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43 #include "gromacs/commandline/pargs.h"
50 #include "gromacs/fileio/futil.h"
57 #include "gromacs/fileio/tpxio.h"
58 #include "gromacs/fileio/trxio.h"
68 static int ocomp(const void *a, const void *b)
85 int gmx_trjorder(int argc, char *argv[])
87 const char *desc[] = {
88 "[THISMODULE] orders molecules according to the smallest distance",
89 "to atoms in a reference group",
90 "or on z-coordinate (with option [TT]-z[tt]).",
91 "With distance ordering, it will ask for a group of reference",
92 "atoms and a group of molecules. For each frame of the trajectory",
93 "the selected molecules will be reordered according to the shortest",
94 "distance between atom number [TT]-da[tt] in the molecule and all the",
95 "atoms in the reference group. The center of mass of the molecules can",
96 "be used instead of a reference atom by setting [TT]-da[tt] to 0.",
97 "All atoms in the trajectory are written",
98 "to the output trajectory.[PAR]",
99 "[THISMODULE] can be useful for e.g. analyzing the n waters closest to a",
101 "In that case the reference group would be the protein and the group",
102 "of molecules would consist of all the water atoms. When an index group",
103 "of the first n waters is made, the ordered trajectory can be used",
104 "with any Gromacs program to analyze the n closest waters.",
106 "If the output file is a [TT].pdb[tt] file, the distance to the reference target",
107 "will be stored in the B-factor field in order to color with e.g. Rasmol.",
109 "With option [TT]-nshell[tt] the number of molecules within a shell",
110 "of radius [TT]-r[tt] around the reference group are printed."
112 static int na = 3, ref_a = 1;
113 static real rcut = 0;
114 static gmx_bool bCOM = FALSE, bZ = FALSE;
116 { "-na", FALSE, etINT, {&na},
117 "Number of atoms in a molecule" },
118 { "-da", FALSE, etINT, {&ref_a},
119 "Atom used for the distance calculation, 0 is COM" },
120 { "-com", FALSE, etBOOL, {&bCOM},
121 "Use the distance to the center of mass of the reference group" },
122 { "-r", FALSE, etREAL, {&rcut},
123 "Cutoff used for the distance calculation when computing the number of molecules in a shell around e.g. a protein" },
124 { "-z", FALSE, etBOOL, {&bZ},
125 "Order molecules on z-coordinate" }
130 gmx_bool bNShell, bPDBout;
133 rvec *x, *xsol, xcom, dx;
137 real t, totmass, mass, rcut2 = 0, n2;
138 int natoms, nwat, ncut;
139 char **grpname, title[256];
140 int i, j, d, *isize, isize_ref = 0, isize_sol;
141 atom_id sa, sr, *swi, **index, *ind_ref = NULL, *ind_sol;
144 { efTRX, "-f", NULL, ffREAD },
145 { efTPS, NULL, NULL, ffREAD },
146 { efNDX, NULL, NULL, ffOPTRD },
147 { efTRO, "-o", "ordered", ffOPTWR },
148 { efXVG, "-nshell", "nshell", ffOPTWR }
150 #define NFILE asize(fnm)
152 if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_BE_NICE,
153 NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
158 read_tps_conf(ftp2fn(efTPS, NFILE, fnm), title, &top, &ePBC, &x, NULL, box, TRUE);
161 /* get index groups */
162 printf("Select %sa group of molecules to be ordered:\n",
163 bZ ? "" : "a group of reference atoms and ");
