| File: | gromacs/gmxana/gmx_make_ndx.c |
| Location: | line 1385, column 13 |
| Description: | Value stored to 'nr1' is never read |
| 1 | /* |
| 2 | * This file is part of the GROMACS molecular simulation package. |
| 3 | * |
| 4 | * Copyright (c) 1991-2000, University of Groningen, The Netherlands. |
| 5 | * Copyright (c) 2001-2004, The GROMACS development team. |
| 6 | * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by |
| 7 | * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, |
| 8 | * and including many others, as listed in the AUTHORS file in the |
| 9 | * top-level source directory and at http://www.gromacs.org. |
| 10 | * |
| 11 | * GROMACS is free software; you can redistribute it and/or |
| 12 | * modify it under the terms of the GNU Lesser General Public License |
| 13 | * as published by the Free Software Foundation; either version 2.1 |
| 14 | * of the License, or (at your option) any later version. |
| 15 | * |
| 16 | * GROMACS is distributed in the hope that it will be useful, |
| 17 | * but WITHOUT ANY WARRANTY; without even the implied warranty of |
| 18 | * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU |
| 19 | * Lesser General Public License for more details. |
| 20 | * |
| 21 | * You should have received a copy of the GNU Lesser General Public |
| 22 | * License along with GROMACS; if not, see |
| 23 | * http://www.gnu.org/licenses, or write to the Free Software Foundation, |
| 24 | * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. |
| 25 | * |
| 26 | * If you want to redistribute modifications to GROMACS, please |
| 27 | * consider that scientific software is very special. Version |
| 28 | * control is crucial - bugs must be traceable. We will be happy to |
| 29 | * consider code for inclusion in the official distribution, but |
| 30 | * derived work must not be called official GROMACS. Details are found |
| 31 | * in the README & COPYING files - if they are missing, get the |
| 32 | * official version at http://www.gromacs.org. |
| 33 | * |
| 34 | * To help us fund GROMACS development, we humbly ask that you cite |
| 35 | * the research papers on the package. Check out http://www.gromacs.org. |
| 36 | */ |
| 37 | #ifdef HAVE_CONFIG_H1 |
| 38 | #include <config.h> |
| 39 | #endif |
| 40 | |
| 41 | #include <ctype.h> |
| 42 | #include <string.h> |
| 43 | |
| 44 | #include "gromacs/utility/futil.h" |
| 45 | #include "macros.h" |
| 46 | #include "gromacs/utility/cstringutil.h" |
| 47 | #include "gromacs/commandline/pargs.h" |
| 48 | #include "gromacs/fileio/confio.h" |
| 49 | #include "typedefs.h" |
| 50 | #include "index.h" |
| 51 | #include "gromacs/utility/smalloc.h" |
| 52 | #include "gromacs/math/vec.h" |
| 53 | #include "index.h" |
| 54 | |
| 55 | #include "gromacs/utility/fatalerror.h" |
| 56 | |
| 57 | #define MAXNAMES30 30 |
| 58 | #define NAME_LEN30 30 |
| 59 | |
| 60 | gmx_bool bCase = FALSE0; |
| 61 | |
| 62 | static int or_groups(atom_id nr1, atom_id *at1, atom_id nr2, atom_id *at2, |
| 63 | atom_id *nr, atom_id *at) |
| 64 | { |
| 65 | atom_id i1, i2, max = 0; |
| 66 | gmx_bool bNotIncr; |
| 67 | |
| 68 | *nr = 0; |
| 69 | |
| 70 | bNotIncr = FALSE0; |
| 71 | for (i1 = 0; i1 < nr1; i1++) |
| 72 | { |
| 73 | if ((i1 > 0) && (at1[i1] <= max)) |
| 74 | { |
| 75 | bNotIncr = TRUE1; |
| 76 | } |
| 77 | max = at1[i1]; |
| 78 | } |
| 79 | for (i1 = 0; i1 < nr2; i1++) |
| 80 | { |
| 81 | if ((i1 > 0) && (at2[i1] <= max)) |
| 82 | { |
| 83 | bNotIncr = TRUE1; |
| 84 | } |
| 85 | max = at2[i1]; |
| 86 | } |
| 87 | |
| 88 | if (bNotIncr) |
| 89 | { |
| 90 | printf("One of your groups is not ascending\n"); |
| 91 | } |
| 92 | else |
| 93 | { |
| 94 | i1 = 0; |
| 95 | i2 = 0; |
| 96 | *nr = 0; |
| 97 | while ((i1 < nr1) || (i2 < nr2)) |
| 98 | { |
| 99 | if ((i2 == nr2) || ((i1 < nr1) && (at1[i1] < at2[i2]))) |
| 100 | { |
| 101 | at[*nr] = at1[i1]; |
| 102 | (*nr)++; |
| 103 | i1++; |
| 104 | } |
| 105 | else |
| 106 | { |
| 107 | if ((i2 < nr2) && ((i1 == nr1) || (at1[i1] > at2[i2]))) |
| 108 | { |
| 109 | at[*nr] = at2[i2]; |
| 110 | (*nr)++; |
| 111 | } |
| 112 | i2++; |
| 113 | } |
| 114 | } |
| 115 | |
| 116 | printf("Merged two groups with OR: %d %d -> %d\n", nr1, nr2, *nr); |
| 117 | } |
| 118 | |
| 119 | return *nr; |
| 120 | } |
| 121 | |
| 122 | static int and_groups(atom_id nr1, atom_id *at1, atom_id nr2, atom_id *at2, |
| 123 | atom_id *nr, atom_id *at) |
| 124 | { |
| 125 | atom_id i1, i2; |
| 126 | |
| 127 | *nr = 0; |
| 128 | for (i1 = 0; i1 < nr1; i1++) |
| 129 | { |
| 130 | for (i2 = 0; i2 < nr2; i2++) |
| 131 | { |
| 132 | if (at1[i1] == at2[i2]) |
| 133 | { |
| 134 | at[*nr] = at1[i1]; |
| 135 | (*nr)++; |
| 136 | } |
| 137 | } |
| 138 | } |
| 139 | |
| 140 | printf("Merged two groups with AND: %d %d -> %d\n", nr1, nr2, *nr); |
| 141 | |
| 142 | return *nr; |
| 143 | } |
