src/gromacs/gmxana/gmx_dyndom.cpp

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  37 #include "gmxpre.h"
  38
  39 #include <cmath>
  40
  41 #include "gromacs/commandline/pargs.h"
  42 #include "gromacs/fileio/confio.h"
  43 #include "gromacs/fileio/trxio.h"
  44 #include "gromacs/gmxana/gmx_ana.h"
  45 #include "gromacs/math/3dtransforms.h"
  46 #include "gromacs/math/units.h"
  47 #include "gromacs/math/vec.h"
  48 #include "gromacs/topology/atoms.h"
  49 #include "gromacs/topology/index.h"
  50 #include "gromacs/topology/topology.h"
  51 #include "gromacs/utility/arraysize.h"
  52 #include "gromacs/utility/fatalerror.h"
  53 #include "gromacs/utility/smalloc.h"
  54
  55 static void rot_conf(t_atoms *atoms, const rvec x[], const rvec v[], real trans, real angle,
  56                      rvec head, rvec tail, int isize, int index[],
  57                      rvec xout[], rvec vout[])
  58 {
  59     rvec     arrow, xcm;
  60     real     theta, phi, arrow_len;
  61     mat4     Rx, Ry, Rz, Rinvy, Rinvz, Mtot;
  62     mat4     temp1, temp2, temp3;
  63     vec4     xv;
  64     int      i, ai;
  65
  66     rvec_sub(tail, head, arrow);
  67     arrow_len = norm(arrow);
  68     if (debug)
  69     {
  70         fprintf(debug, "Arrow vector:   %10.4f  %10.4f  %10.4f\n",
  71                 arrow[XX], arrow[YY], arrow[ZZ]);
  72         fprintf(debug, "Effective translation %g nm\n", trans);
  73     }
  74     if (arrow_len == 0.0)
  75     {
  76         gmx_fatal(FARGS, "Arrow vector not given");
  77     }
  78
  79     /* Copy all aoms to output */
  80     for (i = 0; (i < atoms->nr); i++)
  81     {
  82         copy_rvec(x[i], xout[i]);
  83         copy_rvec(v[i], vout[i]);
  84     }
  85
  86     /* Compute center of mass and move atoms there */
  87     clear_rvec(xcm);
  88     for (i = 0; (i < isize); i++)
  89     {
  90         rvec_inc(xcm, x[index[i]]);
  91     }
  92     for (i = 0; (i < DIM); i++)
  93     {
  94         xcm[i] /= isize;
  95     }
  96     if (debug)
  97     {
  98         fprintf(debug, "Center of mass: %10.4f  %10.4f  %10.4f\n",
  99                 xcm[XX], xcm[YY], xcm[ZZ]);
 100     }
 101     for (i = 0; (i < isize); i++)
 102     {
 103         rvec_sub(x[index[i]], xcm, xout[index[i]]);
 104     }
 105
 106     /* Compute theta and phi that describe the arrow */
 107     theta = std::acos(arrow[ZZ]/arrow_len);
 108     phi   = std::atan2(arrow[YY]/arrow_len, arrow[XX]/arrow_len);
 109     if (debug)
 110     {
 111         fprintf(debug, "Phi = %.1f, Theta = %.1f\n", RAD2DEG*phi, RAD2DEG*theta);
 112     }
 113
 114     /* Now the total rotation matrix: */
 115     /* Rotate a couple of times */
 116     gmx_mat4_init_rotation(ZZ, -phi, Rz);
 117     gmx_mat4_init_rotation(YY, M_PI/2-theta, Ry);
 118     gmx_mat4_init_rotation(XX, angle*DEG2RAD, Rx);
 119     Rx[WW][XX] = trans;
 120     gmx_mat4_init_rotation(YY, theta-M_PI/2, Rinvy);
 121     gmx_mat4_init_rotation(ZZ, phi, Rinvz);
 122
 123     gmx_mat4_mmul(temp1, Ry, Rz);
 124     gmx_mat4_mmul(temp2, Rinvy, Rx);
 125     gmx_mat4_mmul(temp3, temp2, temp1);
 126     gmx_mat4_mmul(Mtot, Rinvz, temp3);
 127
 128     if (debug)
 129     {
 130         gmx_mat4_print(debug, "Rz", Rz);
 131         gmx_mat4_print(debug, "Ry", Ry);
 132         gmx_mat4_print(debug, "Rx", Rx);
 133         gmx_mat4_print(debug, "Rinvy", Rinvy);
 134         gmx_mat4_print(debug, "Rinvz", Rinvz);
 135         gmx_mat4_print(debug, "Mtot", Mtot);
 136     }
 137
 138     for (i = 0; (i < isize); i++)
 139     {
 140         ai = index[i];
 141         gmx_mat4_transform_point(Mtot, xout[ai], xv);
 142         rvec_add(xv, xcm, xout[ai]);
 143         gmx_mat4_transform_point(Mtot, v[ai], xv);
 144         copy_rvec(xv, vout[ai]);
 145     }
 146 }
 147
 148 int gmx_dyndom(int argc, char *argv[])
 149 {
 150     const char       *desc[] = {
 151         "[THISMODULE] reads a [REF].pdb[ref] file output from DynDom",
 152         "(http://www.cmp.uea.ac.uk/dyndom/).",
 153         "It reads the coordinates, the coordinates of the rotation axis,",
 154         "and an index file containing the domains.",
 155         "Furthermore, it takes the first and last atom of the arrow file",
 156         "as command line arguments (head and tail) and",
 157         "finally it takes the translation vector (given in DynDom info file)",
 158         "and the angle of rotation (also as command line arguments). If the angle",
 159         "determined by DynDom is given, one should be able to recover the",
 160         "second structure used for generating the DynDom output.",
 161         "Because of limited numerical accuracy this should be verified by",
 162         "computing an all-atom RMSD (using [gmx-confrms]) rather than by file",
 163         "comparison (using diff).[PAR]",
 164         "The purpose of this program is to interpolate and extrapolate the",
 165         "rotation as found by DynDom. As a result unphysical structures with",
 166         "long or short bonds, or overlapping atoms may be produced. Visual",
 167         "inspection, and energy minimization may be necessary to",
 168         "validate the structure."
