src/gromacs/gmxana/gmx_wheel.cpp

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  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     t_psdata   out;
  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     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     t_psdata   out;
 164     int        i, slen;
 165     real       ring, inner, outer;
 166     real       xc, yc, box;
 167
 168     inner = 60.0;
 169     slen  = 0;
 170     for (i = 0; (i < nres); i++)
 171     {
 172         slen = std::max(slen, static_cast<int>(strlen(resnm[i])));
 173     }
 174     fprintf(stderr, "slen = %d\n", slen);
 175     ring  = slen*fontwidth;
 176     outer = inner+ring;
 177     box   = (1+gmx::exactDiv(nres, 2*angle))*outer;
 178
 179     out = ps_open(fn, 0, 0, 2.0*box, 2.0*box);
 180     xc  = box;
 181     yc  = box;
 182
 183     ps_font(out, efontHELV, 1.5*fontsize);
 184     ps_translate(out, xc, yc);
 185     ps_color(out, 0, 0, 0);
 186     if (title)
 187     {
 188         ps_ctext(out, 0, -fontsize*1.5/2.0, title, eXCenter);
 189     }
 190     ps_font(out, efontHELV, fontsize);
 191
 192     ps_rotate(out, rot0);
 193     for (i = 0; (i < nres); )
 194     {
 195         if ((i % 5) == 4)
 196         {
 197             ps_color(out, gray, gray, 1.0);
 198             ps_fillarcslice(out, 0, 0, inner, outer, -angle, angle);
 199             ps_color(out, 0, 0, 0);
 200         }
 201         ps_arcslice(out, 0, 0, inner, outer, -angle, angle);
 202
 203         ps_ctext(out, inner+fontwidth, -fontsize/2.0, resnm[i], eXLeft);
 204         ps_rotate(out, -2*angle);
 205         i++;
 206
 207         if ((i % (2*angle)) == 0)
 208         {
 209             inner  = outer;
 210             outer += ring;
 211         }
 212     }
 213     ps_close(out);
 214 }
 215
 216 int gmx_wheel(int argc, char *argv[])
 217 {
 218     const char       *desc[] = {
 219         "[THISMODULE] plots a helical wheel representation of your sequence.",
 220         "The input sequence is in the [REF].dat[ref] file where the first line contains",
 221         "the number of residues and each consecutive line contains a residue "
 222         "name."
 223     };
 224     gmx_output_env_t *oenv;
 225     static real       rot0  = 0;
 226     static gmx_bool   bNum  = TRUE;
 227     static char      *title = nullptr;
 228     static int        r0    = 1;
 229     t_pargs           pa [] = {
 230         { "-r0",  FALSE, etINT, {&r0},
 231           "The first residue number in the sequence" },
 232         { "-rot0", FALSE, etREAL, {&rot0},
 233           "Rotate around an angle initially (90 degrees makes sense)" },
 234         { "-T",   FALSE, etSTR, {&title},
 235           "Plot a title in the center of the wheel (must be shorter than 10 characters, or it will overwrite the wheel)" },
 236         { "-nn",  FALSE, etBOOL, {&bNum},
 237           "Toggle numbers" }
 238     };
 239     t_filenm          fnm[] = {
 240         { efDAT, "-f", nullptr,  ffREAD  },
 241         { efEPS, "-o", nullptr,  ffWRITE }
 242     };
 243 #define NFILE asize(fnm)
 244
 245     int    i, nres;
 246     char **resnm;
 247
 248     if (!parse_common_args(&argc, argv, 0, NFILE, fnm, asize(pa), pa,
 249                            asize(desc), desc, 0, nullptr, &oenv))
 250     {
 251         return 0;
 252     }
 253
 254     for (i = 1; (i < argc); i++)
 255     {
 256         if (std::strcmp(argv[i], "-r0") == 0)
 257         {
 258             r0 = std::strtol(argv[++i], nullptr, 10);
 259             fprintf(stderr, "First residue is %d\n", r0);
 260         }
 261         else if (std::strcmp(argv[i], "-rot0") == 0)
 262         {
 263             rot0 = strtod(argv[++i], nullptr);
 264             fprintf(stderr, "Initial rotation is %g\n", rot0);
 265         }
 266         else if (std::strcmp(argv[i], "-T") == 0)
 267         {
 268             title = gmx_strdup(argv[++i]);
 269             fprintf(stderr, "Title will be '%s'\n", title);
 270         }
 271         else if (std::strcmp(argv[i], "-nn") == 0)
 272         {
 273             bNum = FALSE;
 274             fprintf(stderr, "No residue numbers\n");
 275         }
 276         else
 277         {
 278             gmx_fatal(FARGS, "Incorrect usage of option %s", argv[i]);
 279         }
 280     }
 281
 282     nres = get_lines(ftp2fn(efDAT, NFILE, fnm), &resnm);
 283     if (bNum)
 284     {
 285         wheel(ftp2fn(efEPS, NFILE, fnm), nres, resnm, r0, rot0, title);
 286     }
 287     else
 288     {
 289         wheel2(ftp2fn(efEPS, NFILE, fnm), nres, resnm, rot0, title);
 290     }
 291
 292     return 0;
 293 }