             sd->data[iphi1] [ipsi]  * wx1*wy0 +
  98             sd->data[iphi]  [ipsi1] * wx0*wy1 +
  99             sd->data[iphi1] [ipsi1] * wx1*wy1);
 100 }
 101
 102 static void dump_sd(const char *fn, t_shiftdata *sd)
 103 {
 104     FILE  *fp;
 105     int    i, j;
 106     char   buf[256];
 107     int    nnx, nny, nfac = 4, nlevels = 20;
 108     real   phi, psi, *x_phi, *y_psi, **newdata;
 109     real   lo, hi;
 110     t_rgb  rlo = { 1, 0, 0 }, rhi = { 0, 0, 1 };
 111
 112     nnx = sd->nx*nfac+1;
 113     nny = sd->ny*nfac+1;
 114     snew(x_phi, nnx);
 115     snew(y_psi, nny);
 116     snew(newdata, nnx);
 117     lo =  100000;
 118     hi = -100000;
 119     for (i = 0; (i < nnx); i++)
 120     {
 121         snew(newdata[i], nny);
 122         phi      = i*2*M_PI/(nnx-1);
 123         x_phi[i] = phi*RAD2DEG-180;
 124         for (j = 0; (j < nny); j++)
 125         {
 126             psi = j*2*M_PI/(nny-1);
 127             if (i == 0)
 128             {
 129                 y_psi[j] = psi*RAD2DEG-180;
 130             }
 131             /*if (((i % nfac) == 0) && ((j % nfac) == 0))
 132                newdata[i][j] = sd->data[i/nfac][j/nfac];
 133                else*/
 134             newdata[i][j] = interpolate(phi, psi, sd);
 135             lo            = min(lo, newdata[i][j]);
 136             hi            = max(hi, newdata[i][j]);
 137         }
 138     }
 139     sprintf(buf, "%s.xpm", fn);
 140     fp = gmx_ffopen(buf, "w");
 141     write_xpm(fp, 0, fn, fn, "Phi", "Psi", nnx, nny,
 142               x_phi, y_psi, newdata, lo, hi, rlo, rhi, &nlevels);
 143     for (i = 0; (i < nnx); i++)
 144     {
 145         sfree(newdata[i]);
 146     }
 147     sfree(newdata);
 148     sfree(x_phi);
 149     sfree(y_psi);
 150 }
 151
 152 static t_shiftdata *read_shifts(const char *fn)
 153 {
 154     FILE        *fp;
 155     double       xx;
 156     int          i, j, nx, ny;
 157     t_shiftdata *sd;
 158
 159     snew(sd, 1);
 160     fp = libopen(fn);
 161     if (2 != fscanf(fp, "%d%d", &nx, &ny))
 162     {
 163         gmx_fatal(FARGS, "Error reading from file %s", fn);
 164     }
 165
 166     sd->nx = nx;
 167     sd->ny = ny;
 168     sd->dx = nx/(2*M_PI);
 169     sd->dy = ny/(2*M_PI);
 170     snew(sd->data, nx+1);
 171     for (i = 0; (i <= nx); i++)
 172     {
 173         snew(sd->data[i], ny+1);
 174         for (j = 0; (j < ny); j++)
 175         {
 176             if (i == nx)
 177             {
 178                 sd->data[i][j] = sd->data[0][j];
 179             }
 180             else
 181             {
 182                 if (1 != fscanf(fp, "%lf", &xx))
 183                 {
 184                     gmx_fatal(FARGS, "Error reading from file %s", fn);
 185                 }
 186                 sd->data[i][j] = xx;
 187             }
 188         }
 189         sd->data[i][j] = sd->data[i][0];
 190     }
 191     gmx_ffclose(fp);
 192
 193     if (bDebugMode())
 194     {
 195         dump_sd(fn, sd);
 196     }
 197
 198     return sd;
 199 }
 200
 201
 202 static void done_shifts(t_shiftdata *sd)
 203 {
 204     int i;
 205
 206     for (i = 0; (i <= sd->nx); i++)
 207     {
 208         sfree(sd->data[i]);
 209     }
 210     sfree(sd->data);
 211     sfree(sd);
 212 }
 213
 214 void do_pp2shifts(FILE *fp, int nf, int nlist, t_dlist dlist[], real **dih)
 215 {
 216     t_shiftdata *ca_sd, *co_sd, *ha_sd, *cb_sd;
 217     int          i, j, Phi, Psi;
 218     real         phi, psi;
 219     real         ca, co, ha, cb;
 220
 221     /* Read the shift files */
 222     ca_sd = read_shifts("ca-shift.dat");
 223     cb_sd = read_shifts("cb-shift.dat");
 224     ha_sd = read_shifts("ha-shift.dat");
 225     co_sd = read_shifts("co-shift.dat");
 226
 227     fprintf(fp, "\n *** Chemical shifts from the chemical shift index ***\n");
 228     please_cite(fp, "Wishart98a");
 229     fprintf(fp, "%12s  %10s  %10s  %10s  %10s\n",
 230             "Residue", "delta Ca", "delta Ha", "delta CO", "delta Cb");
 231     for (i = 0; (i < nlist); i++)
 232     {
 233         if ((has_dihedral(edPhi, &(dlist[i]))) &&
 234             (has_dihedral(edPsi, &(dlist[i]))))
 235         {
 236             Phi = dlist[i].j0[edPhi];
 237             Psi = dlist[i].j0[edPsi];
 238             ca  = cb = co = ha = 0;
 239             for (j = 0; (j < nf); j++)
 240             {
 241                 phi = dih[Phi][j];
 242                 psi = dih[Psi][j];
 243
 244                 ca += interpolate(phi, psi, ca_sd);
 245                 cb += interpolate(phi, psi, cb_sd);
 246                 co += interpolate(phi, psi, co_sd);
 247                 ha += interpolate(phi, psi, ha_sd);
 248             }
 249             fprintf(fp, "%12s  %10g  %10g  %10g  %10g\n",
 250                     dlist[i].name, ca/nf, ha/nf, co/nf, cb/nf);
 251         }
 252     }
 253     fprintf(fp, "\n");
 254
 255     /* Free memory */
 256     done_shifts(ca_sd);
 257     done_shifts(cb_sd);
 258     done_shifts(co_sd);
 259     done_shifts(ha_sd);
 260 }