| 144 | |
| 145 | static gmx_bool is_name_char(char c) |
| 146 | { |
| 147 | /* This string should contain all characters that can not be |
| 148 | * the first letter of a name due to the make_ndx syntax. |
| 149 | */ |
| 150 | const char *spec = " !&|"; |
| 151 | |
| 152 | return (c != '\0' && strchr(spec, c)(__extension__ (__builtin_constant_p (c) && !__builtin_constant_p (spec) && (c) == '\0' ? (char *) __rawmemchr (spec, c ) : __builtin_strchr (spec, c))) == NULL((void*)0)); |
| 153 | } |
| 154 | |
| 155 | static int parse_names(char **string, int *n_names, char **names) |
| 156 | { |
| 157 | int i; |
| 158 | |
| 159 | *n_names = 0; |
| 160 | while (is_name_char((*string)[0]) || (*string)[0] == ' ') |
| 161 | { |
| 162 | if (is_name_char((*string)[0])) |
| 163 | { |
| 164 | if (*n_names >= MAXNAMES30) |
| 165 | { |
| 166 | gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_make_ndx.c" , 166, "To many names: %d\n", *n_names+1); |
| 167 | } |
| 168 | i = 0; |
| 169 | while (is_name_char((*string)[i])) |
| 170 | { |
| 171 | names[*n_names][i] = (*string)[i]; |
| 172 | i++; |
| 173 | if (i > NAME_LEN30) |
| 174 | { |
| 175 | printf("Name is too long, the maximum is %d characters\n", NAME_LEN30); |
| 176 | return 0; |
| 177 | } |
| 178 | } |
| 179 | names[*n_names][i] = '\0'; |
| 180 | if (!bCase) |
| 181 | { |
| 182 | upstring(names[*n_names]); |
| 183 | } |
| 184 | *string += i; |
| 185 | (*n_names)++; |
| 186 | } |
| 187 | else |
| 188 | { |
| 189 | (*string)++; |
| 190 | } |
| 191 | } |
| 192 | |
| 193 | return *n_names; |
| 194 | } |
| 195 | |
| 196 | static gmx_bool parse_int_char(char **string, int *nr, char *c) |
| 197 | { |
| 198 | char *orig; |
| 199 | gmx_bool bRet; |
| 200 | |
| 201 | orig = *string; |
| 202 | |
| 203 | while ((*string)[0] == ' ') |
| 204 | { |
| 205 | (*string)++; |
| 206 | } |
| 207 | |
| 208 | bRet = FALSE0; |
| 209 | |
| 210 | *c = ' '; |
| 211 | |
| 212 | if (isdigit((*string)[0])((*__ctype_b_loc ())[(int) (((*string)[0]))] & (unsigned short int) _ISdigit)) |
| 213 | { |
| 214 | *nr = (*string)[0]-'0'; |
| 215 | (*string)++; |
| 216 | while (isdigit((*string)[0])((*__ctype_b_loc ())[(int) (((*string)[0]))] & (unsigned short int) _ISdigit)) |
| 217 | { |
| 218 | *nr = (*nr)*10+(*string)[0]-'0'; |
| 219 | (*string)++; |
| 220 | } |
| 221 | if (isalpha((*string)[0])((*__ctype_b_loc ())[(int) (((*string)[0]))] & (unsigned short int) _ISalpha)) |
| 222 | { |
| 223 | *c = (*string)[0]; |
| 224 | (*string)++; |
| 225 | } |
| 226 | /* Check if there is at most one non-digit character */ |
| 227 | if (!isalnum((*string)[0])((*__ctype_b_loc ())[(int) (((*string)[0]))] & (unsigned short int) _ISalnum)) |
| 228 | { |
| 229 | bRet = TRUE1; |
| 230 | } |
| 231 | else |
| 232 | { |
| 233 | *string = orig; |
| 234 | } |
| 235 | } |
| 236 | else |
| 237 | { |
| 238 | *nr = NOTSET-12345; |
| 239 | } |
| 240 | |
| 241 | return bRet; |
| 242 | } |
| 243 | |
| 244 | static gmx_bool parse_int(char **string, int *nr) |
| 245 | { |
| 246 | char *orig, c; |
| 247 | gmx_bool bRet; |
| 248 | |
| 249 | orig = *string; |
| 250 | bRet = parse_int_char(string, nr, &c); |
| 251 | if (bRet && c != ' ') |
| 252 | { |
| 253 | *string = orig; |
| 254 | bRet = FALSE0; |
| 255 | } |
| 256 | |
| 257 | return bRet; |
| 258 | } |
| 259 | |
| 260 | static gmx_bool isquote(char c) |
| 261 | { |
| 262 | return (c == '\"'); |
| 263 | } |
| 264 | |
| 265 | static gmx_bool parse_string(char **string, int *nr, int ngrps, char **grpname) |
| 266 | { |
| 267 | char *s, *sp; |
| 268 | char c; |
| 269 | |
| 270 | while ((*string)[0] == ' ') |
| 271 | { |
| 272 | (*string)++; |
| 273 | } |
| 274 | |
| 275 | (*nr) = NOTSET-12345; |
| 276 | if (isquote((*string)[0])) |
| 277 | { |
| 278 | c = (*string)[0]; |
| 279 | (*string)++; |
| 280 | s = strdup((*string))(__extension__ (__builtin_constant_p ((*string)) && ( (size_t)(const void *)(((*string)) + 1) - (size_t)(const void *)((*string)) == 1) ? (((const char *) ((*string)))[0] == '\0' ? (char *) calloc ((size_t) 1, (size_t) 1) : ({ size_t __len = strlen ((*string)) + 1; char *__retval = (char *) malloc ( __len); if (__retval != ((void*)0)) __retval = (char *) memcpy (__retval, (*string), __len); __retval; })) : __strdup ((*string )))); |
| 281 | sp = strchr(s, c)(__extension__ (__builtin_constant_p (c) && !__builtin_constant_p (s) && (c) == '\0' ? (char *) __rawmemchr (s, c) : __builtin_strchr (s, c))); |
| 282 | if (sp != NULL((void*)0)) |
| 283 | { |
| 284 | (*string) += sp-s + 1; |
| 285 | sp[0] = '\0'; |
| 286 | (*nr) = find_group(s, ngrps, grpname); |
| 287 | } |
| 288 | } |
| 289 | |
| 290 | return (*nr) != NOTSET-12345; |
| 291 | } |
| 292 | |
| 293 | static int select_atomnumbers(char **string, t_atoms *atoms, atom_id n1, |
| 294 | atom_id *nr, atom_id *index, char *gname) |
| 295 | { |
