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44 #include "gromacs/commandline/pargs.h"
45 #include "gromacs/fileio/confio.h"
46 #include "gromacs/fileio/trxio.h"
47 #include "gromacs/fileio/xvgr.h"
48 #include "gromacs/gmxana/gmx_ana.h"
49 #include "gromacs/math/vec.h"
50 #include "gromacs/pbcutil/pbc.h"
51 #include "gromacs/pbcutil/rmpbc.h"
52 #include "gromacs/topology/index.h"
53 #include "gromacs/topology/topology.h"
54 #include "gromacs/trajectory/trajectoryframe.h"
55 #include "gromacs/utility/arraysize.h"
56 #include "gromacs/utility/fatalerror.h"
57 #include "gromacs/utility/futil.h"
58 #include "gromacs/utility/smalloc.h"
66 static t_order* order;
68 static int ocomp(const void* a, const void* b)
70 const t_order *oa, *ob;
72 oa = reinterpret_cast<const t_order*>(a);
73 ob = reinterpret_cast<const t_order*>(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 [REF].pdb[ref] 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 }, "Number of atoms in a molecule" },
117 { "-da", FALSE, etINT, { &ref_a }, "Atom used for the distance calculation, 0 is COM" },
122 "Use the distance to the center of mass of the reference group" },
127 "Cutoff used for the distance calculation when computing the number of molecules in a "
128 "shell around e.g. a protein" },
129 { "-z", FALSE, etBOOL, { &bZ }, "Order molecules on z-coordinate" }
134 gmx_bool bNShell, bPDBout;
137 rvec * x, *xsol, xcom, dx;
141 real t, totmass, mass, rcut2 = 0, n2;
142 int natoms, nwat, ncut;
144 int i, j, d, *isize, isize_ref = 0, isize_sol;
145 int sa, sr, *swi, **index, *ind_ref = nullptr, *ind_sol;
146 gmx_output_env_t* oenv;
147 t_filenm fnm[] = { { efTRX, "-f", nullptr, ffREAD },
148 { efTPS, nullptr, nullptr, ffREAD },
149 { efNDX, nullptr, nullptr, ffOPTRD },
150 { efTRO, "-o", "ordered", ffOPTWR },
151 { efXVG, "-nshell", "nshell", ffOPTWR } };
152 #define NFILE asize(fnm)
154 if (!parse_common_args(&argc, argv, PCA_CAN_TIME, NFILE, fnm, asize(pa), pa, asize(desc), desc,
160 read_tps_conf(ftp2fn(efTPS, NFILE, fnm), &top, &ePBC, &x, nullptr, box, TRUE);
163 /* get index groups */
164 printf("Select %sa group of molecules to be ordered:\n", bZ ? "" : "a group of reference atoms and ");
168 get_index(&top.atoms, ftp2fn_null(efNDX, NFILE, fnm), bZ ? 1 : 2, 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)
195 "An atom number in group %s is larger than the number of atoms in the "
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)",
208 nwat = isize_sol / na;
212 "The reference atom can not be larger than the number of atoms in a molecule");
218 for (i = 0; (i < natoms); i++)
225 bNShell = ((opt2bSet("-nshell", NFILE, fnm)) || (opt2parg_bSet("-r", asize(pa), pa)));
230 fp = xvgropen(opt2fn("-nshell", NFILE, fnm), "Number of molecules", "Time (ps)", "N", oenv);
231 printf("Will compute the number of molecules within a radius of %g\n", rcut);
233 if (!bNShell || opt2bSet("-o", NFILE, fnm))
235 bPDBout = (fn2ftp(opt2fn("-o", NFILE, fnm)) == efPDB);
236 if (bPDBout && !top.atoms.pdbinfo)
238 fprintf(stderr, "Creating pdbfino records\n");
239 snew(top.atoms.pdbinfo, top.atoms.nr);
241 out = open_trx(opt2fn("-o", NFILE, fnm), "w");
243 gpbc = gmx_rmpbc_init(&top.idef, ePBC, natoms);
246 gmx_rmpbc(gpbc, natoms, box, x);
247 set_pbc(&pbc, ePBC, box);
251 /* Calculate the COM of all solvent molecules */
252 for (i = 0; i < nwat; i++)
256 for (j = 0; j < na; j++)
258 sa = ind_sol[i * na + j];
259 mass = top.atoms.atom[sa].m;
261 for (d = 0; d < DIM; d++)
263 xsol[i][d] += mass * x[sa][d];
266 svmul(1.0 / totmass, xsol[i], xsol[i]);
271 /* Copy the reference atom of all solvent molecules */
272 for (i = 0; i < nwat; i++)
274 copy_rvec(x[ind_sol[i * na + ref_a]], xsol[i]);
280 for (i = 0; (i < nwat); i++)
282 sa = ind_sol[na * i];
284 order[i].d2 = xsol[i][ZZ];
291 for (i = 0; i < isize_ref; i++)
293 mass = top.atoms.atom[ind_ref[i]].m;
295 for (j = 0; j < DIM; j++)
297 xcom[j] += mass * x[ind_ref[i]][j];
300 svmul(1 / totmass, xcom, xcom);
301 for (i = 0; (i < nwat); i++)
303 sa = ind_sol[na * i];
304 pbc_dx(&pbc, xcom, xsol[i], dx);
306 order[i].d2 = norm2(dx);
311 /* Set distance to first atom */
312 for (i = 0; (i < nwat); i++)
314 sa = ind_sol[na * i];
315 pbc_dx(&pbc, x[ind_ref[0]], xsol[i], dx);
317 order[i].d2 = norm2(dx);
319 for (j = 1; (j < isize_ref); j++)
322 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 = std::sqrt(order[i].d2);
368 write_trx(out, natoms, swi, &top.atoms, 0, t, box, x, nullptr, nullptr);
370 } while (read_next_x(oenv, status, &t, x, box));
380 gmx_rmpbc_done(gpbc);