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39 #include "gromacs/topology/index.h"
40 #include "gromacs/fileio/confio.h"
41 #include "gromacs/math/units.h"
43 #include "gromacs/legacyheaders/macros.h"
44 #include "gromacs/fileio/trxio.h"
46 #include "gromacs/commandline/pargs.h"
47 #include "gromacs/math/3dtransforms.h"
48 #include "gromacs/math/vec.h"
49 #include "gromacs/topology/atoms.h"
50 #include "gromacs/utility/fatalerror.h"
51 #include "gromacs/utility/smalloc.h"
53 static void rot_conf(t_atoms *atoms, rvec x[], rvec v[], real trans, real angle,
54 rvec head, rvec tail, int isize, atom_id index[],
55 rvec xout[], rvec vout[])
58 real theta, phi, arrow_len;
59 mat4 Rx, Ry, Rz, Rinvy, Rinvz, Mtot;
60 mat4 temp1, temp2, temp3;
64 rvec_sub(tail, head, arrow);
65 arrow_len = norm(arrow);
68 fprintf(debug, "Arrow vector: %10.4f %10.4f %10.4f\n",
69 arrow[XX], arrow[YY], arrow[ZZ]);
70 fprintf(debug, "Effective translation %g nm\n", trans);
74 gmx_fatal(FARGS, "Arrow vector not given");
77 /* Copy all aoms to output */
78 for (i = 0; (i < atoms->nr); i++)
80 copy_rvec(x[i], xout[i]);
81 copy_rvec(v[i], vout[i]);
84 /* Compute center of mass and move atoms there */
86 for (i = 0; (i < isize); i++)
88 rvec_inc(xcm, x[index[i]]);
90 for (i = 0; (i < DIM); i++)
96 fprintf(debug, "Center of mass: %10.4f %10.4f %10.4f\n",
97 xcm[XX], xcm[YY], xcm[ZZ]);
99 for (i = 0; (i < isize); i++)
101 rvec_sub(x[index[i]], xcm, xout[index[i]]);
104 /* Compute theta and phi that describe the arrow */
105 theta = acos(arrow[ZZ]/arrow_len);
106 phi = atan2(arrow[YY]/arrow_len, arrow[XX]/arrow_len);
109 fprintf(debug, "Phi = %.1f, Theta = %.1f\n", RAD2DEG*phi, RAD2DEG*theta);
112 /* Now the total rotation matrix: */
113 /* Rotate a couple of times */
114 gmx_mat4_init_rotation(ZZ, -phi, Rz);
115 gmx_mat4_init_rotation(YY, M_PI/2-theta, Ry);
116 gmx_mat4_init_rotation(XX, angle*DEG2RAD, Rx);
118 gmx_mat4_init_rotation(YY, theta-M_PI/2, Rinvy);
119 gmx_mat4_init_rotation(ZZ, phi, Rinvz);
121 gmx_mat4_mmul(temp1, Ry, Rz);
122 gmx_mat4_mmul(temp2, Rinvy, Rx);
123 gmx_mat4_mmul(temp3, temp2, temp1);
124 gmx_mat4_mmul(Mtot, Rinvz, temp3);
128 gmx_mat4_print(debug, "Rz", Rz);
129 gmx_mat4_print(debug, "Ry", Ry);
130 gmx_mat4_print(debug, "Rx", Rx);
131 gmx_mat4_print(debug, "Rinvy", Rinvy);
132 gmx_mat4_print(debug, "Rinvz", Rinvz);
133 gmx_mat4_print(debug, "Mtot", Mtot);
136 for (i = 0; (i < isize); i++)
139 gmx_mat4_transform_point(Mtot, xout[ai], xv);
140 rvec_add(xv, xcm, xout[ai]);
141 gmx_mat4_transform_point(Mtot, v[ai], xv);
142 copy_rvec(xv, vout[ai]);
146 int gmx_dyndom(int argc, char *argv[])
148 const char *desc[] = {
149 "[THISMODULE] reads a [TT].pdb[tt] file output from DynDom",
150 "(http://www.cmp.uea.ac.uk/dyndom/).",
151 "It reads the coordinates, the coordinates of the rotation axis,",
152 "and an index file containing the domains.",
153 "Furthermore, it takes the first and last atom of the arrow file",
154 "as command line arguments (head and tail) and",
155 "finally it takes the translation vector (given in DynDom info file)",
156 "and the angle of rotation (also as command line arguments). If the angle",
157 "determined by DynDom is given, one should be able to recover the",
158 "second structure used for generating the DynDom output.",
159 "Because of limited numerical accuracy this should be verified by",
160 "computing an all-atom RMSD (using [gmx-confrms]) rather than by file",
161 "comparison (using diff).[PAR]",
162 "The purpose of this program is to interpolate and extrapolate the",
163 "rotation as found by DynDom. As a result unphysical structures with",
164 "long or short bonds, or overlapping atoms may be produced. Visual",
165 "inspection, and energy minimization may be necessary to",
166 "validate the structure."