| 296 | char buf[STRLEN4096]; |
| 297 | int i, up; |
| 298 | |
| 299 | *nr = 0; |
| 300 | while ((*string)[0] == ' ') |
| 301 | { |
| 302 | (*string)++; |
| 303 | } |
| 304 | if ((*string)[0] == '-') |
| 305 | { |
| 306 | (*string)++; |
| 307 | parse_int(string, &up); |
| 308 | if ((n1 < 1) || (n1 > atoms->nr) || (up < 1) || (up > atoms->nr)) |
| 309 | { |
| 310 | printf("Invalid atom range\n"); |
| 311 | } |
| 312 | else |
| 313 | { |
| 314 | for (i = n1-1; i <= up-1; i++) |
| 315 | { |
| 316 | index[*nr] = i; |
| 317 | (*nr)++; |
| 318 | } |
| 319 | printf("Found %d atom%s in range %d-%d\n", *nr, (*nr == 1) ? "" : "s", n1, up); |
| 320 | if (n1 == up) |
| 321 | { |
| 322 | sprintf(buf, "a_%d", n1); |
| 323 | } |
| 324 | else |
| 325 | { |
| 326 | sprintf(buf, "a_%d-%d", n1, up); |
| 327 | } |
| 328 | strcpy(gname, buf); |
| 329 | } |
| 330 | } |
| 331 | else |
| 332 | { |
| 333 | i = n1; |
| 334 | sprintf(gname, "a"); |
| 335 | do |
| 336 | { |
| 337 | if ((i-1 >= 0) && (i-1 < atoms->nr)) |
| 338 | { |
| 339 | index[*nr] = i-1; |
| 340 | (*nr)++; |
| 341 | sprintf(buf, "_%d", i); |
| 342 | strcat(gname, buf); |
| 343 | } |
| 344 | else |
| 345 | { |
| 346 | printf("Invalid atom number %d\n", i); |
| 347 | *nr = 0; |
| 348 | } |
| 349 | } |
| 350 | while ((*nr != 0) && (parse_int(string, &i))); |
| 351 | } |
| 352 | |
| 353 | return *nr; |
| 354 | } |
| 355 | |
| 356 | static int select_residuenumbers(char **string, t_atoms *atoms, |
| 357 | atom_id n1, char c, |
| 358 | atom_id *nr, atom_id *index, char *gname) |
| 359 | { |
| 360 | char buf[STRLEN4096]; |
| 361 | int i, j, up; |
| 362 | t_resinfo *ri; |
| 363 | |
| 364 | *nr = 0; |
| 365 | while ((*string)[0] == ' ') |
| 366 | { |
| 367 | (*string)++; |
| 368 | } |
| 369 | if ((*string)[0] == '-') |
| 370 | { |
| 371 | /* Residue number range selection */ |
| 372 | if (c != ' ') |
| 373 | { |
| 374 | printf("Error: residue insertion codes can not be used with residue range selection\n"); |
| 375 | return 0; |
| 376 | } |
| 377 | (*string)++; |
| 378 | parse_int(string, &up); |
| 379 | |
| 380 | for (i = 0; i < atoms->nr; i++) |
| 381 | { |
| 382 | ri = &atoms->resinfo[atoms->atom[i].resind]; |
| 383 | for (j = n1; (j <= up); j++) |
| 384 | { |
| 385 | if (ri->nr == j && (c == ' ' || ri->ic == c)) |
| 386 | { |
| 387 | index[*nr] = i; |
| 388 | (*nr)++; |
| 389 | } |
| 390 | } |
| 391 | } |
| 392 | printf("Found %d atom%s with res.nr. in range %d-%d\n", |
| 393 | *nr, (*nr == 1) ? "" : "s", n1, up); |
| 394 | if (n1 == up) |
| 395 | { |
| 396 | sprintf(buf, "r_%d", n1); |
| 397 | } |
| 398 | else |
| 399 | { |
| 400 | sprintf(buf, "r_%d-%d", n1, up); |
| 401 | } |
| 402 | strcpy(gname, buf); |
| 403 | } |
| 404 | else |
| 405 | { |
| 406 | /* Individual residue number/insertion code selection */ |
| 407 | j = n1; |
| 408 | sprintf(gname, "r"); |
| 409 | do |
| 410 | { |
| 411 | for (i = 0; i < atoms->nr; i++) |
| 412 | { |
| 413 | ri = &atoms->resinfo[atoms->atom[i].resind]; |
| 414 | if (ri->nr == j && ri->ic == c) |
| 415 | { |
| 416 | index[*nr] = i; |
| 417 | (*nr)++; |
| 418 | } |
| 419 | } |
| 420 | sprintf(buf, "_%d", j); |
| 421 | strcat(gname, buf); |
| 422 | } |
| 423 | while (parse_int_char(string, &j, &c)); |
| 424 | } |
| 425 | |
| 426 | return *nr; |
| 427 | } |
| 428 | |
| 429 | static int select_residueindices(char **string, t_atoms *atoms, |
| 430 | atom_id n1, char c, |
| 431 | atom_id *nr, atom_id *index, char *gname) |
| 432 | { |
| 433 | /*this should be similar to select_residuenumbers except select by index (sequential numbering in file)*/ |
| 434 | /*resind+1 for 1-indexing*/ |
| 435 | char buf[STRLEN4096]; |
| 436 | int i, j, up; |
| 437 | t_resinfo *ri; |
| 438 | |
| 439 | *nr = 0; |
| 440 | while ((*string)[0] == ' ') |
| 441 | { |
| 442 | (*string)++; |
| 443 | } |
| 444 | if ((*string)[0] == '-') |
| 445 | { |
| 446 | /* Residue number range selection */ |
| 447 | if (c != ' ') |
| 448 | { |
| 449 | printf("Error: residue insertion codes can not be used with residue range selection\n"); |
| 450 | return 0; |
| 451 | } |
| 452 | (*string)++; |
| 453 | parse_int(string, &up); |
| 454 | |
| 455 | for (i = 0; i < atoms->nr; i++) |
| 456 | { |
| 457 | ri = &atoms->resinfo[atoms->atom[i].resind]; |
| 458 | for (j = n1; (j <= up); j++) |
| 459 | { |
| 460 | if (atoms->atom[i].resind+1 == j && (c == ' ' || ri->ic == c)) |
| 461 | { |
| 462 | index[*nr] = i; |
| 463 | (*nr)++; |
| 464 | } |
| 465 | } |
| 466 | } |
| 467 | printf("Found %d atom%s with resind.+1 in range %d-%d\n", |
| 468 | *nr, (*nr == 1) ? "" : "s", n1, up); |
| 469 | if (n1 == up) |
| 470 | { |
| 471 | sprintf(buf, "r_%d", n1); |
| 472 | } |
| 473 | else |
| 474 | { |
| 475 | sprintf(buf, "r_%d-%d", n1, up); |
| 476 | } |
| 477 | strcpy(gname, buf); |
| 478 | } |
| 479 | else |
| 480 | { |
