src/gromacs/gmxana/gmx_wheel.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) 2013,2014,2015,2017,2018,2019, 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 <cstdio>
  41 #include <cstdlib>
  42 #include <cstring>
  43
  44 #include <algorithm>
  45
  46 #include "gromacs/commandline/pargs.h"
  47 #include "gromacs/fileio/writeps.h"
  48 #include "gromacs/gmxana/gmx_ana.h"
  49 #include "gromacs/gmxana/gstat.h"
  50 #include "gromacs/math/vec.h"
  51 #include "gromacs/utility/arraysize.h"
  52 #include "gromacs/utility/cstringutil.h"
  53 #include "gromacs/utility/fatalerror.h"
  54 #include "gromacs/utility/futil.h"
  55 #include "gromacs/utility/smalloc.h"
  56 #include "gromacs/utility/strdb.h"
  57
  58 static gmx_bool *bPhobics(int nres, char *resnm[])
  59 {
  60     int       i, nb;
  61     char    **cb;
  62     gmx_bool *bb;
  63
  64     nb = get_lines("phbres.dat", &cb);
  65     snew(bb, nres);
  66
  67     for (i = 0; (i < nres); i++)
  68     {
  69         if (search_str(nb, cb, resnm[i]) != -1)
  70         {
  71             bb[i] = TRUE;
  72         }
  73     }
  74     return bb;
  75 }
  76
  77 static void wheel(const char *fn, int nres, char *resnm[], int r0, real rot0, char *title)
  78 {
  79     const real fontsize  = 16;
  80     const real gray      = 0.9;
  81     const real fontasp   = 0.6;
  82     const real fontwidth = fontsize*fontasp;
  83
  84     int        i, sl, slen;
  85     real       ring, inner, outer;
  86     real       xc, yc, box;
  87     gmx_bool  *bPh;
  88     char     **rnms;
  89     char       sign;
  90
  91     inner = 75.0;
  92     slen  = 0;
  93     snew(rnms, nres);
  94     for (i = 0; (i < nres); i++)
  95     {
  96         snew(rnms[i], 256);
  97         sl   = std::strlen(resnm[i]);
  98         sign = resnm[i][sl-1];
  99         if ((sign == '+') || (sign == '-'))
 100         {
 101             resnm[i][sl-1] = '\0';
 102         }
 103         sprintf(rnms[i], "%s-%d", resnm[i], i+r0);
 104         if ((sign == '+') || (sign == '-'))
 105         {
 106             sl            = std::strlen(rnms[i]);
 107             rnms[i][sl]   = sign;
 108             rnms[i][sl+1] = '\0';
 109         }
 110
 111         slen = std::max(slen, static_cast<int>(std::strlen(rnms[i])));
 112     }
 113     ring  = (2+slen)*fontwidth;
 114     outer = inner+ring;
 115     box   = inner*1.5+(1+int{nres/18})*ring;
 116
 117     bPh = bPhobics(nres, resnm);
 118
 119     t_psdata out = ps_open(fn, 0, 0, 2.0*box, 2.0*box);
 120     xc  = box;
 121     yc  = box;
 122
 123     ps_font(&out, efontHELV, 1.5*fontsize);
 124     ps_translate(&out, xc, yc);
 125     if (title)
 126     {
 127         ps_ctext(&out, 0, -fontsize*1.5/2.0, title, eXCenter);
 128     }
 129     ps_font(&out, efontHELV, fontsize);
 130     ps_rotate(&out, rot0);
 131     for (i = 0; (i < nres); )
 132     {
 133         if (bPh[i])
 134         {
 135             ps_color(&out, gray, gray, gray);
 136             ps_fillarcslice(&out, 0, 0, inner, outer, -10, 10);
 137             ps_color(&out, 0, 0, 0);
 138         }
 139         ps_arcslice(&out, 0, 0, inner, outer, -10, 10);
 140
 141         ps_ctext(&out, inner+fontwidth, -fontsize/2.0, rnms[i], eXLeft);
 142         ps_rotate(&out, -100);
 143         i++;
 144
 145         if ((i % 18) == 0)
 146         {
 147             inner  = outer;
 148             outer += ring;
 149         }
 150     }
 151     ps_close(&out);
 152 }
 153
 154 static void wheel2(const char *fn, int nres, char *resnm[], real rot0, char *title)
 155 {
 156     const real fontsize  = 14;
 157     const real gray      = 0.9;
 158     const real fontasp   = 0.45;
 159     const int  angle     = 9;
 160     const real fontwidth = fontsize*fontasp;
 161
 162     int        i, slen;
 163     real       ring, inner, outer;
 164     real       xc, yc, box;
 165
 166     inner = 60.0;
 167     slen  = 0;
 168     for (i = 0; (i < nres); i++)
 169     {
 170         slen = std::max(slen, static_cast<int>(strlen(resnm[i])));
 171     }
