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45 #include "gromacs/commandline/pargs.h"
47 #include "gromacs/utility/smalloc.h"
51 #include "gromacs/utility/futil.h"
54 #include "gromacs/fileio/xvgr.h"
58 #include "gromacs/fileio/tpxio.h"
59 #include "gromacs/fileio/trxio.h"
62 #include "gromacs/utility/fatalerror.h"
71 static int ocomp(const void *a, const void *b)
88 int gmx_trjorder(int argc, char *argv[])
90 const char *desc[] = {
91 "[THISMODULE] orders molecules according to the smallest distance",
92 "to atoms in a reference group",
93 "or on z-coordinate (with option [TT]-z[tt]).",
94 "With distance ordering, it will ask for a group of reference",
95 "atoms and a group of molecules. For each frame of the trajectory",
96 "the selected molecules will be reordered according to the shortest",
97 "distance between atom number [TT]-da[tt] in the molecule and all the",
98 "atoms in the reference group. The center of mass of the molecules can",
99 "be used instead of a reference atom by setting [TT]-da[tt] to 0.",
100 "All atoms in the trajectory are written",
101 "to the output trajectory.[PAR]",
102 "[THISMODULE] can be useful for e.g. analyzing the n waters closest to a",
104 "In that case the reference group would be the protein and the group",
105 "of molecules would consist of all the water atoms. When an index group",
106 "of the first n waters is made, the ordered trajectory can be used",
107 "with any Gromacs program to analyze the n closest waters.",
109 "If the output file is a [TT].pdb[tt] file, the distance to the reference target",
110 "will be stored in the B-factor field in order to color with e.g. Rasmol.",
112 "With option [TT]-nshell[tt] the number of molecules within a shell",
113 "of radius [TT]-r[tt] around the reference group are printed."
115 static int na = 3, ref_a = 1;
116 static real rcut = 0;
117 static gmx_bool bCOM = FALSE, bZ = FALSE;
119 { "-na", FALSE, etINT, {&na},
120 "Number of atoms in a molecule" },
121 { "-da", FALSE, etINT, {&ref_a},
122 "Atom used for the distance calculation, 0 is COM" },
123 { "-com", FALSE, etBOOL, {&bCOM},
124 "Use the distance to the center of mass of the reference group" },
125 { "-r", FALSE, etREAL, {&rcut},
126 "Cutoff used for the distance calculation when computing the number of molecules in a shell around e.g. a protein" },
127 { "-z", FALSE, etBOOL, {&bZ},
128 "Order molecules on z-coordinate" }
133 gmx_bool bNShell, bPDBout;
136 rvec *x, *xsol, xcom, dx;
140 real t, totmass, mass, rcut2 = 0, n2;
141 int natoms, nwat, ncut;
142 char **grpname, title[256];
143 int i, j, d, *isize, isize_ref = 0, isize_sol;
144 atom_id sa, sr, *swi, **index, *ind_ref = NULL, *ind_sol;
147 { efTRX, "-f", NULL, ffREAD },
148 { efTPS, NULL, NULL, ffREAD },
149 { efNDX, NULL, NULL, ffOPTRD },
150 { efTRO, "-o", "ordered", ffOPTWR },
151 { efXVG, "-nshell", "nshell", ffOPTWR }
153 #define NFILE asize(fnm)
155 if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_BE_NICE,
156 NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
161 read_tps_conf(ftp2fn(efTPS, NFILE, fnm), title, &top, &ePBC, &x, NULL, box, TRUE);
164 /* get index groups */
165 printf("Select %sa group of molecules to be ordered:\n",