| 481 | /* Individual residue number/insertion code selection */ |
| 482 | j = n1; |
| 483 | sprintf(gname, "r"); |
| 484 | do |
| 485 | { |
| 486 | for (i = 0; i < atoms->nr; i++) |
| 487 | { |
| 488 | ri = &atoms->resinfo[atoms->atom[i].resind]; |
| 489 | if (atoms->atom[i].resind+1 == j && ri->ic == c) |
| 490 | { |
| 491 | index[*nr] = i; |
| 492 | (*nr)++; |
| 493 | } |
| 494 | } |
| 495 | sprintf(buf, "_%d", j); |
| 496 | strcat(gname, buf); |
| 497 | } |
| 498 | while (parse_int_char(string, &j, &c)); |
| 499 | } |
| 500 | |
| 501 | return *nr; |
| 502 | } |
| 503 | |
| 504 | |
| 505 | static gmx_bool atoms_from_residuenumbers(t_atoms *atoms, int group, t_blocka *block, |
| 506 | atom_id *nr, atom_id *index, char *gname) |
| 507 | { |
| 508 | int i, j, j0, j1, resnr, nres; |
| 509 | |
| 510 | j0 = block->index[group]; |
| 511 | j1 = block->index[group+1]; |
| 512 | nres = atoms->nres; |
| 513 | for (j = j0; j < j1; j++) |
| 514 | { |
| 515 | if (block->a[j] >= nres) |
| 516 | { |
| 517 | printf("Index %s contains number>nres (%d>%d)\n", |
| 518 | gname, block->a[j]+1, nres); |
| 519 | return FALSE0; |
| 520 | } |
| 521 | } |
| 522 | for (i = 0; i < atoms->nr; i++) |
| 523 | { |
| 524 | resnr = atoms->resinfo[atoms->atom[i].resind].nr; |
| 525 | for (j = j0; j < j1; j++) |
| 526 | { |
| 527 | if (block->a[j]+1 == resnr) |
| 528 | { |
| 529 | index[*nr] = i; |
| 530 | (*nr)++; |
| 531 | break; |
| 532 | } |
| 533 | } |
| 534 | } |
| 535 | printf("Found %d atom%s in %d residues from group %s\n", |
| 536 | *nr, (*nr == 1) ? "" : "s", j1-j0, gname); |
| 537 | return *nr; |
| 538 | } |
| 539 | |
| 540 | static gmx_bool comp_name(char *name, char *search) |
| 541 | { |
| 542 | while (name[0] != '\0' && search[0] != '\0') |
| 543 | { |
| 544 | switch (search[0]) |
| 545 | { |
| 546 | case '?': |
| 547 | /* Always matches */ |
| 548 | break; |
| 549 | case '*': |
| 550 | if (search[1] != '\0') |
| 551 | { |
| 552 | printf("WARNING: Currently '*' is only supported at the end of an expression\n"); |
| 553 | return FALSE0; |
| 554 | } |
| 555 | else |
| 556 | { |
| 557 | return TRUE1; |
| 558 | } |
| 559 | break; |
| 560 | default: |
| 561 | /* Compare a single character */ |
| 562 | if (( bCase && strncmp(name, search, 1)(__extension__ (__builtin_constant_p (1) && ((__builtin_constant_p (name) && strlen (name) < ((size_t) (1))) || (__builtin_constant_p (search) && strlen (search) < ((size_t) (1)))) ? __extension__ ({ size_t __s1_len, __s2_len; (__builtin_constant_p (name) && __builtin_constant_p (search) && (__s1_len = strlen ( name), __s2_len = strlen (search), (!((size_t)(const void *)( (name) + 1) - (size_t)(const void *)(name) == 1) || __s1_len >= 4) && (!((size_t)(const void *)((search) + 1) - (size_t )(const void *)(search) == 1) || __s2_len >= 4)) ? __builtin_strcmp (name, search) : (__builtin_constant_p (name) && ((size_t )(const void *)((name) + 1) - (size_t)(const void *)(name) == 1) && (__s1_len = strlen (name), __s1_len < 4) ? ( __builtin_constant_p (search) && ((size_t)(const void *)((search) + 1) - (size_t)(const void *)(search) == 1) ? __builtin_strcmp (name, search) : (__extension__ ({ const unsigned char *__s2 = (const unsigned char *) (const char *) (search); int __result = (((const unsigned char *) (const char *) (name))[0] - __s2 [0]); if (__s1_len > 0 && __result == 0) { __result = (((const unsigned char *) (const char *) (name))[1] - __s2 [1]); if (__s1_len > 1 && __result == 0) { __result = (((const unsigned char *) (const char *) (name))[2] - __s2 [2]); if (__s1_len > 2 && __result == 0) __result = (((const unsigned char *) (const char *) (name))[3] - __s2[3 ]); } } __result; }))) : (__builtin_constant_p (search) && ((size_t)(const void *)((search) + 1) - (size_t)(const void * )(search) == 1) && (__s2_len = strlen (search), __s2_len < 4) ? (__builtin_constant_p (name) && ((size_t)( const void *)((name) + 1) - (size_t)(const void *)(name) == 1 ) ? __builtin_strcmp (name, search) : (- (__extension__ ({ const unsigned char *__s2 = (const unsigned char *) (const char *) (name); int __result = (((const unsigned char *) (const char *) (search))[0] - __s2[0]); if (__s2_len > 0 && __result == 0) { __result = (((const unsigned char *) (const char *) ( search))[1] - __s2[1]); if (__s2_len > 1 && __result == 0) { __result = (((const unsigned char *) (const char *) ( search))[2] - __s2[2]); if (__s2_len > 2 && __result == 0) __result = (((const unsigned char *) (const char *) (search ))[3] - __s2[3]); } } __result; })))) : __builtin_strcmp (name , search)))); }) : strncmp (name, search, 1)))) || |
| 563 | (!bCase && gmx_strncasecmp(name, search, 1))) |
| 564 | { |
| 565 | return FALSE0; |
| 566 | } |
| 567 | } |
| 568 | name++; |
| 569 | search++; |
| 570 | } |
| 571 | |
| 572 | return (name[0] == '\0' && (search[0] == '\0' || search[0] == '*')); |
