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37 #include "insert-molecules.h"
44 #include "gromacs/math/utilities.h"
45 #include "gromacs/fileio/confio.h"
48 #include "gromacs/math/vec.h"
49 #include "gromacs/gmxlib/conformation-utilities.h"
51 #include "read-conformation.h"
53 #include "gromacs/commandline/pargs.h"
54 #include "gromacs/fileio/xvgr.h"
55 #include "gromacs/pbcutil/ishift.h"
56 #include "gromacs/pbcutil/pbc.h"
57 #include "gromacs/random/random.h"
58 #include "gromacs/topology/atomprop.h"
59 #include "gromacs/utility/cstringutil.h"
60 #include "gromacs/utility/fatalerror.h"
61 #include "gromacs/utility/futil.h"
62 #include "gromacs/utility/smalloc.h"
64 static gmx_bool in_box(t_pbc *pbc, rvec x)
69 /* pbc_dx_aiuc only works correctly with the rectangular box center */
70 calc_box_center(ecenterRECT, pbc->box, box_center);
72 shift = pbc_dx_aiuc(pbc, x, box_center, dx);
74 return (shift == CENTRAL);
77 /* This is a (maybe) slow workaround to avoid the neighbor searching in addconf.c, which
78 * leaks memory (May 2012). The function could be deleted as soon as the memory leaks
80 * However, when inserting a small molecule in a system containing not too many atoms,
81 * allPairsDistOk is probably even faster than the other code.
84 allPairsDistOk(t_atoms *atoms, rvec *x, real *exclusionDistances,
86 t_atoms *atoms_insrt, rvec *x_n, real *exclusionDistances_insrt)
93 set_pbc(&pbc, ePBC, box);
94 for (i = 0; i < atoms->nr; i++)
96 for (j = 0; j < atoms_insrt->nr; j++)
98 pbc_dx(&pbc, x[i], x_n[j], dx);
100 r2 = sqr(exclusionDistances[i]+exclusionDistances_insrt[j]);
110 /* enum for random rotations of inserted solutes */
112 en_rot, en_rotXYZ, en_rotZ, en_rotNone, en_NR
115 static char *insert_mols(const char *mol_insrt, int nmol_insrt, int ntry, int seed,
116 t_atoms *atoms, rvec **x, real **exclusionDistances, int ePBC, matrix box,
118 real defaultDistance, real scaleFactor, real rshell,
119 const output_env_t oenv,
120 const char* posfn, const rvec deltaR, int enum_rot,
121 gmx_bool bCheckAllPairDist)
124 static char *title_insrt;
127 real *exclusionDistances_insrt;
130 int i, mol, onr, ncol;
131 real alfa = 0., beta = 0., gamma = 0.;
137 rng = gmx_rng_init(seed);
138 set_pbc(&pbc, ePBC, box);
140 /* read number of atoms of insert molecules */
143 get_stx_coordnum(mol_insrt, &natoms);
146 gmx_fatal(FARGS, "No molecule in %s, please check your input\n", mol_insrt);
148 init_t_atoms(&atoms_insrt, natoms, FALSE);
150 /* allocate memory for atom coordinates of insert molecules */
151 snew(x_insrt, atoms_insrt.nr);
152 snew(atoms_insrt.resinfo, atoms_insrt.nr);
153 snew(atoms_insrt.atomname, atoms_insrt.nr);
154 snew(atoms_insrt.atom, atoms_insrt.nr);
155 atoms_insrt.pdbinfo = NULL;
156 snew(x_n, atoms_insrt.nr);
157 snew(title_insrt, STRLEN);
159 /* read residue number, residue names, atomnames, coordinates etc. */
160 fprintf(stderr, "Reading molecule configuration \n");
161 read_stx_conf(mol_insrt, title_insrt, &atoms_insrt, x_insrt, NULL,
162 &ePBC_insrt, box_insrt);
163 fprintf(stderr, "%s\nContaining %d atoms in %d residue\n",
164 title_insrt, atoms_insrt.nr, atoms_insrt.nres);
165 srenew(atoms_insrt.resinfo, atoms_insrt.nres);
