src/gromacs/fileio/confio.cpp

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  37 #include "gmxpre.h"
  38
  39 #include "confio.h"
  40
  41 #include <cstdio>
  42 #include <cstring>
  43
  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"
  63
  64 void write_sto_conf_indexed(const char *outfile, const char *title,
  65                             const t_atoms *atoms,
  66                             const rvec x[], const rvec *v, int ePBC, const matrix box,
  67                             int nindex, int index[])
  68 {
  69     FILE       *out;
  70     int         ftp;
  71     t_trxframe  fr;
  72
  73     ftp = fn2ftp(outfile);
  74     switch (ftp)
  75     {
  76         case efGRO:
  77             out = gmx_fio_fopen(outfile, "w");
  78             write_hconf_indexed_p(out, title, atoms, nindex, index, x, v, box);
  79             gmx_fio_fclose(out);
  80             break;
  81         case efG96:
  82             clear_trxframe(&fr, TRUE);
  83             fr.bTitle = TRUE;
  84             fr.title  = title;
  85             fr.natoms = atoms->nr;
  86             fr.bAtoms = TRUE;
  87             fr.atoms  = const_cast<t_atoms *>(atoms);
  88             fr.bX     = TRUE;
  89             fr.x      = const_cast<rvec *>(x);
  90             if (v)
  91             {
  92                 fr.bV = TRUE;
  93                 fr.v  = const_cast<rvec *>(v);
  94             }
  95             fr.bBox = TRUE;
  96             copy_mat(box, fr.box);
  97             out = gmx_fio_fopen(outfile, "w");
  98             write_g96_conf(out, &fr, nindex, index);
  99             gmx_fio_fclose(out);
 100             break;
 101         case efPDB:
 102         case efBRK:
 103         case efENT:
 104         case efPQR:
 105             out = gmx_fio_fopen(outfile, "w");
 106             write_pdbfile_indexed(out, title, atoms, x, ePBC, box, ' ', -1, nindex, index, NULL, TRUE);
 107             gmx_fio_fclose(out);
 108             break;
 109         case efESP:
 110             out = gmx_fio_fopen(outfile, "w");
 111             write_espresso_conf_indexed(out, title, atoms, nindex, index, x, v, box);
 112             gmx_fio_fclose(out);
 113             break;
 114         case efTPR:
 115             gmx_fatal(FARGS, "Sorry, can not write a topology to %s", outfile);
 116             break;
 117         default:
 118             gmx_incons("Not supported in write_sto_conf_indexed");
 119     }
 120 }
 121
 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)
 124 {
 125     FILE       *out;
 126     int         ftp;
 127     t_trxframe  fr;
 128
 129     ftp = fn2ftp(outfile);
 130     switch (ftp)
 131     {
 132         case efGRO:
 133             write_conf_p(outfile, title, atoms, x, v, box);
 134             break;
 135         case efG96:
 136             clear_trxframe(&fr, TRUE);
 137             fr.bTitle = TRUE;
 138             fr.title  = title;
 139             fr.natoms = atoms->nr;
 140             fr.bAtoms = TRUE;
 141             fr.atoms  = const_cast<t_atoms *>(atoms); // TODO check
 142             fr.bX     = TRUE;
 143             fr.x      = const_cast<rvec *>(x);
 144             if (v)
 145             {
 146                 fr.bV = TRUE;
 147                 fr.v  = const_cast<rvec *>(v);
 148             }
 149             fr.bBox = TRUE;
 150             copy_mat(box, fr.box);
 151             out = gmx_fio_fopen(outfile, "w");
 152             write_g96_conf(out, &fr, -1, NULL);
 153             gmx_fio_fclose(out);
 154             break;
 155         case efPDB:
 156         case efBRK:
 157         case efENT:
 158             out = gmx_fio_fopen(outfile, "w");
 159             write_pdbfile(out, title, atoms, x, ePBC, box, ' ', -1, NULL, TRUE);
 160             gmx_fio_fclose(out);
 161             break;
 162         case efESP:
 163             out = gmx_fio_fopen(outfile, "w");
 164             write_espresso_conf_indexed(out, title, atoms, atoms->nr, NULL, x, v, box);
 165             gmx_fio_fclose(out);
 166             break;
 167         case efTPR:
 168             gmx_fatal(FARGS, "Sorry, can not write a topology to %s", outfile);
 169             break;
 170         default:
 171             gmx_incons("Not supported in write_sto_conf");
 172     }
 173 }
 174
 175 void write_sto_conf_mtop(const char *outfile, const char *title,
 176                          gmx_mtop_t *mtop,
 177                          const rvec x[], const rvec *v, int ePBC, const matrix box)
 178 {
 179     int     ftp;
 180     FILE   *out;
 181     t_atoms atoms;
 182
 183     ftp = fn2ftp(outfile);
 184     switch (ftp)
 185     {
 186         case efGRO:
 187             out = gmx_fio_fopen(outfile, "w");
 188             write_hconf_mtop(out, title, mtop, x, v, box);
 189             gmx_fio_fclose(out);
 190             break;
 191         default:
 192             /* This is a brute force approach which requires a lot of memory.
