src/gromacs/gmxana/gmx_helix.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/confio.h"
  45 #include "gromacs/fileio/tpxio.h"
  46 #include "gromacs/fileio/trxio.h"
  47 #include "gromacs/fileio/xvgr.h"
  48 #include "gromacs/gmxana/fitahx.h"
  49 #include "gromacs/gmxana/gmx_ana.h"
  50 #include "gromacs/gmxana/gstat.h"
  51 #include "gromacs/gmxana/hxprops.h"
  52 #include "gromacs/math/utilities.h"
  53 #include "gromacs/math/vec.h"
  54 #include "gromacs/pbcutil/rmpbc.h"
  55 #include "gromacs/topology/topology.h"
  56 #include "gromacs/utility/arraysize.h"
  57 #include "gromacs/utility/fatalerror.h"
  58 #include "gromacs/utility/futil.h"
  59 #include "gromacs/utility/smalloc.h"
  60
  61 int gmx_helix(int argc, char *argv[])
  62 {
  63     const char        *desc[] = {
  64         "[THISMODULE] computes all kinds of helix properties. First, the peptide",
  65         "is checked to find the longest helical part, as determined by",
  66         "hydrogen bonds and [GRK]phi[grk]/[GRK]psi[grk] angles.",
  67         "That bit is fitted",
  68         "to an ideal helix around the [IT]z[it]-axis and centered around the origin.",
  69         "Then the following properties are computed:",
  70         "",
  71         " * Helix radius (file [TT]radius.xvg[tt]). This is merely the",
  72         "   RMS deviation in two dimensions for all C[GRK]alpha[grk] atoms.",
  73         "   it is calculated as [SQRT]([SUM][sum][SUB]i[sub] (x^2(i)+y^2(i)))/N[sqrt] where N is the number",
  74         "   of backbone atoms. For an ideal helix the radius is 0.23 nm.",
  75         " * Twist (file [TT]twist.xvg[tt]). The average helical angle per",
  76         "   residue is calculated. For an [GRK]alpha[grk]-helix it is 100 degrees,",
  77         "   for 3-10 helices it will be smaller, and ",
  78         "   for 5-helices it will be larger.",
  79         " * Rise per residue (file [TT]rise.xvg[tt]). The helical rise per",
  80         "   residue is plotted as the difference in [IT]z[it]-coordinate between C[GRK]alpha[grk]",
  81         "   atoms. For an ideal helix, this is 0.15 nm.",
  82         " * Total helix length (file [TT]len-ahx.xvg[tt]). The total length",
  83         "   of the",
  84         "   helix in nm. This is simply the average rise (see above) times the",
  85         "   number of helical residues (see below).",
  86         " * Helix dipole, backbone only (file [TT]dip-ahx.xvg[tt]).",
  87         " * RMS deviation from ideal helix, calculated for the C[GRK]alpha[grk]",
  88         "   atoms only (file [TT]rms-ahx.xvg[tt]).",
  89         " * Average C[GRK]alpha[grk] - C[GRK]alpha[grk] dihedral angle (file [TT]phi-ahx.xvg[tt]).",
  90         " * Average [GRK]phi[grk] and [GRK]psi[grk] angles (file [TT]phipsi.xvg[tt]).",
  91         " * Ellipticity at 222 nm according to Hirst and Brooks."
  92     };
  93     static gmx_bool    bCheck = FALSE, bFit = TRUE, bDBG = FALSE, bEV = FALSE;
  94     static int         rStart = 0, rEnd = 0, r0 = 1;
  95     t_pargs            pa []  = {
  96         { "-r0", FALSE, etINT, {&r0},
  97           "The first residue number in the sequence" },
  98         { "-q",  FALSE, etBOOL, {&bCheck},
  99           "Check at every step which part of the sequence is helical" },
 100         { "-F",  FALSE, etBOOL, {&bFit},
 101           "Toggle fit to a perfect helix" },
 102         { "-db", FALSE, etBOOL, {&bDBG},
 103           "Print debug info" },
 104         { "-ev", FALSE, etBOOL, {&bEV},
 105           "Write a new 'trajectory' file for ED" },
 106         { "-ahxstart", FALSE, etINT, {&rStart},
 107           "First residue in helix" },
 108         { "-ahxend", FALSE, etINT, {&rEnd},
 109           "Last residue in helix" }
 110     };
 111
 112     typedef struct { //NOLINT(clang-analyzer-optin.performance.Padding)
 113         FILE       *fp, *fp2;
 114         gmx_bool    bfp2;
 115         const char *filenm;