167 /* initialise distance arrays for inserted molecules */
168 exclusionDistances_insrt = makeExclusionDistances(&atoms_insrt, aps, defaultDistance, scaleFactor);
170 /* With -ip, take nmol_insrt from file posfn */
173 nmol_insrt = read_xvg(posfn, &rpos, &ncol);
176 gmx_fatal(FARGS, "Expected 3 columns (x/y/z coordinates) in file %s\n", ncol, posfn);
178 fprintf(stderr, "Read %d positions from file %s\n\n", nmol_insrt, posfn);
181 srenew(atoms->resinfo, (atoms->nres+nmol_insrt*atoms_insrt.nres));
182 srenew(atoms->atomname, (atoms->nr+atoms_insrt.nr*nmol_insrt));
183 srenew(atoms->atom, (atoms->nr+atoms_insrt.nr*nmol_insrt));
184 srenew(*x, (atoms->nr+atoms_insrt.nr*nmol_insrt));
185 srenew(*exclusionDistances, (atoms->nr+atoms_insrt.nr*nmol_insrt));
188 while ((mol < nmol_insrt) && (trial < ntry*nmol_insrt))
190 fprintf(stderr, "\rTry %d", trial++);
191 for (i = 0; (i < atoms_insrt.nr); i++)
193 copy_rvec(x_insrt[i], x_n[i]);
198 alfa = 2*M_PI * gmx_rng_uniform_real(rng);
199 beta = 2*M_PI * gmx_rng_uniform_real(rng);
200 gamma = 2*M_PI * gmx_rng_uniform_real(rng);
204 gamma = 2*M_PI * gmx_rng_uniform_real(rng);
207 alfa = beta = gamma = 0.;
210 if (enum_rot == en_rotXYZ || (enum_rot == en_rotZ))
212 rotate_conf(atoms_insrt.nr, x_n, NULL, alfa, beta, gamma);
216 /* insert at random positions */
217 offset_x[XX] = box[XX][XX] * gmx_rng_uniform_real(rng);
218 offset_x[YY] = box[YY][YY] * gmx_rng_uniform_real(rng);
219 offset_x[ZZ] = box[ZZ][ZZ] * gmx_rng_uniform_real(rng);
220 make_new_box(atoms_insrt.nr, x_n, box_insrt, offset_x, TRUE);
221 if (!in_box(&pbc, x_n[0]) || !in_box(&pbc, x_n[atoms_insrt.nr-1]))
228 /* Insert at positions taken from option -ip file */
229 offset_x[XX] = rpos[XX][mol] + deltaR[XX]*(2 * gmx_rng_uniform_real(rng)-1);
230 offset_x[YY] = rpos[YY][mol] + deltaR[YY]*(2 * gmx_rng_uniform_real(rng)-1);
231 offset_x[ZZ] = rpos[ZZ][mol] + deltaR[ZZ]*(2 * gmx_rng_uniform_real(rng)-1);
232 for (i = 0; i < atoms_insrt.nr; i++)
234 rvec_inc(x_n[i], offset_x);
240 /* This is a (maybe) slow workaround to avoid too many calls of add_conf, which
241 * leaks memory (status May 2012). If the momory leaks in add_conf() are fixed,
242 * this check could be removed. Note, however, that allPairsDistOk is probably
243 * even faster than add_conf() when inserting a small molecule into a moderately
246 if (bCheckAllPairDist && !allPairsDistOk(atoms, *x, *exclusionDistances, ePBC, box, &atoms_insrt, x_n, exclusionDistances_insrt))
251 add_conf(atoms, x, NULL, exclusionDistances, FALSE, ePBC, box, TRUE,
252 &atoms_insrt, x_n, NULL, exclusionDistances_insrt, FALSE, rshell, 0, oenv);
254 if (atoms->nr == (atoms_insrt.nr+onr))
257 fprintf(stderr, " success (now %d atoms)!\n", atoms->nr);
260 gmx_rng_destroy(rng);
261 srenew(atoms->resinfo, atoms->nres);
262 srenew(atoms->atomname, atoms->nr);
263 srenew(atoms->atom, atoms->nr);
264 srenew(*x, atoms->nr);
265 srenew(*exclusionDistances, atoms->nr);
267 fprintf(stderr, "\n");
268 /* print number of molecules added */
269 fprintf(stderr, "Added %d molecules (out of %d requested) of %s\n",
270 mol, nmol_insrt, *atoms_insrt.resinfo[0].name);
273 sfree(exclusionDistances_insrt);