 172     fprintf(stderr, "slen = %d\n", slen);
 173     ring  = slen*fontwidth;
 174     outer = inner+ring;
 175     box   = (1+gmx::exactDiv(nres, 2*angle))*outer;
 176
 177     t_psdata out = ps_open(fn, 0, 0, 2.0*box, 2.0*box);
 178     xc  = box;
 179     yc  = box;
 180
 181     ps_font(&out, efontHELV, 1.5*fontsize);
 182     ps_translate(&out, xc, yc);
 183     ps_color(&out, 0, 0, 0);
 184     if (title)
 185     {
 186         ps_ctext(&out, 0, -fontsize*1.5/2.0, title, eXCenter);
 187     }
 188     ps_font(&out, efontHELV, fontsize);
 189
 190     ps_rotate(&out, rot0);
 191     for (i = 0; (i < nres); )
 192     {
 193         if ((i % 5) == 4)
 194         {
 195             ps_color(&out, gray, gray, 1.0);
 196             ps_fillarcslice(&out, 0, 0, inner, outer, -angle, angle);
 197             ps_color(&out, 0, 0, 0);
 198         }
 199         ps_arcslice(&out, 0, 0, inner, outer, -angle, angle);
 200
 201         ps_ctext(&out, inner+fontwidth, -fontsize/2.0, resnm[i], eXLeft);
 202         ps_rotate(&out, -2*angle);
 203         i++;
 204
 205         if ((i % (2*angle)) == 0)
 206         {
 207             inner  = outer;
 208             outer += ring;
 209         }
 210     }
 211     ps_close(&out);
 212 }
 213
 214 int gmx_wheel(int argc, char *argv[])
 215 {
 216     const char       *desc[] = {
 217         "[THISMODULE] plots a helical wheel representation of your sequence.",
 218         "The input sequence is in the [REF].dat[ref] file where the first line contains",
 219         "the number of residues and each consecutive line contains a residue "
 220         "name."
 221     };
 222     gmx_output_env_t *oenv;
 223     static real       rot0  = 0;
 224     static gmx_bool   bNum  = TRUE;
 225     static char      *title = nullptr;
 226     static int        r0    = 1;
 227     t_pargs           pa [] = {
 228         { "-r0",  FALSE, etINT, {&r0},
 229           "The first residue number in the sequence" },
 230         { "-rot0", FALSE, etREAL, {&rot0},
 231           "Rotate around an angle initially (90 degrees makes sense)" },
 232         { "-T",   FALSE, etSTR, {&title},
 233           "Plot a title in the center of the wheel (must be shorter than 10 characters, or it will overwrite the wheel)" },
 234         { "-nn",  FALSE, etBOOL, {&bNum},
 235           "Toggle numbers" }
 236     };
 237     t_filenm          fnm[] = {
 238         { efDAT, "-f", nullptr,  ffREAD  },
 239         { efEPS, "-o", nullptr,  ffWRITE }
 240     };
 241 #define NFILE asize(fnm)
 242
 243     int    i, nres;
 244     char **resnm;
 245
 246     if (!parse_common_args(&argc, argv, 0, NFILE, fnm, asize(pa), pa,
 247                            asize(desc), desc, 0, nullptr, &oenv))
 248     {
 249         return 0;
 250     }
 251
 252     for (i = 1; (i < argc); i++)
 253     {
 254         if (std::strcmp(argv[i], "-r0") == 0)
 255         {
 256             r0 = std::strtol(argv[++i], nullptr, 10);
 257             fprintf(stderr, "First residue is %d\n", r0);
 258         }
 259         else if (std::strcmp(argv[i], "-rot0") == 0)
 260         {
 261             rot0 = strtod(argv[++i], nullptr);
 262             fprintf(stderr, "Initial rotation is %g\n", rot0);
 263         }
 264         else if (std::strcmp(argv[i], "-T") == 0)
 265         {
 266             title = gmx_strdup(argv[++i]);
 267             fprintf(stderr, "Title will be '%s'\n", title);
 268         }
 269         else if (std::strcmp(argv[i], "-nn") == 0)
 270         {
 271             bNum = FALSE;
 272             fprintf(stderr, "No residue numbers\n");
 273         }
 274         else
 275         {
 276             gmx_fatal(FARGS, "Incorrect usage of option %s", argv[i]);
 277         }
 278     }
 279
 280     nres = get_lines(ftp2fn(efDAT, NFILE, fnm), &resnm);
 281     if (bNum)
 282     {
 283         wheel(ftp2fn(efEPS, NFILE, fnm), nres, resnm, r0, rot0, title);
 284     }
 285     else
 286     {
 287         wheel2(ftp2fn(efEPS, NFILE, fnm), nres, resnm, rot0, title);
 288     }
 289
 290     return 0;
 291 }