src/gromacs/gmxana/pp2shift.c

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