167 get_index(&top.atoms, ftp2fn_null(efNDX, NFILE, fnm), bZ ? 1 : 2,
168 isize, index, grpname);
172 isize_ref = isize[0];
173 isize_sol = isize[1];
179 isize_sol = isize[0];
183 natoms = read_first_x(oenv, &status, ftp2fn(efTRX, NFILE, fnm), &t, &x, box);
184 if (natoms > top.atoms.nr)
186 gmx_fatal(FARGS, "Number of atoms in the run input file is larger than in the trjactory");
188 for (i = 0; (i < 2); i++)
190 for (j = 0; (j < isize[i]); j++)
192 if (index[i][j] > natoms)
194 gmx_fatal(FARGS, "An atom number in group %s is larger than the number of atoms in the trajectory");
199 if ((isize_sol % na) != 0)
201 gmx_fatal(FARGS, "Number of atoms in the molecule group (%d) is not a multiple of na (%d)",
208 gmx_fatal(FARGS, "The reference atom can not be larger than the number of atoms in a molecule");
214 for (i = 0; (i < natoms); i++)
221 bNShell = ((opt2bSet("-nshell", NFILE, fnm)) ||
222 (opt2parg_bSet("-r", asize(pa), pa)));
227 fp = xvgropen(opt2fn("-nshell", NFILE, fnm), "Number of molecules",
228 "Time (ps)", "N", oenv);
229 printf("Will compute the number of molecules within a radius of %g\n",
232 if (!bNShell || opt2bSet("-o", NFILE, fnm))
234 bPDBout = (fn2ftp(opt2fn("-o", NFILE, fnm)) == efPDB);
235 if (bPDBout && !top.atoms.pdbinfo)
237 fprintf(stderr, "Creating pdbfino records\n");
238 snew(top.atoms.pdbinfo, top.atoms.nr);
240 out = open_trx(opt2fn("-o", NFILE, fnm), "w");
242 gpbc = gmx_rmpbc_init(&top.idef, ePBC, natoms);
245 gmx_rmpbc(gpbc, natoms, box, x);
246 set_pbc(&pbc, ePBC, box);
250 /* Calculate the COM of all solvent molecules */
251 for (i = 0; i < nwat; i++)
255 for (j = 0; j < na; j++)
257 sa = ind_sol[i*na+j];
258 mass = top.atoms.atom[sa].m;
260 for (d = 0; d < DIM; d++)
262 xsol[i][d] += mass*x[sa][d];
265 svmul(1/totmass, xsol[i], xsol[i]);
270 /* Copy the reference atom of all solvent molecules */
271 for (i = 0; i < nwat; i++)
273 copy_rvec(x[ind_sol[i*na+ref_a]], xsol[i]);
279 for (i = 0; (i < nwat); i++)
283 order[i].d2 = xsol[i][ZZ];
290 for (i = 0; i < isize_ref; i++)
292 mass = top.atoms.atom[ind_ref[i]].m;
294 for (j = 0; j < DIM; j++)
296 xcom[j] += mass*x[ind_ref[i]][j];
299 svmul(1/totmass, xcom, xcom);
300 for (i = 0; (i < nwat); i++)
303 pbc_dx(&pbc, xcom, xsol[i], dx);
305 order[i].d2 = norm2(dx);
310 /* Set distance to first atom */
311 for (i = 0; (i < nwat); i++)
314 pbc_dx(&pbc, x[ind_ref[0]], xsol[i], dx);
316 order[i].d2 = norm2(dx);
318 for (j = 1; (j < isize_ref); j++)
321 for (i = 0; (i < nwat); i++)
324 pbc_dx(&pbc, x[sr], xsol[i], dx);
326 if (n2 < order[i].d2)
337 for (i = 0; (i < nwat); i++)
339 if (order[i].d2 <= rcut2)
344 fprintf(fp, "%10.3f %8d\n", t, ncut);
348 qsort(order, nwat, sizeof(*order), ocomp);
349 for (i = 0; (i < nwat); i++)
351 for (j = 0; (j < na); j++)
353 swi[ind_sol[na*i]+j] = order[i].i+j;
357 /* Store the distance as the B-factor */
360 for (i = 0; (i < nwat); i++)
362 for (j = 0; (j < na); j++)
364 top.atoms.pdbinfo[order[i].i+j].bfac = sqrt(order[i].d2);
368 write_trx(out, natoms, swi, &top.atoms, 0, t, box, x, NULL, NULL);
371 while (read_next_x(oenv, status, &t, x, box));
381 gmx_rmpbc_done(gpbc);