166 bZ ? "" : "a group of reference atoms and ");
170 get_index(&top.atoms, ftp2fn_null(efNDX, NFILE, fnm), bZ ? 1 : 2,
171 isize, index, grpname);
175 isize_ref = isize[0];
176 isize_sol = isize[1];
182 isize_sol = isize[0];
186 natoms = read_first_x(oenv, &status, ftp2fn(efTRX, NFILE, fnm), &t, &x, box);
187 if (natoms > top.atoms.nr)
189 gmx_fatal(FARGS, "Number of atoms in the run input file is larger than in the trjactory");
191 for (i = 0; (i < 2); i++)
193 for (j = 0; (j < isize[i]); j++)
195 if (index[i][j] > natoms)
197 gmx_fatal(FARGS, "An atom number in group %s is larger than the number of atoms in the trajectory");
202 if ((isize_sol % na) != 0)
204 gmx_fatal(FARGS, "Number of atoms in the molecule group (%d) is not a multiple of na (%d)",
211 gmx_fatal(FARGS, "The reference atom can not be larger than the number of atoms in a molecule");
217 for (i = 0; (i < natoms); i++)
224 bNShell = ((opt2bSet("-nshell", NFILE, fnm)) ||
225 (opt2parg_bSet("-r", asize(pa), pa)));
230 fp = xvgropen(opt2fn("-nshell", NFILE, fnm), "Number of molecules",
231 "Time (ps)", "N", oenv);
232 printf("Will compute the number of molecules within a radius of %g\n",
235 if (!bNShell || opt2bSet("-o", NFILE, fnm))
237 bPDBout = (fn2ftp(opt2fn("-o", NFILE, fnm)) == efPDB);
238 if (bPDBout && !top.atoms.pdbinfo)
240 fprintf(stderr, "Creating pdbfino records\n");
241 snew(top.atoms.pdbinfo, top.atoms.nr);
243 out = open_trx(opt2fn("-o", NFILE, fnm), "w");
245 gpbc = gmx_rmpbc_init(&top.idef, ePBC, natoms);
248 gmx_rmpbc(gpbc, natoms, box, x);
249 set_pbc(&pbc, ePBC, box);
253 /* Calculate the COM of all solvent molecules */
254 for (i = 0; i < nwat; i++)
258 for (j = 0; j < na; j++)
260 sa = ind_sol[i*na+j];
261 mass = top.atoms.atom[sa].m;
263 for (d = 0; d < DIM; d++)
265 xsol[i][d] += mass*x[sa][d];
268 svmul(1/totmass, xsol[i], xsol[i]);
273 /* Copy the reference atom of all solvent molecules */
274 for (i = 0; i < nwat; i++)
276 copy_rvec(x[ind_sol[i*na+ref_a]], xsol[i]);
282 for (i = 0; (i < nwat); i++)
286 order[i].d2 = xsol[i][ZZ];
293 for (i = 0; i < isize_ref; i++)
295 mass = top.atoms.atom[ind_ref[i]].m;
297 for (j = 0; j < DIM; j++)
299 xcom[j] += mass*x[ind_ref[i]][j];
302 svmul(1/totmass, xcom, xcom);
303 for (i = 0; (i < nwat); i++)
306 pbc_dx(&pbc, xcom, xsol[i], dx);
308 order[i].d2 = norm2(dx);
313 /* Set distance to first atom */
314 for (i = 0; (i < nwat); i++)
317 pbc_dx(&pbc, x[ind_ref[0]], xsol[i], dx);
319 order[i].d2 = norm2(dx);
321 for (j = 1; (j < isize_ref); j++)
324 for (i = 0; (i < nwat); i++)
327 pbc_dx(&pbc, x[sr], xsol[i], dx);
329 if (n2 < order[i].d2)
340 for (i = 0; (i < nwat); i++)
342 if (order[i].d2 <= rcut2)
347 fprintf(fp, "%10.3f %8d\n", t, ncut);
351 qsort(order, nwat, sizeof(*order), ocomp);
352 for (i = 0; (i < nwat); i++)
354 for (j = 0; (j < na); j++)
356 swi[ind_sol[na*i]+j] = order[i].i+j;
360 /* Store the distance as the B-factor */
363 for (i = 0; (i < nwat); i++)
365 for (j = 0; (j < na); j++)
367 top.atoms.pdbinfo[order[i].i+j].bfac = sqrt(order[i].d2);
371 write_trx(out, natoms, swi, &top.atoms, 0, t, box, x, NULL, NULL);
374 while (read_next_x(oenv, status, &t, x, box));
384 gmx_rmpbc_done(gpbc);