| 573 | } |
| 574 | |
| 575 | static int select_chainnames(t_atoms *atoms, int n_names, char **names, |
| 576 | atom_id *nr, atom_id *index) |
| 577 | { |
| 578 | char name[2]; |
| 579 | int j; |
| 580 | atom_id i; |
| 581 | |
| 582 | name[1] = 0; |
| 583 | *nr = 0; |
| 584 | for (i = 0; i < atoms->nr; i++) |
| 585 | { |
| 586 | name[0] = atoms->resinfo[atoms->atom[i].resind].chainid; |
| 587 | j = 0; |
| 588 | while (j < n_names && !comp_name(name, names[j])) |
| 589 | { |
| 590 | j++; |
| 591 | } |
| 592 | if (j < n_names) |
| 593 | { |
| 594 | index[*nr] = i; |
| 595 | (*nr)++; |
| 596 | } |
| 597 | } |
| 598 | printf("Found %d atom%s with chain identifier%s", |
| 599 | *nr, (*nr == 1) ? "" : "s", (n_names == 1) ? "" : "s"); |
| 600 | for (j = 0; (j < n_names); j++) |
| 601 | { |
| 602 | printf(" %s", names[j]); |
| 603 | } |
| 604 | printf("\n"); |
| 605 | |
| 606 | return *nr; |
| 607 | } |
| 608 | |
| 609 | static int select_atomnames(t_atoms *atoms, int n_names, char **names, |
| 610 | atom_id *nr, atom_id *index, gmx_bool bType) |
| 611 | { |
| 612 | char *name; |
| 613 | int j; |
| 614 | atom_id i; |
| 615 | |
| 616 | *nr = 0; |
| 617 | for (i = 0; i < atoms->nr; i++) |
| 618 | { |
| 619 | if (bType) |
| 620 | { |
| 621 | name = *(atoms->atomtype[i]); |
| 622 | } |
| 623 | else |
| 624 | { |
| 625 | name = *(atoms->atomname[i]); |
| 626 | } |
| 627 | j = 0; |
| 628 | while (j < n_names && !comp_name(name, names[j])) |
| 629 | { |
| 630 | j++; |
| 631 | } |
| 632 | if (j < n_names) |
| 633 | { |
| 634 | index[*nr] = i; |
| 635 | (*nr)++; |
| 636 | } |
| 637 | } |
| 638 | printf("Found %d atoms with %s%s", |
| 639 | *nr, bType ? "type" : "name", (n_names == 1) ? "" : "s"); |
| 640 | for (j = 0; (j < n_names); j++) |
| 641 | { |
| 642 | printf(" %s", names[j]); |
| 643 | } |
| 644 | printf("\n"); |
| 645 | |
| 646 | return *nr; |
| 647 | } |
| 648 | |
| 649 | static int select_residuenames(t_atoms *atoms, int n_names, char **names, |
| 650 | atom_id *nr, atom_id *index) |
| 651 | { |
| 652 | char *name; |
| 653 | int j; |
| 654 | atom_id i; |
| 655 | |
| 656 | *nr = 0; |
| 657 | for (i = 0; i < atoms->nr; i++) |
| 658 | { |
| 659 | name = *(atoms->resinfo[atoms->atom[i].resind].name); |
| 660 | j = 0; |
| 661 | while (j < n_names && !comp_name(name, names[j])) |
| 662 | { |
| 663 | j++; |
| 664 | } |
| 665 | if (j < n_names) |
| 666 | { |
| 667 | index[*nr] = i; |
| 668 | (*nr)++; |
| 669 | } |
| 670 | } |
| 671 | printf("Found %d atoms with residue name%s", *nr, (n_names == 1) ? "" : "s"); |
| 672 | for (j = 0; (j < n_names); j++) |
| 673 | { |
| 674 | printf(" %s", names[j]); |
| 675 | } |
| 676 | printf("\n"); |
| 677 | |
| 678 | return *nr; |
| 679 | } |
| 680 | |
| 681 | static void copy2block(int n, atom_id *index, t_blocka *block) |
| 682 | { |
| 683 | int i, n0; |
| 684 | |
| 685 | block->nr++; |
| 686 | n0 = block->nra; |
| 687 | block->nra = n0+n; |
| 688 | srenew(block->index, block->nr+1)(block->index) = save_realloc("block->index", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_make_ndx.c" , 688, (block->index), (block->nr+1), sizeof(*(block-> index))); |
| 689 | block->index[block->nr] = n0+n; |
| 690 | srenew(block->a, n0+n)(block->a) = save_realloc("block->a", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_make_ndx.c" , 690, (block->a), (n0+n), sizeof(*(block->a))); |
| 691 | for (i = 0; (i < n); i++) |
| 692 | { |
| 693 | block->a[n0+i] = index[i]; |
| 694 | } |
| 695 | } |
| 696 | |
| 697 | static void make_gname(int n, char **names, char *gname) |
| 698 | { |
| 699 | int i; |
| 700 | |
| 701 | strcpy(gname, names[0]); |
| 702 | for (i = 1; i < n; i++) |
| 703 | { |
| 704 | strcat(gname, "_"); |
| 705 | strcat(gname, names[i]); |
| 706 | } |
| 707 | } |
| 708 | |
| 709 | static void copy_group(int g, t_blocka *block, atom_id *nr, atom_id *index) |
| 710 | { |
| 711 | int i, i0; |
| 712 | |
| 713 | i0 = block->index[g]; |
| 714 | *nr = block->index[g+1]-i0; |
| 715 | for (i = 0; i < *nr; i++) |
| 716 | { |
| 717 | index[i] = block->a[i0+i]; |
| 718 | } |
| 719 | } |
| 720 | |
| 721 | static void remove_group(int nr, int nr2, t_blocka *block, char ***gn) |
| 722 | { |
| 723 | int i, j, shift; |
| 724 | char *name; |
| 725 | |
| 726 | if (nr2 == NOTSET-12345) |
| 727 | { |
| 728 | nr2 = nr; |
| 729 | } |
| 730 | |
| 731 | for (j = 0; j <= nr2-nr; j++) |
| 732 | { |
| 733 | if ((nr < 0) || (nr >= block->nr)) |
| 734 | { |
| 735 | printf("Group %d does not exist\n", nr+j); |
| 736 | } |
| 737 | else |
| 738 | { |
| 739 | shift = block->index[nr+1]-block->index[nr]; |
| 740 | for (i = block->index[nr+1]; i < block->nra; i++) |
| 741 | { |
| 742 | block->a[i-shift] = block->a[i]; |
| 743 | } |
| 744 | |
| 745 | for (i = nr; i < block->nr; i++) |
| 746 | { |
| 747 | block->index[i] = block->index[i+1]-shift; |