 193              * We should implement mtop versions of all writing routines.
 194              */
 195             atoms = gmx_mtop_global_atoms(mtop);
 196
 197             write_sto_conf(outfile, title, &atoms, x, v, ePBC, box);
 198
 199             done_atom(&atoms);
 200             break;
 201     }
 202 }
 203
 204 static void get_stx_coordnum(const char *infile, int *natoms)
 205 {
 206     FILE      *in;
 207     int        ftp;
 208     t_trxframe fr;
 209     char       g96_line[STRLEN+1];
 210
 211     ftp = fn2ftp(infile);
 212     range_check(ftp, 0, efNR);
 213     switch (ftp)
 214     {
 215         case efGRO:
 216             get_coordnum(infile, natoms);
 217             break;
 218         case efG96:
 219         {
 220             in        = gmx_fio_fopen(infile, "r");
 221             fr.title  = NULL;
 222             fr.natoms = -1;
 223             fr.atoms  = NULL;
 224             fr.x      = NULL;
 225             fr.v      = NULL;
 226             fr.f      = NULL;
 227             *natoms   = read_g96_conf(in, infile, &fr, NULL, g96_line);
 228             sfree(const_cast<char *>(fr.title));
 229             gmx_fio_fclose(in);
 230             break;
 231         }
 232         case efPDB:
 233         case efBRK:
 234         case efENT:
 235             in = gmx_fio_fopen(infile, "r");
 236             get_pdb_coordnum(in, natoms);
 237             gmx_fio_fclose(in);
 238             break;
 239         case efESP:
 240             *natoms = get_espresso_coordnum(infile);
 241             break;
 242         default:
 243             gmx_fatal(FARGS, "File type %s not supported in get_stx_coordnum",
 244                       ftp2ext(ftp));
 245     }
 246 }
 247
 248 static void tpx_make_chain_identifiers(t_atoms *atoms, t_block *mols)
 249 {
 250     /* We always assign a new chain number, but save the chain id characters
 251      * for larger molecules.
 252      */
 253     const int chainMinAtoms = 15;
 254
 255     int       chainnum = 0;
 256     char      chainid  = 'A';
 257     bool      outOfIds = false;
 258     for (int m = 0; m < mols->nr; m++)
 259     {
 260         int a0 = mols->index[m];
 261         int a1 = mols->index[m+1];
 262         int c;
 263         if (a1 - a0 >= chainMinAtoms && !outOfIds)
 264         {
 265             /* Set the chain id for the output */
 266             c = chainid;
 267             /* Here we allow for the max possible 2*26+10=62 chain ids */
 268             if (chainid == 'Z')
 269             {
 270                 chainid = 'a';
 271             }
 272             else if (chainid == 'z')
 273             {
 274                 chainid = '0';
 275             }
 276             else if (chainid == '9')
 277             {
 278                 outOfIds = true;
 279             }
 280             else
 281             {
 282                 chainid++;
 283             }
 284         }
 285         else
 286         {
 287             c = ' ';
 288         }
 289         for (int a = a0; a < a1; a++)
 290         {
 291             atoms->resinfo[atoms->atom[a].resind].chainnum = chainnum;
 292             atoms->resinfo[atoms->atom[a].resind].chainid  = c;
 293         }
 294         chainnum++;
 295     }
 296
 297     /* Blank out the chain id if there was only one chain */
 298     if (chainid == 'B')
 299     {
 300         for (int r = 0; r < atoms->nres; r++)
 301         {
 302             atoms->resinfo[r].chainid = ' ';
 303         }
 304     }
 305 }
 306
 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)
 310 {
 311     FILE       *in;
 312     t_trxframe  fr;
 313     int         ftp;
 314     char        g96_line[STRLEN+1];
 315
 316     if (atoms->nr == 0)
 317     {
 318         fprintf(stderr, "Warning: Number of atoms in %s is 0\n", infile);
 319     }
 320     else if (atoms->atom == NULL)
 321     {
 322         gmx_mem("Uninitialized array atom");
 323     }
 324
 325     if (ePBC)
 326     {
 327         *ePBC = -1;
 328     }
 329
 330     ftp = fn2ftp(infile);
 331     switch (ftp)
 332     {
 333         case efGRO:
 334             gmx_gro_read_conf(infile, symtab, name, atoms, x, v, box);
 335             break;
 336         case efG96:
 337             fr.title  = NULL;
 338             fr.natoms = atoms->nr;
 339             fr.atoms  = atoms;
 340             fr.x      = x;
 341             fr.v      = v;
 342             fr.f      = NULL;
 343             in        = gmx_fio_fopen(infile, "r");
