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/matio.h"
  45 #include "gromacs/gmxana/gstat.h"
  46 #include "gromacs/math/units.h"
  47 #include "gromacs/utility/fatalerror.h"
  48 #include "gromacs/utility/futil.h"
  49 #include "gromacs/utility/gmxassert.h"
  50 #include "gromacs/utility/pleasecite.h"
  51 #include "gromacs/utility/smalloc.h"
  52
  53 typedef struct
  54 {
  55     int    nx, ny;
  56     real   dx, dy;
  57     real** data;
  58 } t_shiftdata;
  59
  60 static real interpolate(real phi, real psi, t_shiftdata* sd)
  61 {
  62     int  iphi, ipsi, iphi1, ipsi1;
  63     real fphi, fpsi, wx0, wx1, wy0, wy1;
  64
  65     /*phi  += M_PI;
  66        if (phi > 2*M_PI) phi -= 2*M_PI;
  67        psi  += M_PI;
  68        if (psi > 2*M_PI) psi -= 2*M_PI;
  69      */
  70     while (phi < 0)
  71     {
  72         phi += 2 * M_PI;
  73     }
  74     while (psi < 0)
  75     {
  76         psi += 2 * M_PI;
  77     }
  78     phi = 2 * M_PI - phi;
  79
  80     fphi = phi * sd->dx;
  81     fpsi = psi * sd->dy;
  82
  83     iphi = static_cast<int>(fphi);
  84     ipsi = static_cast<int>(fpsi);
  85     fphi -= iphi; /* Fraction (offset from gridpoint) */
  86     fpsi -= ipsi;
  87
  88     wx0   = 1.0 - fphi;
  89     wx1   = fphi;
  90     wy0   = 1.0 - fpsi;
  91     wy1   = fpsi;
  92     iphi  = iphi % sd->nx;
  93     ipsi  = ipsi % sd->ny;
  94     iphi1 = (iphi + 1) % sd->nx;
  95     ipsi1 = (ipsi + 1) % sd->ny;
  96
  97     return (sd->data[iphi][ipsi] * wx0 * wy0 + sd->data[iphi1][ipsi] * wx1 * wy0
  98             + sd->data[iphi][ipsi1] * wx0 * wy1 + 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, 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     double       xx;
 153     int          i, j, nx, ny;
 154     t_shiftdata* sd;
 155
 156     snew(sd, 1);
 157     gmx::FilePtr fp = gmx::openLibraryFile(fn);
 158     if (2 != fscanf(fp.get(), "%d%d", &nx, &ny))
 159     {
 160         gmx_fatal(FARGS, "Error reading from file %s", fn);
 161     }
 162     GMX_ASSERT(nx > 0, "");
 163     sd->nx = nx;
 164     sd->ny = ny;
 165     sd->dx = nx / (2 * M_PI);
 166     sd->dy = ny / (2 * M_PI);
 167     snew(sd->data, nx + 1);
 168     for (i = 0; (i <= nx); i++)
 169     {
 170         snew(sd->data[i], ny + 1);
 171         for (j = 0; (j < ny); j++)
 172         {
 173             if (i == nx)
 174             {
 175                 sd->data[i][j] = sd->data[0][j];
 176             }
 177             else
 178             {
 179                 if (1 != fscanf(fp.get(), "%lf", &xx))
 180                 {
 181                     gmx_fatal(FARGS, "Error reading from file %s", fn);
 182                 }
 183                 sd->data[i][j] = xx;
 184             }
 185         }
 186         sd->data[i][j] = sd->data[i][0];
 187     }
 188
 189     if (bDebugMode())
 190     {
 191         dump_sd(fn, sd);
 192     }
 193
 194     return sd;
 195 }
 196
 197
 198 static void done_shifts(t_shiftdata* sd)
 199 {
 200     int i;
 201
 202     for (i = 0; (i <= sd->nx); i++)
 203     {
 204         sfree(sd->data[i]);
 205     }
 206     sfree(sd->data);
 207     sfree(sd);
 208 }
 209
 210 void do_pp2shifts(FILE* fp, int nf, int nlist, t_dlist dlist[], real** dih)
 211 {
 212     t_shiftdata *ca_sd, *co_sd, *ha_sd, *cb_sd;
 213     int          i, j, Phi, Psi;
 214     real         phi, psi;
 215     real         ca, co, ha, cb;
 216
 217     /* Read the shift files */
 218     ca_sd = read_shifts("ca-shift.dat");
 219     cb_sd = read_shifts("cb-shift.dat");
 220     ha_sd = read_shifts("ha-shift.dat");
 221     co_sd = read_shifts("co-shift.dat");
 222
 223     fprintf(fp, "\n *** Chemical shifts from the chemical shift index ***\n");
 224     please_cite(fp, "Wishart98a");
 225     fprintf(fp, "%12s  %10s  %10s  %10s  %10s\n", "Residue", "delta Ca", "delta Ha", "delta CO",
 226             "delta Cb");
 227     for (i = 0; (i < nlist); i++)
 228     {
 229         if ((has_dihedral(edPhi, &(dlist[i]))) && (has_dihedral(edPsi, &(dlist[i]))))
 230         {
 231             Phi = dlist[i].j0[edPhi];
 232             Psi = dlist[i].j0[edPsi];
 233             ca = cb = co = ha = 0;
 234             for (j = 0; (j < nf); j++)
 235             {
 236                 phi = dih[Phi][j];
 237                 psi = dih[Psi][j];
 238
 239                 ca += interpolate(phi, psi, ca_sd);
 240                 cb += interpolate(phi, psi, cb_sd);
 241                 co += interpolate(phi, psi, co_sd);
 242                 ha += interpolate(phi, psi, ha_sd);
 243             }
 244             fprintf(fp, "%12s  %10g  %10g  %10g  %10g\n", dlist[i].name, ca / nf, ha / nf, co / nf,
 245                     cb / nf);
 246         }
 247     }
 248     fprintf(fp, "\n");
 249
 250     /* Free memory */
 251     done_shifts(ca_sd);
 252     done_shifts(cb_sd);
 253     done_shifts(co_sd);
 254     done_shifts(ha_sd);
 255 }