 169     };
 170     static real       trans0 = 0;
 171     static rvec       head   = { 0, 0, 0 };
 172     static rvec       tail   = { 0, 0, 0 };
 173     static real       angle0 = 0, angle1 = 0, maxangle = 0;
 174     static int        label  = 0, nframes = 11;
 175     t_pargs           pa[]   = {
 176         { "-firstangle",    FALSE, etREAL, {&angle0},
 177           "Angle of rotation about rotation vector" },
 178         { "-lastangle",    FALSE, etREAL, {&angle1},
 179           "Angle of rotation about rotation vector" },
 180         { "-nframe",   FALSE, etINT,  {&nframes},
 181           "Number of steps on the pathway" },
 182         { "-maxangle", FALSE, etREAL, {&maxangle},
 183           "DymDom dtermined angle of rotation about rotation vector" },
 184         { "-trans",    FALSE, etREAL, {&trans0},
 185           "Translation (Angstrom) along rotation vector (see DynDom info file)" },
 186         { "-head",     FALSE, etRVEC, {head},
 187           "First atom of the arrow vector" },
 188         { "-tail",     FALSE, etRVEC, {tail},
 189           "Last atom of the arrow vector" }
 190     };
 191     int               i, j, natoms, isize;
 192     t_trxstatus      *status;
 193     int              *index = nullptr, *index_all;
 194     char             *grpname;
 195     real              angle, trans;
 196     rvec             *x, *v, *xout, *vout;
 197     matrix            box;
 198     gmx_output_env_t *oenv;
 199
 200     t_filenm          fnm[] = {
 201         { efPDB, "-f", "dyndom",  ffREAD },
 202         { efTRO, "-o", "rotated", ffWRITE },
 203         { efNDX, "-n", "domains", ffREAD }
 204     };
 205 #define NFILE asize(fnm)
 206
 207     if (!parse_common_args(&argc, argv, 0, NFILE, fnm, asize(pa), pa,
 208                            asize(desc), desc, 0, nullptr, &oenv))
 209     {
 210         return 0;
 211     }
 212
 213     if (maxangle == 0)
 214     {
 215         gmx_fatal(FARGS, "maxangle not given");
 216     }
 217
 218     t_topology *top;
 219     snew(top, 1);
 220     read_tps_conf(opt2fn("-f", NFILE, fnm), top, nullptr, &x, &v, box, FALSE);
 221     t_atoms  &atoms = top->atoms;
 222     if (atoms.pdbinfo == nullptr)
 223     {
 224         snew(atoms.pdbinfo, atoms.nr);
 225     }
 226     atoms.havePdbInfo = TRUE;
 227     natoms            = atoms.nr;
 228     snew(xout, natoms);
 229     snew(vout, natoms);
 230
 231     printf("Select group to rotate:\n");
 232     rd_index(ftp2fn(efNDX, NFILE, fnm), 1, &isize, &index, &grpname);
 233     printf("Going to rotate %s containing %d atoms\n", grpname, isize);
 234
 235     snew(index_all, atoms.nr);
 236     for (i = 0; (i < atoms.nr); i++)
 237     {
 238         index_all[i] = i;
 239     }
 240
 241     status = open_trx(opt2fn("-o", NFILE, fnm), "w");
 242
 243     label = 'A';
 244     for (i = 0; (i < nframes); i++, label++)
 245     {
 246         angle = angle0 + (i*(angle1-angle0))/(nframes-1);
 247         trans = trans0*0.1*angle/maxangle;
 248         printf("Frame: %2d (label %c), angle: %8.3f deg., trans: %8.3f nm\n",
 249                i, label, angle, trans);
 250         rot_conf(&atoms, x, v, trans, angle, head, tail, isize, index, xout, vout);
 251
 252         if (label > 'Z')
 253         {
 254             label -= 26;
 255         }
 256         for (j = 0; (j < atoms.nr); j++)
 257         {
 258             atoms.resinfo[atoms.atom[j].resind].chainid = label;
 259         }
 260
 261         write_trx(status, atoms.nr, index_all, &atoms, i, angle, box, xout, vout, nullptr);
 262     }
 263     close_trx(status);
 264
 265     return 0;
 266 }