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44 #include "gromacs/fileio/espio.h"
45 #include "gromacs/fileio/filetypes.h"
46 #include "gromacs/fileio/g96io.h"
47 #include "gromacs/fileio/gmxfio.h"
48 #include "gromacs/fileio/groio.h"
49 #include "gromacs/fileio/pdbio.h"
50 #include "gromacs/fileio/tpxio.h"
51 #include "gromacs/fileio/trxio.h"
52 #include "gromacs/math/vec.h"
53 #include "gromacs/topology/atoms.h"
54 #include "gromacs/topology/block.h"
55 #include "gromacs/topology/mtop_util.h"
56 #include "gromacs/topology/symtab.h"
57 #include "gromacs/topology/topology.h"
58 #include "gromacs/trajectory/trajectoryframe.h"
59 #include "gromacs/utility/cstringutil.h"
60 #include "gromacs/utility/fatalerror.h"
61 #include "gromacs/utility/gmxassert.h"
62 #include "gromacs/utility/smalloc.h"
64 void write_sto_conf_indexed(const char *outfile, const char *title,
66 const rvec x[], const rvec *v, int ePBC, const matrix box,
67 int nindex, int index[])
73 ftp = fn2ftp(outfile);
77 out = gmx_fio_fopen(outfile, "w");
78 write_hconf_indexed_p(out, title, atoms, nindex, index, x, v, box);
82 clear_trxframe(&fr, TRUE);
85 fr.natoms = atoms->nr;
87 fr.atoms = const_cast<t_atoms *>(atoms);
89 fr.x = const_cast<rvec *>(x);
93 fr.v = const_cast<rvec *>(v);
96 copy_mat(box, fr.box);
97 out = gmx_fio_fopen(outfile, "w");
98 write_g96_conf(out, &fr, nindex, index);
105 out = gmx_fio_fopen(outfile, "w");
106 write_pdbfile_indexed(out, title, atoms, x, ePBC, box, ' ', -1, nindex, index, nullptr, TRUE);
110 out = gmx_fio_fopen(outfile, "w");
111 write_espresso_conf_indexed(out, title, atoms, nindex, index, x, v, box);
115 gmx_fatal(FARGS, "Sorry, can not write a topology to %s", outfile);
118 gmx_incons("Not supported in write_sto_conf_indexed");
122 void write_sto_conf(const char *outfile, const char *title, const t_atoms *atoms,
123 const rvec x[], const rvec *v, int ePBC, const matrix box)
129 ftp = fn2ftp(outfile);
133 write_conf_p(outfile, title, atoms, x, v, box);
136 clear_trxframe(&fr, TRUE);
139 fr.natoms = atoms->nr;
141 fr.atoms = const_cast<t_atoms *>(atoms); // TODO check
143 fr.x = const_cast<rvec *>(x);
147 fr.v = const_cast<rvec *>(v);
150 copy_mat(box, fr.box);
151 out = gmx_fio_fopen(outfile, "w");
152 write_g96_conf(out, &fr, -1, nullptr);
158 out = gmx_fio_fopen(outfile, "w");
159 write_pdbfile(out, title, atoms, x, ePBC, box, ' ', -1, nullptr, TRUE);
163 out = gmx_fio_fopen(outfile, "w");
164 write_espresso_conf_indexed(out, title, atoms, atoms->nr, nullptr, x, v, box);
168 gmx_fatal(FARGS, "Sorry, can not write a topology to %s", outfile);
171 gmx_incons("Not supported in write_sto_conf");
175 void write_sto_conf_mtop(const char *outfile, const char *title,
177 const rvec x[], const rvec *v, int ePBC, const matrix box)
183 ftp = fn2ftp(outfile);
187 out = gmx_fio_fopen(outfile, "w");
188 write_hconf_mtop(out, title, mtop, x, v, box);
192 /* This is a brute force approach which requires a lot of memory.
193 * We should implement mtop versions of all writing routines.
195 atoms = gmx_mtop_global_atoms(mtop);
197 write_sto_conf(outfile, title, &atoms, x, v, ePBC, box);
204 static void get_stx_coordnum(const char *infile, int *natoms)
209 char g96_line[STRLEN+1];
211 ftp = fn2ftp(infile);
212 range_check(ftp, 0, efNR);
216 get_coordnum(infile, natoms);
220 in = gmx_fio_fopen(infile, "r");
227 *natoms = read_g96_conf(in, infile, &fr, nullptr, g96_line);
228 sfree(const_cast<char *>(fr.title));
235 in = gmx_fio_fopen(infile, "r");
236 get_pdb_coordnum(in, natoms);
240 *natoms = get_espresso_coordnum(infile);
243 gmx_fatal(FARGS, "File type %s not supported in get_stx_coordnum",
248 static void tpx_make_chain_identifiers(t_atoms *atoms, t_block *mols)
250 /* We always assign a new chain number, but save the chain id characters
251 * for larger molecules.