| 748 | } |
| 749 | name = strdup((*gn)[nr])(__extension__ (__builtin_constant_p ((*gn)[nr]) && ( (size_t)(const void *)(((*gn)[nr]) + 1) - (size_t)(const void *)((*gn)[nr]) == 1) ? (((const char *) ((*gn)[nr]))[0] == '\0' ? (char *) calloc ((size_t) 1, (size_t) 1) : ({ size_t __len = strlen ((*gn)[nr]) + 1; char *__retval = (char *) malloc ( __len); if (__retval != ((void*)0)) __retval = (char *) memcpy (__retval, (*gn)[nr], __len); __retval; })) : __strdup ((*gn )[nr]))); |
| 750 | sfree((*gn)[nr])save_free("(*gn)[nr]", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_make_ndx.c" , 750, ((*gn)[nr])); |
| 751 | for (i = nr; i < block->nr-1; i++) |
| 752 | { |
| 753 | (*gn)[i] = (*gn)[i+1]; |
| 754 | } |
| 755 | block->nr--; |
| 756 | block->nra = block->index[block->nr]; |
| 757 | printf("Removed group %d '%s'\n", nr+j, name); |
| 758 | sfree(name)save_free("name", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_make_ndx.c" , 758, (name)); |
| 759 | } |
| 760 | } |
| 761 | } |
| 762 | |
| 763 | static void split_group(t_atoms *atoms, int sel_nr, t_blocka *block, char ***gn, |
| 764 | gmx_bool bAtom) |
| 765 | { |
| 766 | char buf[STRLEN4096], *name; |
| 767 | int i, resind; |
| 768 | atom_id a, n0, n1; |
| 769 | |
| 770 | printf("Splitting group %d '%s' into %s\n", sel_nr, (*gn)[sel_nr], |
| 771 | bAtom ? "atoms" : "residues"); |
| 772 | |
| 773 | n0 = block->index[sel_nr]; |
| 774 | n1 = block->index[sel_nr+1]; |
| 775 | srenew(block->a, block->nra+n1-n0)(block->a) = save_realloc("block->a", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_make_ndx.c" , 775, (block->a), (block->nra+n1-n0), sizeof(*(block-> a))); |
| 776 | for (i = n0; i < n1; i++) |
| 777 | { |
| 778 | a = block->a[i]; |
| 779 | resind = atoms->atom[a].resind; |
| 780 | name = *(atoms->resinfo[resind].name); |
| 781 | if (bAtom || (i == n0) || (atoms->atom[block->a[i-1]].resind != resind)) |
| 782 | { |
| 783 | if (i > n0) |
| 784 | { |
| 785 | block->index[block->nr] = block->nra; |
| 786 | } |
| 787 | block->nr++; |
| 788 | srenew(block->index, block->nr+1)(block->index) = save_realloc("block->index", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_make_ndx.c" , 788, (block->index), (block->nr+1), sizeof(*(block-> index))); |
| 789 | srenew(*gn, block->nr)(*gn) = save_realloc("*gn", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_make_ndx.c" , 789, (*gn), (block->nr), sizeof(*(*gn))); |
| 790 | if (bAtom) |
| 791 | { |
| 792 | sprintf(buf, "%s_%s_%d", (*gn)[sel_nr], *atoms->atomname[a], a+1); |
| 793 | } |
| 794 | else |
| 795 | { |
| 796 | sprintf(buf, "%s_%s_%d", (*gn)[sel_nr], name, atoms->resinfo[resind].nr); |
| 797 | } |
| 798 | (*gn)[block->nr-1] = strdup(buf)(__extension__ (__builtin_constant_p (buf) && ((size_t )(const void *)((buf) + 1) - (size_t)(const void *)(buf) == 1 ) ? (((const char *) (buf))[0] == '\0' ? (char *) calloc ((size_t ) 1, (size_t) 1) : ({ size_t __len = strlen (buf) + 1; char * __retval = (char *) malloc (__len); if (__retval != ((void*)0 )) __retval = (char *) memcpy (__retval, buf, __len); __retval ; })) : __strdup (buf))); |
| 799 | } |
| 800 | block->a[block->nra] = a; |
| 801 | block->nra++; |
| 802 | } |
| 803 | block->index[block->nr] = block->nra; |
| 804 | } |
| 805 | |
| 806 | static int split_chain(t_atoms *atoms, rvec *x, |
| 807 | int sel_nr, t_blocka *block, char ***gn) |
| 808 | { |
| 809 | char buf[STRLEN4096]; |
| 810 | int j, nchain; |
| 811 | atom_id i, a, natoms, *start = NULL((void*)0), *end = NULL((void*)0), ca_start, ca_end; |
| 812 | rvec vec; |
| 813 | |
| 814 | natoms = atoms->nr; |
| 815 | nchain = 0; |
| 816 | ca_start = 0; |
| 817 | |
| 818 | while (ca_start < natoms) |
| 819 | { |
| 820 | while ((ca_start < natoms) && strcmp(*atoms->atomname[ca_start], "CA")__extension__ ({ size_t __s1_len, __s2_len; (__builtin_constant_p (*atoms->atomname[ca_start]) && __builtin_constant_p ("CA") && (__s1_len = strlen (*atoms->atomname[ca_start ]), __s2_len = strlen ("CA"), (!((size_t)(const void *)((*atoms ->atomname[ca_start]) + 1) - (size_t)(const void *)(*atoms ->atomname[ca_start]) == 1) || __s1_len >= 4) && (!