168 static real trans0 = 0;
169 static rvec head = { 0, 0, 0 };
170 static rvec tail = { 0, 0, 0 };
171 static real angle0 = 0, angle1 = 0, maxangle = 0;
172 static int label = 0, nframes = 11;
174 { "-firstangle", FALSE, etREAL, {&angle0},
175 "Angle of rotation about rotation vector" },
176 { "-lastangle", FALSE, etREAL, {&angle1},
177 "Angle of rotation about rotation vector" },
178 { "-nframe", FALSE, etINT, {&nframes},
179 "Number of steps on the pathway" },
180 { "-maxangle", FALSE, etREAL, {&maxangle},
181 "DymDom dtermined angle of rotation about rotation vector" },
182 { "-trans", FALSE, etREAL, {&trans0},
183 "Translation (Angstrom) along rotation vector (see DynDom info file)" },
184 { "-head", FALSE, etRVEC, {head},
185 "First atom of the arrow vector" },
186 { "-tail", FALSE, etRVEC, {tail},
187 "Last atom of the arrow vector" }
189 int i, j, natoms, isize;
191 atom_id *index = NULL, *index_all;
192 char title[256], *grpname;
195 rvec *x, *v, *xout, *vout;
200 { efPDB, "-f", "dyndom", ffREAD },
201 { efTRO, "-o", "rotated", ffWRITE },
202 { efNDX, "-n", "domains", ffREAD }
204 #define NFILE asize(fnm)
206 if (!parse_common_args(&argc, argv, 0, NFILE, fnm, asize(pa), pa,
207 asize(desc), desc, 0, NULL, &oenv))
212 get_stx_coordnum (opt2fn("-f", NFILE, fnm), &natoms);
213 init_t_atoms(&atoms, natoms, TRUE);
216 read_stx_conf(opt2fn("-f", NFILE, fnm), title, &atoms, x, v, NULL, box);
220 printf("Select group to rotate:\n");
221 rd_index(ftp2fn(efNDX, NFILE, fnm), 1, &isize, &index, &grpname);
222 printf("Going to rotate %s containg %d atoms\n", grpname, isize);
224 snew(index_all, atoms.nr);
225 for (i = 0; (i < atoms.nr); i++)
230 status = open_trx(opt2fn("-o", NFILE, fnm), "w");
233 for (i = 0; (i < nframes); i++, label++)
235 angle = angle0 + (i*(angle1-angle0))/(nframes-1);
236 trans = trans0*0.1*angle/maxangle;
237 printf("Frame: %2d (label %c), angle: %8.3f deg., trans: %8.3f nm\n",
238 i, label, angle, trans);
239 rot_conf(&atoms, x, v, trans, angle, head, tail, isize, index, xout, vout);
245 for (j = 0; (j < atoms.nr); j++)
247 atoms.resinfo[atoms.atom[j].resind].chainid = label;
250 write_trx(status, atoms.nr, index_all, &atoms, i, angle, box, xout, vout, NULL);