src/gromacs/gmxana/gmx_rama.cpp

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  37 #include "gmxpre.h"
  38
  39 #include <cmath>
  40 #include <cstring>
  41
  42 #include "gromacs/commandline/pargs.h"
  43 #include "gromacs/commandline/viewit.h"
  44 #include "gromacs/fileio/xvgr.h"
  45 #include "gromacs/gmxana/gmx_ana.h"
  46 #include "gromacs/gmxana/nrama.h"
  47 #include "gromacs/math/units.h"
  48 #include "gromacs/math/vec.h"
  49 #include "gromacs/utility/arraysize.h"
  50 #include "gromacs/utility/futil.h"
  51 #include "gromacs/utility/smalloc.h"
  52
  53
  54 static void plot_rama(FILE *out, t_xrama *xr)
  55 {
  56     int  i;
  57     real phi, psi;
  58
  59     for (i = 0; (i < xr->npp); i++)
  60     {
  61         phi = xr->dih[xr->pp[i].iphi].ang*RAD2DEG;
  62         psi = xr->dih[xr->pp[i].ipsi].ang*RAD2DEG;
  63         fprintf(out, "%g  %g  %s\n", phi, psi, xr->pp[i].label);
  64     }
  65 }
  66
  67 int gmx_rama(int argc, char *argv[])
  68 {
  69     const char       *desc[] = {
  70         "[THISMODULE] selects the [GRK]phi[grk]/[GRK]psi[grk] dihedral combinations from your topology file",
  71         "and computes these as a function of time.",
  72         "Using simple Unix tools such as [IT]grep[it] you can select out",
  73         "specific residues."
  74     };
  75
  76     FILE             *out;
  77     t_xrama          *xr;
  78     int               j;
  79     gmx_output_env_t *oenv;
  80     t_filenm          fnm[] = {
  81         { efTRX, "-f", nullptr,  ffREAD },
  82         { efTPR, nullptr, nullptr,  ffREAD },
  83         { efXVG, nullptr, "rama", ffWRITE }
  84     };
  85 #define NFILE asize(fnm)
  86
  87     if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME,
  88                            NFILE, fnm, 0, nullptr, asize(desc), desc, 0, nullptr, &oenv))
  89     {
  90         return 0;
  91     }
  92
  93
  94     snew(xr, 1);
  95     init_rama(oenv, ftp2fn(efTRX, NFILE, fnm), ftp2fn(efTPR, NFILE, fnm), xr, 3);
  96
  97     out = xvgropen(ftp2fn(efXVG, NFILE, fnm), "Ramachandran Plot", "Phi", "Psi", oenv);
  98     xvgr_line_props(out, 0, elNone, ecFrank, oenv);
  99     xvgr_view(out, 0.2, 0.2, 0.8, 0.8, oenv);
 100     xvgr_world(out, -180, -180, 180, 180, oenv);
 101     if (output_env_get_print_xvgr_codes(oenv))
 102     {
 103         fprintf(out, "@    xaxis  tick on\n@    xaxis  tick major 60\n@    xaxis  tick minor 30\n");
 104         fprintf(out, "@    yaxis  tick on\n@    yaxis  tick major 60\n@    yaxis  tick minor 30\n");
 105         fprintf(out, "@ s0 symbol 2\n@ s0 symbol size 0.4\n@ s0 symbol fill 1\n");
 106     }
 107     j = 0;
 108     do
 109     {
 110         plot_rama(out, xr);
 111         j++;
 112     }
 113     while (new_data(xr));
 114     fprintf(stderr, "\n");
 115     xvgrclose(out);
 116
 117     do_view(oenv, ftp2fn(efXVG, NFILE, fnm), nullptr);
 118
 119     return 0;
 120 }