src/gromacs/gmxana/gmx_wheel.cpp

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  38 #include "gmxpre.h"
  39
  40 #include <cmath>
  41 #include <cstdio>
  42 #include <cstdlib>
  43 #include <cstring>
  44
  45 #include <algorithm>
  46
  47 #include "gromacs/commandline/pargs.h"
  48 #include "gromacs/fileio/writeps.h"
  49 #include "gromacs/gmxana/gmx_ana.h"
  50 #include "gromacs/gmxana/gstat.h"
  51 #include "gromacs/math/vec.h"
  52 #include "gromacs/utility/arraysize.h"
  53 #include "gromacs/utility/cstringutil.h"
  54 #include "gromacs/utility/fatalerror.h"
  55 #include "gromacs/utility/futil.h"
  56 #include "gromacs/utility/smalloc.h"
  57 #include "gromacs/utility/strdb.h"
  58
  59 static gmx_bool* bPhobics(int nres, char* resnm[])
  60 {
  61     int       i, nb;
  62     char**    cb;
  63     gmx_bool* bb;
  64
  65     nb = get_lines("phbres.dat", &cb);
  66     snew(bb, nres);
  67
  68     for (i = 0; (i < nres); i++)
  69     {
  70         if (search_str(nb, cb, resnm[i]) != -1)
  71         {
  72             bb[i] = TRUE;
  73         }
  74     }
  75     return bb;
  76 }
  77
  78 static void wheel(const char* fn, int nres, char* resnm[], int r0, real rot0, char* title)
  79 {
  80     const real fontsize  = 16;
  81     const real gray      = 0.9;
  82     const real fontasp   = 0.6;
  83     const real fontwidth = fontsize * fontasp;
  84
  85     int       i, sl, slen;
  86     real      ring, inner, outer;
  87     real      xc, yc, box;
  88     gmx_bool* bPh;
  89     char**    rnms;
  90     char      sign;
  91
  92     inner = 75.0;
  93     slen  = 0;
  94     snew(rnms, nres);
  95     for (i = 0; (i < nres); i++)
  96     {
  97         snew(rnms[i], 256);
  98         sl   = std::strlen(resnm[i]);
  99         sign = resnm[i][sl - 1];
 100         if ((sign == '+') || (sign == '-'))
 101         {
 102             resnm[i][sl - 1] = '\0';
 103         }
 104         sprintf(rnms[i], "%s-%d", resnm[i], i + r0);
 105         if ((sign == '+') || (sign == '-'))
 106         {
 107             sl              = std::strlen(rnms[i]);
 108             rnms[i][sl]     = sign;
 109             rnms[i][sl + 1] = '\0';
 110         }
 111
 112         slen = std::max(slen, static_cast<int>(std::strlen(rnms[i])));
 113     }
 114     ring  = (2 + slen) * fontwidth;
 115     outer = inner + ring;
 116     box   = inner * 1.5 + (1 + int{ nres / 18 }) * ring;
 117
 118     bPh = bPhobics(nres, resnm);
 119
 120     t_psdata out = ps_open(fn, 0, 0, 2.0 * box, 2.0 * box);
 121     xc           = box;
 122     yc           = box;
 123
 124     ps_font(&out, efontHELV, 1.5 * fontsize);
 125     ps_translate(&out, xc, yc);
 126     if (title)
 127     {
 128         ps_ctext(&out, 0, -fontsize * 1.5 / 2.0, title, eXCenter);
 129     }
 130     ps_font(&out, efontHELV, fontsize);
 131     ps_rotate(&out, rot0);
 132     for (i = 0; (i < nres);)
 133     {
 134         if (bPh[i])
 135         {
 136             ps_color(&out, gray, gray, gray);
 137             ps_fillarcslice(&out, 0, 0, inner, outer, -10, 10);
 138             ps_color(&out, 0, 0, 0);
 139         }
 140         ps_arcslice(&out, 0, 0, inner, outer, -10, 10);
 141
 142         ps_ctext(&out, inner + fontwidth, -fontsize / 2.0, rnms[i], eXLeft);
 143         ps_rotate(&out, -100);
 144         i++;
 145
 146         if ((i % 18) == 0)
 147         {
 148             inner = outer;
 149             outer += ring;
 150         }
 151     }
 152     ps_close(&out);
