src/gromacs/gmxana/pp2shift.cpp

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
   5  * Copyright (c) 2001-2004, The GROMACS development team.
   6  * Copyright (c) 2013,2014,2015,2018, by the GROMACS development team, led by
   7  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
   8  * and including many others, as listed in the AUTHORS file in the
   9  * top-level source directory and at http://www.gromacs.org.
  10  *
  11  * GROMACS is free software; you can redistribute it and/or
  12  * modify it under the terms of the GNU Lesser General Public License
  13  * as published by the Free Software Foundation; either version 2.1
  14  * of the License, or (at your option) any later version.
  15  *
  16  * GROMACS is distributed in the hope that it will be useful,
  17  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  18  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  19  * Lesser General Public License for more details.
  20  *
  21  * You should have received a copy of the GNU Lesser General Public
  22  * License along with GROMACS; if not, see
  23  * http://www.gnu.org/licenses, or write to the Free Software Foundation,
  24  * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
  25  *
  26  * If you want to redistribute modifications to GROMACS, please
  27  * consider that scientific software is very special. Version
  28  * control is crucial - bugs must be traceable. We will be happy to
  29  * consider code for inclusion in the official distribution, but
  30  * derived work must not be called official GROMACS. Details are found
  31  * in the README & COPYING files - if they are missing, get the
  32  * official version at http://www.gromacs.org.
  33  *
  34  * To help us fund GROMACS development, we humbly ask that you cite
  35  * the research papers on the package. Check out http://www.gromacs.org.
  36  */
  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/pleasecite.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     double       xx;
 154     int          i, j, nx, ny;
 155     t_shiftdata *sd;
 156
 157     snew(sd, 1);
 158     gmx::FilePtr fp = gmx::openLibraryFile(fn);
 159     if (2 != fscanf(fp.get(), "%d%d", &nx, &ny))
 160     {
 161         gmx_fatal(FARGS, "Error reading from file %s", fn);
 162     }
 163     GMX_ASSERT(nx > 0, "");
 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.get(), "%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
 190     if (bDebugMode())
 191     {
 192         dump_sd(fn, sd);
 193     }
 194
 195     return sd;
 196 }
 197
 198
 199 static void done_shifts(t_shiftdata *sd)
 200 {
 201     int i;
 202
 203     for (i = 0; (i <= sd->nx); i++)
 204     {
 205         sfree(sd->data[i]);
 206     }
 207     sfree(sd->data);
 208     sfree(sd);
 209 }
 210
 211 void do_pp2shifts(FILE *fp, int nf, int nlist, t_dlist dlist[], real **dih)
 212 {
 213     t_shiftdata *ca_sd, *co_sd, *ha_sd, *cb_sd;
 214     int          i, j, Phi, Psi;
 215     real         phi, psi;
 216     real         ca, co, ha, cb;
 217
 218     /* Read the shift files */
 219     ca_sd = read_shifts("ca-shift.dat");
 220     cb_sd = read_shifts("cb-shift.dat");
 221     ha_sd = read_shifts("ha-shift.dat");
 222     co_sd = read_shifts("co-shift.dat");
 223
 224     fprintf(fp, "\n *** Chemical shifts from the chemical shift index ***\n");
 225     please_cite(fp, "Wishart98a");
 226     fprintf(fp, "%12s  %10s  %10s  %10s  %10s\n",
 227             "Residue", "delta Ca", "delta Ha", "delta CO", "delta Cb");
 228     for (i = 0; (i < nlist); i++)
 229     {
 230         if ((has_dihedral(edPhi, &(dlist[i]))) &&
 231             (has_dihedral(edPsi, &(dlist[i]))))
 232         {
 233             Phi = dlist[i].j0[edPhi];
 234             Psi = dlist[i].j0[edPsi];
 235             ca  = cb = co = ha = 0;
 236             for (j = 0; (j < nf); j++)
 237             {
 238                 phi = dih[Phi][j];
 239                 psi = dih[Psi][j];
 240
 241                 ca += interpolate(phi, psi, ca_sd);
 242                 cb += interpolate(phi, psi, cb_sd);
 243                 co += interpolate(phi, psi, co_sd);
 244                 ha += interpolate(phi, psi, ha_sd);
 245             }
 246             fprintf(fp, "%12s  %10g  %10g  %10g  %10g\n",
 247                     dlist[i].name, ca/nf, ha/nf, co/nf, cb/nf);
 248         }
 249     }
 250     fprintf(fp, "\n");
 251
 252     /* Free memory */
 253     done_shifts(ca_sd);
 254     done_shifts(cb_sd);
 255     done_shifts(co_sd);
 256     done_shifts(ha_sd);
 257 }