((size_t)(const void *)(("CA") + 1) - (size_t)(const void * )("CA") == 1) || __s2_len >= 4)) ? __builtin_strcmp (*atoms ->atomname[ca_start], "CA") : (__builtin_constant_p (*atoms ->atomname[ca_start]) && ((size_t)(const void *)(( *atoms->atomname[ca_start]) + 1) - (size_t)(const void *)( *atoms->atomname[ca_start]) == 1) && (__s1_len = strlen (*atoms->atomname[ca_start]), __s1_len < 4) ? (__builtin_constant_p ("CA") && ((size_t)(const void *)(("CA") + 1) - (size_t )(const void *)("CA") == 1) ? __builtin_strcmp (*atoms->atomname [ca_start], "CA") : (__extension__ ({ const unsigned char *__s2 = (const unsigned char *) (const char *) ("CA"); int __result = (((const unsigned char *) (const char *) (*atoms->atomname [ca_start]))[0] - __s2[0]); if (__s1_len > 0 && __result == 0) { __result = (((const unsigned char *) (const char *) ( *atoms->atomname[ca_start]))[1] - __s2[1]); if (__s1_len > 1 && __result == 0) { __result = (((const unsigned char *) (const char *) (*atoms->atomname[ca_start]))[2] - __s2 [2]); if (__s1_len > 2 && __result == 0) __result = (((const unsigned char *) (const char *) (*atoms->atomname [ca_start]))[3] - __s2[3]); } } __result; }))) : (__builtin_constant_p ("CA") && ((size_t)(const void *)(("CA") + 1) - (size_t )(const void *)("CA") == 1) && (__s2_len = strlen ("CA" ), __s2_len < 4) ? (__builtin_constant_p (*atoms->atomname [ca_start]) && ((size_t)(const void *)((*atoms->atomname [ca_start]) + 1) - (size_t)(const void *)(*atoms->atomname [ca_start]) == 1) ? __builtin_strcmp (*atoms->atomname[ca_start ], "CA") : (- (__extension__ ({ const unsigned char *__s2 = ( const unsigned char *) (const char *) (*atoms->atomname[ca_start ]); int __result = (((const unsigned char *) (const char *) ( "CA"))[0] - __s2[0]); if (__s2_len > 0 && __result == 0) { __result = (((const unsigned char *) (const char *) ( "CA"))[1] - __s2[1]); if (__s2_len > 1 && __result == 0) { __result = (((const unsigned char *) (const char *) ( "CA"))[2] - __s2[2]); if (__s2_len > 2 && __result == 0) __result = (((const unsigned char *) (const char *) ("CA" ))[3] - __s2[3]); } } __result; })))) : __builtin_strcmp (*atoms ->atomname[ca_start], "CA")))); })) |
| 821 | { |
| 822 | ca_start++; |
| 823 | } |
| 824 | if (ca_start < natoms) |
| 825 | { |
| 826 | srenew(start, nchain+1)(start) = save_realloc("start", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_make_ndx.c" , 826, (start), (nchain+1), sizeof(*(start))); |
| 827 | srenew(end, nchain+1)(end) = save_realloc("end", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_make_ndx.c" , 827, (end), (nchain+1), sizeof(*(end))); |
| 828 | start[nchain] = ca_start; |
| 829 | while ((start[nchain] > 0) && |
| 830 | (atoms->atom[start[nchain]-1].resind == |
| 831 | atoms->atom[ca_start].resind)) |
| 832 | { |
| 833 | start[nchain]--; |
| 834 | } |
| 835 | |
| 836 | i = ca_start; |
| 837 | do |
| 838 | { |
| 839 | ca_end = i; |
| 840 | do |
| 841 | { |
| 842 | i++; |
| 843 | } |
| 844 | while ((i < natoms) && strcmp(*atoms->atomname[i], "CA")__extension__ ({ size_t __s1_len, __s2_len; (__builtin_constant_p (*atoms->atomname[i]) && __builtin_constant_p ("CA" ) && (__s1_len = strlen (*atoms->atomname[i]), __s2_len = strlen ("CA"), (!((size_t)(const void *)((*atoms->atomname [i]) + 1) - (size_t)(const void *)(*atoms->atomname[i]) == 1) || __s1_len >= 4) && (!((size_t)(const void *) (("CA") + 1) - (size_t)(const void *)("CA") == 1) || __s2_len >= 4)) ? __builtin_strcmp (*atoms->atomname[i], "CA") : (__builtin_constant_p (*atoms->atomname[i]) && (( size_t)(const void *)((*atoms->atomname[i]) + 1) - (size_t )(const void *)(*atoms->atomname[i]) == 1) && (__s1_len = strlen (*atoms->atomname[i]), __s1_len < 4) ? (__builtin_constant_p ("CA") && ((size_t)(const void *)(("CA") + 1) - (size_t )(const void *)("CA") == 1) ? __builtin_strcmp (*atoms->atomname [i], "CA") : (__extension__ ({ const unsigned char *__s2 = (const unsigned char *) (const char *) ("CA"); int __result = (((const unsigned char *) (const char *) (*atoms->atomname[i]))[0] - __s2[0]); if (__s1_len > 0 && __result == 0) { __result = (((const unsigned char *) (const char *) (*atoms->atomname [i]))[1] - __s2[1]); if (__s1_len > 1 && __result == 0) { __result = (((const unsigned char *) (const char *) (*atoms ->atomname[i]))[2] - __s2[2]); if (__s1_len > 2 && __result == 0) __result = (((const unsigned char *) (const char *) (*atoms->atomname[i]))[3] - __s2[3]); } } __result; }) )) : (__builtin_constant_p ("CA") && ((size_t)(const void *)(("CA") + 1) - (size_t)(const void *)("CA") == 1) && (__s2_len = strlen ("CA"), __s2_len < 4) ? (__builtin_constant_p (*atoms->atomname[i]) && ((size_t)(const void *)( (*atoms->atomname[i]) + 1) - (size_t)(const void *)(*atoms ->atomname[i]) == 1) ? __builtin_strcmp (*atoms->atomname [i], "CA") : (- (__extension__ ({ const unsigned char *__s2 = (const unsigned char *) (const char *) (*atoms->atomname[ i]); int __result = (((const unsigned char *) (const char *) ( "CA"))[0] - __s2[0]); if (__s2_len > 0 && __result == 0) { __result = (((const unsigned char *) (const char *) ( "CA"))[1] - __s2[1]); if (__s2_len > 1 && __result == 0) { __result = (((const unsigned char *) (const char *) ( "CA"))[2] - __s2[2]); if (__s2_len > 2 && __result == 0) __result = (((const unsigned char *) (const char *) ("CA" ))[3] - __s2[3]); } } __result; })))) : __builtin_strcmp (*atoms ->atomname[i], "CA")))); })); |
| 845 | if (i < natoms) |
| 846 | { |
| 847 | rvec_sub(x[ca_end], x[i], vec); |
| 848 | } |