 153 }
 154
 155 static void wheel2(const char* fn, int nres, char* resnm[], real rot0, char* title)
 156 {
 157     const real fontsize  = 14;
 158     const real gray      = 0.9;
 159     const real fontasp   = 0.45;
 160     const int  angle     = 9;
 161     const real fontwidth = fontsize * fontasp;
 162
 163     int  i, slen;
 164     real ring, inner, outer;
 165     real xc, yc, box;
 166
 167     inner = 60.0;
 168     slen  = 0;
 169     for (i = 0; (i < nres); i++)
 170     {
 171         slen = std::max(slen, static_cast<int>(strlen(resnm[i])));
 172     }
 173     fprintf(stderr, "slen = %d\n", slen);
 174     ring  = slen * fontwidth;
 175     outer = inner + ring;
 176     box   = (1 + gmx::exactDiv(nres, 2 * angle)) * outer;
 177
 178     t_psdata out = ps_open(fn, 0, 0, 2.0 * box, 2.0 * box);
 179     xc           = box;
 180     yc           = box;
 181
 182     ps_font(&out, efontHELV, 1.5 * fontsize);
 183     ps_translate(&out, xc, yc);
 184     ps_color(&out, 0, 0, 0);
 185     if (title)
 186     {
 187         ps_ctext(&out, 0, -fontsize * 1.5 / 2.0, title, eXCenter);
 188     }
 189     ps_font(&out, efontHELV, fontsize);
 190
 191     ps_rotate(&out, rot0);
 192     for (i = 0; (i < nres);)
 193     {
 194         if ((i % 5) == 4)
 195         {
 196             ps_color(&out, gray, gray, 1.0);
 197             ps_fillarcslice(&out, 0, 0, inner, outer, -angle, angle);
 198             ps_color(&out, 0, 0, 0);
 199         }
 200         ps_arcslice(&out, 0, 0, inner, outer, -angle, angle);
 201
 202         ps_ctext(&out, inner + fontwidth, -fontsize / 2.0, resnm[i], eXLeft);
 203         ps_rotate(&out, -2 * angle);
 204         i++;
 205
 206         if ((i % (2 * angle)) == 0)
 207         {
 208             inner = outer;
 209             outer += ring;
 210         }
 211     }
 212     ps_close(&out);
 213 }
 214
 215 int gmx_wheel(int argc, char* argv[])
 216 {
 217     const char* desc[] = {
 218         "[THISMODULE] plots a helical wheel representation of your sequence.",
 219         "The input sequence is in the [REF].dat[ref] file where the first line contains",
 220         "the number of residues and each consecutive line contains a residue "
 221         "name."
 222     };
 223     gmx_output_env_t* oenv;
 224     static real       rot0  = 0;
 225     static gmx_bool   bNum  = TRUE;
 226     static char*      title = nullptr;
 227     static int        r0    = 1;
 228     t_pargs  pa[]  = { { "-r0", FALSE, etINT, { &r0 }, "The first residue number in the sequence" },
 229                      { "-rot0",
 230                        FALSE,
 231                        etREAL,
 232                        { &rot0 },
 233                        "Rotate around an angle initially (90 degrees makes sense)" },
 234                      { "-T",
 235                        FALSE,
 236                        etSTR,
 237                        { &title },
 238                        "Plot a title in the center of the wheel (must be shorter than 10 "
 239                        "characters, or it will overwrite the wheel)" },
 240                      { "-nn", FALSE, etBOOL, { &bNum }, "Toggle numbers" } };
 241     t_filenm fnm[] = { { efDAT, "-f", nullptr, ffREAD }, { efEPS, "-o", nullptr, ffWRITE } };
 242 #define NFILE asize(fnm)
 243
 244     int    i, nres;
 245     char** resnm;
 246
 247     if (!parse_common_args(&argc, argv, 0, NFILE, fnm, asize(pa), pa, 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 }