src/gromacs/gmxana/pp2shift.cpp

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