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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"
54 static void plot_rama(FILE* out, t_xrama* xr)
59 for (i = 0; (i < xr->npp); i++)
61 phi = xr->dih[xr->pp[i].iphi].ang * gmx::c_rad2Deg;
62 psi = xr->dih[xr->pp[i].ipsi].ang * gmx::c_rad2Deg;
63 fprintf(out, "%g %g %s\n", phi, psi, xr->pp[i].label);
67 int gmx_rama(int argc, char* argv[])
69 const char* desc[] = {
70 "[THISMODULE] selects the [GRK]phi[grk]/[GRK]psi[grk] dihedral combinations from ",
71 "your topology file and computes these as a function of time.",
72 "Using simple Unix tools such as [IT]grep[it] you can select out specific residues."
78 gmx_output_env_t* oenv;
79 t_filenm fnm[] = { { efTRX, "-f", nullptr, ffREAD },
80 { efTPR, nullptr, nullptr, ffREAD },
81 { efXVG, nullptr, "rama", ffWRITE } };
82 #define NFILE asize(fnm)
84 if (!parse_common_args(
85 &argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME, NFILE, fnm, 0, nullptr, asize(desc), desc, 0, nullptr, &oenv))
92 init_rama(oenv, ftp2fn(efTRX, NFILE, fnm), ftp2fn(efTPR, NFILE, fnm), xr, 3);
94 out = xvgropen(ftp2fn(efXVG, NFILE, fnm), "Ramachandran Plot", "Phi", "Psi", oenv);
95 xvgr_line_props(out, 0, elNone, ecFrank, oenv);
96 xvgr_view(out, 0.2, 0.2, 0.8, 0.8, oenv);
97 xvgr_world(out, -180, -180, 180, 180, oenv);
98 if (output_env_get_print_xvgr_codes(oenv))
100 fprintf(out, "@ xaxis tick on\n@ xaxis tick major 60\n@ xaxis tick minor 30\n");
101 fprintf(out, "@ yaxis tick on\n@ yaxis tick major 60\n@ yaxis tick minor 30\n");
102 fprintf(out, "@ s0 symbol 2\n@ s0 symbol size 0.4\n@ s0 symbol fill 1\n");
109 } while (new_data(xr));
110 fprintf(stderr, "\n");
113 do_view(oenv, ftp2fn(efXVG, NFILE, fnm), nullptr);