274 done_atom(&atoms_insrt);
279 int gmx_insert_molecules(int argc, char *argv[])
281 const char *desc[] = {
282 "[THISMODULE] inserts [TT]-nmol[tt] copies of the system specified in",
283 "the [TT]-ci[tt] input file. The insertions take place either into",
284 "vacant space in the solute conformation given with [TT]-f[tt], or",
285 "into an empty box given by [TT]-box[tt]. Specifying both [TT]-f[tt]",
286 "and [TT]-box[tt] behaves like [TT]-f[tt], but places a new box",
287 "around the solute before insertions. Any velocities present are",
290 "By default, the insertion positions are random (with initial seed",
291 "specified by [TT]-seed[tt]). The program iterates until [TT]-nmol[tt]",
292 "molecules have been inserted in the box. Molecules are not inserted",
293 "where the distance between any existing atom and any atom of the",
294 "inserted molecule is less than the sum based on the van der Waals",
295 "radii of both atoms. A database ([TT]vdwradii.dat[tt]) of van der",
296 "Waals radii is read by the program, and the resulting radii scaled",
297 "by [TT]-scale[tt]. If radii are not found in the database, those"
298 "atoms are assigned the (pre-scaled) distance [TT]-radius[tt].[PAR]",
300 "A total of [TT]-nmol[tt] * [TT]-try[tt] insertion attempts are made",
301 "before giving up. Increase [TT]-try[tt] if you have several small",
302 "holes to fill. Option [TT]-rot[tt] specifies whether the insertion",
303 "molecules are randomly oriented before insertion attempts.[PAR]",
305 "Alternatively, the molecules can be inserted only at positions defined in",
306 "positions.dat ([TT]-ip[tt]). That file should have 3 columns (x,y,z),",
307 "that give the displacements compared to the input molecule position",
308 "([TT]-ci[tt]). Hence, if that file should contain the absolute",
309 "positions, the molecule must be centered on (0,0,0) before using",
310 "[THISMODULE] (e.g. from [gmx-editconf] [TT]-center[tt]).",
311 "Comments in that file starting with # are ignored. Option [TT]-dr[tt]",
312 "defines the maximally allowed displacements during insertial trials.",
313 "[TT]-try[tt] and [TT]-rot[tt] work as in the default mode (see above).",
317 const char *bugs[] = {
318 "Molecules must be whole in the initial configurations.",
319 "Many repeated neighbor searchings with -ci blows up the allocated memory. "
320 "Option -allpair avoids this using all-to-all distance checks (slow for large systems)"
324 gmx_bool bProt, bBox;
325 const char *conf_prot, *confout;
326 real *exclusionDistances = NULL;
327 char *title_ins = NULL;
330 /* protein configuration data */
338 { efSTX, "-f", "protein", ffOPTRD },
339 { efSTX, "-ci", "insert", ffREAD},
340 { efDAT, "-ip", "positions", ffOPTRD},
341 { efSTO, NULL, NULL, ffWRITE},
343 #define NFILE asize(fnm)
345 static int nmol_ins = 0, nmol_try = 10, seed = 1997, enum_rot;
346 static real defaultDistance = 0.105, scaleFactor = 0.57;
347 static rvec new_box = {0.0, 0.0, 0.0}, deltaR = {0.0, 0.0, 0.0};
348 static gmx_bool bCheckAllPairDist = FALSE;
350 const char *enum_rot_string[] = {NULL, "xyz", "z", "none", NULL};
352 { "-box", FALSE, etRVEC, {new_box},
353 "Box size (in nm)" },