 116         const char *title;
 117         const char *xaxis;
 118         const char *yaxis;
 119         real        val;
 120     } t_xvgrfile;
 121
 122     t_xvgrfile        xf[efhNR] = {
 123         { nullptr, nullptr, TRUE,  "radius",  "Helix radius",               nullptr, "r (nm)", 0.0 },
 124         { nullptr, nullptr, TRUE,  "twist",   "Twist per residue",          nullptr, "Angle (deg)", 0.0 },
 125         { nullptr, nullptr, TRUE,  "rise",    "Rise per residue",           nullptr, "Rise (nm)", 0.0 },
 126         { nullptr, nullptr, FALSE, "len-ahx", "Length of the Helix",        nullptr, "Length (nm)", 0.0 },
 127         { nullptr, nullptr, FALSE, "dip-ahx", "Helix Backbone Dipole",      nullptr, "rq (nm e)", 0.0 },
 128         { nullptr, nullptr, TRUE,  "rms-ahx", "RMS Deviation from Ideal Helix", nullptr, "RMS (nm)", 0.0 },
 129         { nullptr, nullptr, FALSE, "rmsa-ahx", "Average RMSD per Residue",   "Residue", "RMS (nm)", 0.0 },
 130         { nullptr, nullptr, FALSE,  "cd222",   "Ellipticity at 222 nm", nullptr, "nm", 0.0 },
 131         { nullptr, nullptr, TRUE,  "pprms",   "RMS Distance from \\8a\\4-helix", nullptr, "deg", 0.0 },
 132         { nullptr, nullptr, TRUE,  "caphi",   "Average Ca-Ca Dihedral",     nullptr, "\\8F\\4(deg)", 0.0 },
 133         { nullptr, nullptr, TRUE,  "phi",     "Average \\8F\\4 angles", nullptr, "deg", 0.0 },
 134         { nullptr, nullptr, TRUE,  "psi",     "Average \\8Y\\4 angles", nullptr, "deg", 0.0 },
 135         { nullptr, nullptr, TRUE,  "hb3",     "Average n-n+3 hbond length", nullptr, "nm", 0.0 },
 136         { nullptr, nullptr, TRUE,  "hb4",     "Average n-n+4 hbond length", nullptr, "nm", 0.0 },
 137         { nullptr, nullptr, TRUE,  "hb5",     "Average n-n+5 hbond length", nullptr, "nm", 0.0 },
 138         { nullptr, nullptr, FALSE,  "JCaHa",   "J-Coupling Values",        "Residue", "Hz", 0.0 },
 139         { nullptr, nullptr, FALSE,  "helicity", "Helicity per Residue",     "Residue", "% of time", 0.0 }
 140     };
 141
 142     gmx_output_env_t *oenv;
 143     char              buf[54];
 144     t_trxstatus      *status;
 145     int               natoms, nres;
 146     t_bb             *bb;
 147     int               i, j, nall, nbb, nca, teller;
 148     int              *bbindex, *caindex, *allindex;
 149     t_topology       *top;
 150     int               ePBC;
 151     rvec             *x, *xref;
 152     real              t;
 153     real              rms;
 154     matrix            box;
 155     gmx_rmpbc_t       gpbc = nullptr;
 156     gmx_bool          bRange;
 157     t_filenm          fnm[] = {
 158         { efTPR, nullptr,  nullptr,   ffREAD  },
 159         { efNDX, nullptr,  nullptr,   ffREAD  },
 160         { efTRX, "-f",  nullptr,   ffREAD  },
 161         { efSTO, "-cz", "zconf", ffWRITE },
 162     };
 163 #define NFILE asize(fnm)
 164
 165     if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME,
 166                            NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, nullptr, &oenv))
 167     {
 168         return 0;
 169     }
 170
 171     bRange = (opt2parg_bSet("-ahxstart", asize(pa), pa) &&
 172               opt2parg_bSet("-ahxend", asize(pa), pa));
 173
 174     top = read_top(ftp2fn(efTPR, NFILE, fnm), &ePBC);
 175
 176     natoms = read_first_x(oenv, &status, opt2fn("-f", NFILE, fnm), &t, &x, box);
 177
 178     if (natoms != top->atoms.nr)
 179     {
 180         gmx_fatal(FARGS, "Sorry can only run when the number of atoms in the run input file (%d) is equal to the number in the trajectory (%d)",
 181                   top->atoms.nr, natoms);
 182     }
 183
 184     bb = mkbbind(ftp2fn(efNDX, NFILE, fnm), &nres, &nbb, r0, &nall, &allindex,
 185                  top->atoms.atomname, top->atoms.atom, top->atoms.resinfo);
 186     snew(bbindex, natoms);
 187     snew(caindex, nres);
 188
 189     fprintf(stderr, "nall=%d\n", nall);
 190