253 const int chainMinAtoms = 15;
257 bool outOfIds = false;
258 for (int m = 0; m < mols->nr; m++)
260 int a0 = mols->index[m];
261 int a1 = mols->index[m+1];
263 if (a1 - a0 >= chainMinAtoms && !outOfIds)
265 /* Set the chain id for the output */
267 /* Here we allow for the max possible 2*26+10=62 chain ids */
272 else if (chainid == 'z')
276 else if (chainid == '9')
289 for (int a = a0; a < a1; a++)
291 atoms->resinfo[atoms->atom[a].resind].chainnum = chainnum;
292 atoms->resinfo[atoms->atom[a].resind].chainid = c;
297 /* Blank out the chain id if there was only one chain */
300 for (int r = 0; r < atoms->nres; r++)
302 atoms->resinfo[r].chainid = ' ';
307 static void read_stx_conf(const char *infile,
308 t_symtab *symtab, char ***name, t_atoms *atoms,
309 rvec x[], rvec *v, int *ePBC, matrix box)
314 char g96_line[STRLEN+1];
318 fprintf(stderr, "Warning: Number of atoms in %s is 0\n", infile);
320 else if (atoms->atom == nullptr)
322 gmx_mem("Uninitialized array atom");
330 ftp = fn2ftp(infile);
334 gmx_gro_read_conf(infile, symtab, name, atoms, x, v, box);
338 fr.natoms = atoms->nr;
343 in = gmx_fio_fopen(infile, "r");
344 read_g96_conf(in, infile, &fr, symtab, g96_line);
346 copy_mat(fr.box, box);
347 *name = put_symtab(symtab, fr.title);
348 sfree(const_cast<char *>(fr.title));
353 gmx_pdb_read_conf(infile, symtab, name, atoms, x, ePBC, box);
356 gmx_espresso_read_conf(infile, symtab, name, atoms, x, v, box);
359 gmx_incons("Not supported in read_stx_conf");
363 static void readConfAndAtoms(const char *infile,
364 t_symtab *symtab, char ***name, t_atoms *atoms,
366 rvec **x, rvec **v, matrix box)
369 get_stx_coordnum(infile, &natoms);
371 init_t_atoms(atoms, natoms, (fn2ftp(infile) == efPDB));
373 bool xIsNull = false;
384 read_stx_conf(infile,
386 *x, (v == nullptr) ? nullptr : *v, ePBC, box);
394 void readConfAndTopology(const char *infile,
395 bool *haveTopology, gmx_mtop_t *mtop,
397 rvec **x, rvec **v, matrix box)
399 GMX_RELEASE_ASSERT(mtop != nullptr, "readConfAndTopology requires mtop!=NULL");
406 *haveTopology = fn2bTPX(infile);
410 read_tpxheader(infile, &header, TRUE);
413 snew(*x, header.natoms);
417 snew(*v, header.natoms);
421 = read_tpx(infile, nullptr, box, &natoms,
422 (x == nullptr) ? nullptr : *x, (v == nullptr) ? nullptr : *v, mtop);
434 open_symtab(&symtab);
436 readConfAndAtoms(infile, &symtab, &name, &atoms, ePBC, x, v, box);
439 convertAtomsToMtop(&symtab, name, &atoms, mtop);
443 gmx_bool read_tps_conf(const char *infile, t_topology *top, int *ePBC,
444 rvec **x, rvec **v, matrix box, gmx_bool requireMasses)
449 // Note: We should have an initializer instead of relying on snew
451 readConfAndTopology(infile, &haveTopology, mtop, ePBC, x, v, box);
453 *top = gmx_mtop_t_to_t_topology(mtop, true);
456 tpx_make_chain_identifiers(&top->atoms, &top->mols);
458 if (requireMasses && !top->atoms.haveMass)
460 atomsSetMassesBasedOnNames(&top->atoms, TRUE);
462 if (!top->atoms.haveMass)
464 gmx_fatal(FARGS, "Masses were requested, but for some atom(s) masses could not be found in the database. Use a tpr file as input, if possible, or add these atoms to the mass database.");