354 { "-nmol", FALSE, etINT, {&nmol_ins},
355 "Number of extra molecules to insert" },
356 { "-try", FALSE, etINT, {&nmol_try},
357 "Try inserting [TT]-nmol[tt] times [TT]-try[tt] times" },
358 { "-seed", FALSE, etINT, {&seed},
359 "Random generator seed"},
360 { "-radius", FALSE, etREAL, {&defaultDistance},
361 "Default van der Waals distance"},
362 { "-scale", FALSE, etREAL, {&scaleFactor},
363 "Scale factor to multiply Van der Waals radii from the database in share/gromacs/top/vdwradii.dat. The default value of 0.57 yields density close to 1000 g/l for proteins in water." },
364 { "-dr", FALSE, etRVEC, {deltaR},
365 "Allowed displacement in x/y/z from positions in [TT]-ip[tt] file" },
366 { "-rot", FALSE, etENUM, {enum_rot_string},
367 "rotate inserted molecules randomly" },
368 { "-allpair", FALSE, etBOOL, {&bCheckAllPairDist},
369 "Avoid momory leaks during neighbor searching with option -ci. May be slow for large systems." },
372 if (!parse_common_args(&argc, argv, PCA_BE_NICE, NFILE, fnm, asize(pa), pa,
373 asize(desc), desc, asize(bugs), bugs, &oenv))
378 bProt = opt2bSet("-f", NFILE, fnm);
379 bBox = opt2parg_bSet("-box", asize(pa), pa);
380 enum_rot = nenum(enum_rot_string);
383 const char *insertionMoleculeFileName = opt2fn("-ci", NFILE, fnm);
384 if (!gmx_fexist(insertionMoleculeFileName))
387 "A molecule conformation to insert is required in -ci. %s was not found!",
388 insertionMoleculeFileName);
390 if (nmol_ins <= 0 && !opt2bSet("-ip", NFILE, fnm))
392 gmx_fatal(FARGS, "Either -nmol must be larger than 0, "
393 "or positions must be given with -ip");
397 gmx_fatal(FARGS, "When no solute (-f) is specified, "
398 "a box size (-box) must be specified");
401 aps = gmx_atomprop_init();
404 init_t_atoms(atoms, 0, FALSE);
407 /* Generate a solute configuration */
408 conf_prot = opt2fn("-f", NFILE, fnm);
409 title = readConformation(conf_prot, atoms, &x, NULL,
411 exclusionDistances = makeExclusionDistances(atoms, aps, defaultDistance, scaleFactor);
414 fprintf(stderr, "Note: no atoms in %s\n", conf_prot);
422 box[XX][XX] = new_box[XX];
423 box[YY][YY] = new_box[YY];
424 box[ZZ][ZZ] = new_box[ZZ];
428 gmx_fatal(FARGS, "Undefined solute box.\nCreate one with gmx editconf "
429 "or give explicit -box command line option");
432 /* add nmol_ins molecules of atoms_ins
433 in random orientation at random place */
434 title_ins = insert_mols(insertionMoleculeFileName, nmol_ins, nmol_try, seed,
435 atoms, &x, &exclusionDistances, ePBC, box, aps,
436 defaultDistance, scaleFactor, 0,
437 oenv, opt2fn_null("-ip", NFILE, fnm), deltaR, enum_rot,
440 /* write new configuration to file confout */
441 confout = ftp2fn(efSTO, NFILE, fnm);
442 fprintf(stderr, "Writing generated configuration to %s\n", confout);
445 write_sto_conf(confout, title, atoms, x, NULL, ePBC, box);
446 /* print box sizes and box type to stderr */
447 fprintf(stderr, "%s\n", title);
451 write_sto_conf(confout, title_ins, atoms, x, NULL, ePBC, box);
454 /* print size of generated configuration */
455 fprintf(stderr, "\nOutput configuration contains %d atoms in %d residues\n",
456 atoms->nr, atoms->nres);
458 gmx_atomprop_destroy(aps);
459 sfree(exclusionDistances);