 191     /* Open output files, default x-axis is time */
 192     for (i = 0; (i < efhNR); i++)
 193     {
 194         sprintf(buf, "%s.xvg", xf[i].filenm);
 195         remove(buf);
 196         xf[i].fp = xvgropen(buf, xf[i].title,
 197                             xf[i].xaxis ? xf[i].xaxis : "Time (ps)",
 198                             xf[i].yaxis, oenv);
 199         if (xf[i].bfp2)
 200         {
 201             sprintf(buf, "%s.out", xf[i].filenm);
 202             remove(buf);
 203             xf[i].fp2 = gmx_ffopen(buf, "w");
 204         }
 205     }
 206
 207     /* Read reference frame from tpx file to compute helix length */
 208     snew(xref, top->atoms.nr);
 209     read_tpx(ftp2fn(efTPR, NFILE, fnm),
 210              nullptr, nullptr, nullptr, xref, nullptr, nullptr);
 211     calc_hxprops(nres, bb, xref);
 212     do_start_end(nres, bb, &nbb, bbindex, &nca, caindex, bRange, rStart, rEnd);
 213     sfree(xref);
 214     if (bDBG)
 215     {
 216         fprintf(stderr, "nca=%d, nbb=%d\n", nca, nbb);
 217         pr_bb(stdout, nres, bb);
 218     }
 219
 220     gpbc = gmx_rmpbc_init(&top->idef, ePBC, natoms);
 221
 222     teller = 0;
 223     do
 224     {
 225         if ((teller++ % 10) == 0)
 226         {
 227             fprintf(stderr, "\rt=%.2f", t);
 228             fflush(stderr);
 229         }
 230         gmx_rmpbc(gpbc, natoms, box, x);
 231
 232
 233         calc_hxprops(nres, bb, x);
 234         if (bCheck)
 235         {
 236             do_start_end(nres, bb, &nbb, bbindex, &nca, caindex, FALSE, 0, 0);
 237         }
 238
 239         if (nca >= 5)
 240         {
 241             rms = fit_ahx(nres, bb, natoms, nall, allindex, x, nca, caindex, bFit);
 242
 243             if (teller == 1)
 244             {
 245                 write_sto_conf(opt2fn("-cz", NFILE, fnm), "Helix fitted to Z-Axis",
 246                                &(top->atoms), x, nullptr, ePBC, box);
 247             }
 248
 249             xf[efhRAD].val   = radius(xf[efhRAD].fp2, nca, caindex, x);
 250             xf[efhTWIST].val = twist(nca, caindex, x);
 251             xf[efhRISE].val  = rise(nca, caindex, x);
 252             xf[efhLEN].val   = ahx_len(nca, caindex, x);
 253             xf[efhCD222].val = ellipticity(nres, bb);
 254             xf[efhDIP].val   = dip(nbb, bbindex, x, top->atoms.atom);
 255             xf[efhRMS].val   = rms;
 256             xf[efhCPHI].val  = ca_phi(nca, caindex, x);
 257             xf[efhPPRMS].val = pprms(xf[efhPPRMS].fp2, nres, bb);
 258
 259             for (j = 0; (j <= efhCPHI); j++)
 260             {
 261                 fprintf(xf[j].fp,   "%10g  %10g\n", t, xf[j].val);
 262             }
 263
 264             av_phipsi(xf[efhPHI].fp, xf[efhPSI].fp, xf[efhPHI].fp2, xf[efhPSI].fp2,
 265                       t, nres, bb);
 266             av_hblen(xf[efhHB3].fp, xf[efhHB3].fp2,
 267                      xf[efhHB4].fp, xf[efhHB4].fp2,
 268                      xf[efhHB5].fp, xf[efhHB5].fp2,
 269                      t, nres, bb);
 270         }
 271     }
 272     while (read_next_x(oenv, status, &t, x, box));
 273     fprintf(stderr, "\n");
 274
 275     gmx_rmpbc_done(gpbc);
 276
 277     close_trx(status);
 278
 279     for (i = 0; (i < nres); i++)
 280     {
 281         if (bb[i].nrms > 0)
 282         {
 283             fprintf(xf[efhRMSA].fp, "%10d  %10g\n", r0+i, bb[i].rmsa/bb[i].nrms);
 284         }
 285         fprintf(xf[efhAHX].fp, "%10d  %10g\n", r0+i, (bb[i].nhx*100.0)/static_cast<real>(teller));
 286         fprintf(xf[efhJCA].fp, "%10d  %10g\n",
 287                 r0+i, 140.3+(bb[i].jcaha/static_cast<double>(teller)));
 288     }
 289
 290     for (i = 0; (i < efhNR); i++)
 291     {
 292         xvgrclose(xf[i].fp);
 293         if (xf[i].bfp2)
 294         {
 295             xvgrclose(xf[i].fp2);
 296         }
 297         do_view(oenv, xf[i].filenm, "-nxy");
 298     }
 299
 300     return 0;
 301 }