 344             read_g96_conf(in, infile, &fr, symtab, g96_line);
 345             gmx_fio_fclose(in);
 346             copy_mat(fr.box, box);
 347             *name     = put_symtab(symtab, fr.title);
 348             sfree(const_cast<char *>(fr.title));
 349             break;
 350         case efPDB:
 351         case efBRK:
 352         case efENT:
 353             gmx_pdb_read_conf(infile, symtab, name, atoms, x, ePBC, box);
 354             break;
 355         case efESP:
 356             gmx_espresso_read_conf(infile, symtab, name, atoms, x, v, box);
 357             break;
 358         default:
 359             gmx_incons("Not supported in read_stx_conf");
 360     }
 361 }
 362
 363 static void done_gmx_groups_t(gmx_groups_t *g)
 364 {
 365     int i;
 366
 367     for (i = 0; (i < egcNR); i++)
 368     {
 369         if (NULL != g->grps[i].nm_ind)
 370         {
 371             sfree(g->grps[i].nm_ind);
 372             g->grps[i].nm_ind = NULL;
 373         }
 374         if (NULL != g->grpnr[i])
 375         {
 376             sfree(g->grpnr[i]);
 377             g->grpnr[i] = NULL;
 378         }
 379     }
 380     /* The contents of this array is in symtab, don't free it here */
 381     sfree(g->grpname);
 382 }
 383
 384 static void readConfAndAtoms(const char *infile,
 385                              t_symtab *symtab, char ***name, t_atoms *atoms,
 386                              int *ePBC,
 387                              rvec **x, rvec **v, matrix box)
 388 {
 389     int natoms;
 390     get_stx_coordnum(infile, &natoms);
 391
 392     init_t_atoms(atoms, natoms, (fn2ftp(infile) == efPDB));
 393
 394     bool xIsNull = false;
 395     if (x == NULL)
 396     {
 397         snew(x, 1);
 398         xIsNull = true;
 399     }
 400     snew(*x, natoms);
 401     if (v)
 402     {
 403         snew(*v, natoms);
 404     }
 405     read_stx_conf(infile,
 406                   symtab, name, atoms,
 407                   *x, (v == NULL) ? NULL : *v, ePBC, box);
 408     if (xIsNull)
 409     {
 410         sfree(*x);
 411         sfree(x);
 412     }
 413 }
 414
 415 void readConfAndTopology(const char *infile,
 416                          bool *haveTopology, gmx_mtop_t *mtop,
 417                          int *ePBC,
 418                          rvec **x, rvec **v, matrix box)
 419 {
 420     GMX_RELEASE_ASSERT(mtop != NULL, "readConfAndTopology requires mtop!=NULL");
 421
 422     if (ePBC != NULL)
 423     {
 424         *ePBC = -1;
 425     }
 426
 427     *haveTopology = fn2bTPX(infile);
 428     if (*haveTopology)
 429     {
 430         t_tpxheader header;
 431         read_tpxheader(infile, &header, TRUE);
 432         if (x)
 433         {
 434             snew(*x, header.natoms);
 435         }
 436         if (v)
 437         {
 438             snew(*v, header.natoms);
 439         }
 440         int natoms;
 441         int ePBC_tmp
 442             = read_tpx(infile, NULL, box, &natoms,
 443                        (x == NULL) ? NULL : *x, (v == NULL) ? NULL : *v, mtop);
 444         if (ePBC != NULL)
 445         {
 446             *ePBC = ePBC_tmp;
 447         }
 448     }
 449     else
 450     {
 451         t_symtab   symtab;
 452         char     **name;
 453         t_atoms    atoms;
 454
 455         open_symtab(&symtab);
 456
 457         readConfAndAtoms(infile, &symtab, &name, &atoms, ePBC, x, v, box);
 458
 459         init_mtop(mtop);
 460         convertAtomsToMtop(&symtab, name, &atoms, mtop);
 461     }
 462 }
 463
 464 gmx_bool read_tps_conf(const char *infile, t_topology *top, int *ePBC,
 465                        rvec **x, rvec **v, matrix box, gmx_bool requireMasses)
 466 {
 467     bool        haveTopology;
 468     gmx_mtop_t *mtop;
 469
 470     // Note: We should have an initializer instead of relying on snew
 471     snew(mtop, 1);
 472     readConfAndTopology(infile, &haveTopology, mtop, ePBC, x, v, box);
 473
 474     *top = gmx_mtop_t_to_t_topology(mtop);
 475     /* In this case we need to throw away the group data too */
 476     done_gmx_groups_t(&mtop->groups);
 477     sfree(mtop);
 478
 479     tpx_make_chain_identifiers(&top->atoms, &top->mols);
 480
 481     if (requireMasses && !top->atoms.haveMass)
 482     {
 483         atomsSetMassesBasedOnNames(&top->atoms, TRUE);
 484
 485         if (!top->atoms.haveMass)
 486         {
 487             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.");
 488         }
 489     }
 490
 491     return haveTopology;
 492 }