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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);
83 fr.natoms = atoms->nr;
85 fr.atoms = const_cast<t_atoms *>(atoms);
87 fr.x = const_cast<rvec *>(x);
91 fr.v = const_cast<rvec *>(v);
94 copy_mat(box, fr.box);
95 out = gmx_fio_fopen(outfile, "w");
96 write_g96_conf(out, title, &fr, nindex, index);
103 out = gmx_fio_fopen(outfile, "w");
104 write_pdbfile_indexed(out, title, atoms, x, ePBC, box, ' ', -1, nindex, index, nullptr, TRUE);
108 out = gmx_fio_fopen(outfile, "w");
109 write_espresso_conf_indexed(out, title, atoms, nindex, index, x, v, box);
113 gmx_fatal(FARGS, "Sorry, can not write a topology to %s", outfile);
116 gmx_incons("Not supported in write_sto_conf_indexed");
120 void write_sto_conf(const char *outfile, const char *title, const t_atoms *atoms,
121 const rvec x[], const rvec *v, int ePBC, const matrix box)
127 ftp = fn2ftp(outfile);
131 write_conf_p(outfile, title, atoms, x, v, box);
134 clear_trxframe(&fr, TRUE);
135 fr.natoms = atoms->nr;
137 fr.atoms = const_cast<t_atoms *>(atoms); // TODO check
139 fr.x = const_cast<rvec *>(x);
143 fr.v = const_cast<rvec *>(v);
146 copy_mat(box, fr.box);
147 out = gmx_fio_fopen(outfile, "w");
148 write_g96_conf(out, title, &fr, -1, nullptr);
154 out = gmx_fio_fopen(outfile, "w");
155 write_pdbfile(out, title, atoms, x, ePBC, box, ' ', -1, nullptr, TRUE);
159 out = gmx_fio_fopen(outfile, "w");
160 write_espresso_conf_indexed(out, title, atoms, atoms->nr, nullptr, x, v, box);
164 gmx_fatal(FARGS, "Sorry, can not write a topology to %s", outfile);
167 gmx_incons("Not supported in write_sto_conf");
171 void write_sto_conf_mtop(const char *outfile, const char *title,
173 const rvec x[], const rvec *v, int ePBC, const matrix box)
179 ftp = fn2ftp(outfile);
183 out = gmx_fio_fopen(outfile, "w");
184 write_hconf_mtop(out, title, mtop, x, v, box);
188 /* This is a brute force approach which requires a lot of memory.
189 * We should implement mtop versions of all writing routines.
191 atoms = gmx_mtop_global_atoms(mtop);
193 write_sto_conf(outfile, title, &atoms, x, v, ePBC, box);
200 static void get_stx_coordnum(const char *infile, int *natoms)
205 char g96_line[STRLEN+1];
207 ftp = fn2ftp(infile);
208 range_check(ftp, 0, efNR);
212 get_coordnum(infile, natoms);
216 in = gmx_fio_fopen(infile, "r");
222 *natoms = read_g96_conf(in, infile, nullptr, &fr, nullptr, g96_line);
229 in = gmx_fio_fopen(infile, "r");
230 get_pdb_coordnum(in, natoms);
234 *natoms = get_espresso_coordnum(infile);
237 gmx_fatal(FARGS, "File type %s not supported in get_stx_coordnum",
242 static void tpx_make_chain_identifiers(t_atoms *atoms, t_block *mols)
244 /* We always assign a new chain number, but save the chain id characters
245 * for larger molecules.
247 const int chainMinAtoms = 15;
251 bool outOfIds = false;
252 for (int m = 0; m < mols->nr; m++)
254 int a0 = mols->index[m];
255 int a1 = mols->index[m+1];
257 if (a1 - a0 >= chainMinAtoms && !outOfIds)
259 /* Set the chain id for the output */
261 /* Here we allow for the max possible 2*26+10=62 chain ids */
266 else if (chainid == 'z')
270 else if (chainid == '9')
283 for (int a = a0; a < a1; a++)
285 atoms->resinfo[atoms->atom[a].resind].chainnum = chainnum;
286 atoms->resinfo[atoms->atom[a].resind].chainid = c;
291 /* Blank out the chain id if there was only one chain */
294 for (int r = 0; r < atoms->nres; r++)
296 atoms->resinfo[r].chainid = ' ';
301 static void read_stx_conf(const char *infile,
302 t_symtab *symtab, char **name, t_atoms *atoms,
303 rvec x[], rvec *v, int *ePBC, matrix box)
308 char g96_line[STRLEN+1];
312 fprintf(stderr, "Warning: Number of atoms in %s is 0\n", infile);
314 else if (atoms->atom == nullptr)
316 gmx_mem("Uninitialized array atom");
324 ftp = fn2ftp(infile);
328 gmx_gro_read_conf(infile, symtab, name, atoms, x, v, box);
331 fr.natoms = atoms->nr;
336 in = gmx_fio_fopen(infile, "r");
337 read_g96_conf(in, infile, name, &fr, symtab, g96_line);
339 copy_mat(fr.box, box);
344 gmx_pdb_read_conf(infile, symtab, name, atoms, x, ePBC, box);
347 gmx_espresso_read_conf(infile, symtab, name, atoms, x, v, box);
350 gmx_incons("Not supported in read_stx_conf");
354 static void readConfAndAtoms(const char *infile,
355 t_symtab *symtab, char **name, t_atoms *atoms,
357 rvec **x, rvec **v, matrix box)
360 get_stx_coordnum(infile, &natoms);
362 init_t_atoms(atoms, natoms, (fn2ftp(infile) == efPDB));
364 bool xIsNull = false;
375 read_stx_conf(infile,
377 *x, (v == nullptr) ? nullptr : *v, ePBC, box);
385 void readConfAndTopology(const char *infile,
386 bool *haveTopology, gmx_mtop_t *mtop,
388 rvec **x, rvec **v, matrix box)
390 GMX_RELEASE_ASSERT(mtop != nullptr, "readConfAndTopology requires mtop!=NULL");
397 *haveTopology = fn2bTPX(infile);
401 read_tpxheader(infile, &header, TRUE);
404 snew(*x, header.natoms);
408 snew(*v, header.natoms);
412 = read_tpx(infile, nullptr, box, &natoms,
413 (x == nullptr) ? nullptr : *x, (v == nullptr) ? nullptr : *v, mtop);
425 open_symtab(&symtab);
427 readConfAndAtoms(infile, &symtab, &name, &atoms, ePBC, x, v, box);
430 convertAtomsToMtop(&symtab, put_symtab(&symtab, name), &atoms, mtop);
435 gmx_bool read_tps_conf(const char *infile, t_topology *top, int *ePBC,
436 rvec **x, rvec **v, matrix box, gmx_bool requireMasses)
441 // Note: We should have an initializer instead of relying on snew
443 readConfAndTopology(infile, &haveTopology, mtop, ePBC, x, v, box);
445 *top = gmx_mtop_t_to_t_topology(mtop, true);
448 tpx_make_chain_identifiers(&top->atoms, &top->mols);
450 if (requireMasses && !top->atoms.haveMass)
452 atomsSetMassesBasedOnNames(&top->atoms, TRUE);
454 if (!top->atoms.haveMass)
456 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.");