| 849 | } |
| 850 | while ((i < natoms) && (norm(vec) < 0.45)); |
| 851 | |
| 852 | end[nchain] = ca_end; |
| 853 | while ((end[nchain]+1 < natoms) && |
| 854 | (atoms->atom[end[nchain]+1].resind == atoms->atom[ca_end].resind)) |
| 855 | { |
| 856 | end[nchain]++; |
| 857 | } |
| 858 | ca_start = end[nchain]+1; |
| 859 | nchain++; |
| 860 | } |
| 861 | } |
| 862 | if (nchain == 1) |
| 863 | { |
| 864 | printf("Found 1 chain, will not split\n"); |
| 865 | } |
| 866 | else |
| 867 | { |
| 868 | printf("Found %d chains\n", nchain); |
| 869 | } |
| 870 | for (j = 0; j < nchain; j++) |
| 871 | { |
| 872 | printf("%d:%6d atoms (%d to %d)\n", |
| 873 | j+1, end[j]-start[j]+1, start[j]+1, end[j]+1); |
| 874 | } |
| 875 | |
| 876 | if (nchain > 1) |
| 877 | { |
| 878 | srenew(block->a, block->nra+block->index[sel_nr+1]-block->index[sel_nr])(block->a) = save_realloc("block->a", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_make_ndx.c" , 878, (block->a), (block->nra+block->index[sel_nr+1 ]-block->index[sel_nr]), sizeof(*(block->a))); |
| 879 | for (j = 0; j < nchain; j++) |
| 880 | { |
| 881 | block->nr++; |
| 882 | srenew(block->index, block->nr+1)(block->index) = save_realloc("block->index", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_make_ndx.c" , 882, (block->index), (block->nr+1), sizeof(*(block-> index))); |
| 883 | srenew(*gn, block->nr)(*gn) = save_realloc("*gn", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_make_ndx.c" , 883, (*gn), (block->nr), sizeof(*(*gn))); |
| 884 | sprintf(buf, "%s_chain%d", (*gn)[sel_nr], j+1); |
| 885 | (*gn)[block->nr-1] = strdup(buf)(__extension__ (__builtin_constant_p (buf) && ((size_t )(const void *)((buf) + 1) - (size_t)(const void *)(buf) == 1 ) ? (((const char *) (buf))[0] == '\0' ? (char *) calloc ((size_t ) 1, (size_t) 1) : ({ size_t __len = strlen (buf) + 1; char * __retval = (char *) malloc (__len); if (__retval != ((void*)0 )) __retval = (char *) memcpy (__retval, buf, __len); __retval ; })) : __strdup (buf))); |
| 886 | for (i = block->index[sel_nr]; i < block->index[sel_nr+1]; i++) |
| 887 | { |
| 888 | a = block->a[i]; |
| 889 | if ((a >= start[j]) && (a <= end[j])) |
| 890 | { |
| 891 | block->a[block->nra] = a; |
| 892 | block->nra++; |
| 893 | } |
| 894 | } |
| 895 | block->index[block->nr] = block->nra; |
| 896 | if (block->index[block->nr-1] == block->index[block->nr]) |
| 897 | { |
| 898 | remove_group(block->nr-1, NOTSET-12345, block, gn); |
| 899 | } |
| 900 | } |
| 901 | } |
| 902 | sfree(start)save_free("start", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_make_ndx.c" , 902, (start)); |
| 903 | sfree(end)save_free("end", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_make_ndx.c" , 903, (end)); |
| 904 | |
| 905 | return nchain; |
| 906 | } |
| 907 | |
| 908 | static gmx_bool check_have_atoms(t_atoms *atoms, char *string) |
| 909 | { |
| 910 | if (atoms == NULL((void*)0)) |
| 911 | { |
| 912 | printf("Can not process '%s' without atom info, use option -f\n", string); |
| 913 | return FALSE0; |
| 914 | } |
| 915 | else |
| 916 | { |
| 917 | return TRUE1; |
| 918 | } |
| 919 | } |
| 920 | |
| 921 | static gmx_bool parse_entry(char **string, int natoms, t_atoms *atoms, |
| 922 | t_blocka *block, char ***gn, |
| 923 | atom_id *nr, atom_id *index, char *gname) |
| 924 | { |
| 925 | static char **names, *ostring; |
| 926 | static gmx_bool bFirst = TRUE1; |
| 927 | int j, n_names, sel_nr1; |
| 928 | atom_id i, nr1, *index1; |
| 929 | char c; |
| 930 | gmx_bool bRet, bCompl; |
| 931 | |
| 932 | if (bFirst) |
| 933 | { |
| 934 | bFirst = FALSE0; |
| 935 | snew(names, MAXNAMES)(names) = save_calloc("names", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_make_ndx.c" , 935, (30), sizeof(*(names))); |
| 936 | for (i = 0; i < MAXNAMES30; i++) |
| 937 | { |
| 938 | snew(names[i], NAME_LEN+1)(names[i]) = save_calloc("names[i]", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_make_ndx.c" , 938, (30 +1), sizeof(*(names[i]))); |
| 939 | } |
| 940 | } |
| 941 | |
| 942 | bRet = FALSE0; |
| 943 | sel_nr1 = NOTSET-12345; |
| 944 | |
| 945 | while (*string[0] == ' ') |
| 946 | { |
| 947 | (*string)++; |
| 948 | } |
| 949 | |
| 950 | if ((*string)[0] == '!') |
| 951 | { |
| 952 | bCompl = TRUE1; |
| 953 | (*string)++; |
| 954 | while (*string[0] == ' ') |
| 955 | { |
| 956 | (*string)++; |
| 957 | } |
| 958 | } |
| 959 | else |
| 960 | { |
| 961 | bCompl = FALSE0; |
| 962 | } |
| 963 | |
| 964 | ostring = *string; |
| 965 | |
| 966 | if (parse_int(string, &sel_nr1) || |
| 967 | parse_string(string, &sel_nr1, block->nr, *gn)) |
| 968 | { |
| 969 | if ((sel_nr1 >= 0) && (sel_nr1 < block->nr)) |
| 970 | { |
| 971 | copy_group(sel_nr1, block, nr, index); |
| 972 | strcpy(gname, (*gn)[sel_nr1]); |
| 973 | printf("Copied index group %d '%s'\n", sel_nr1, (*gn)[sel_nr1]); |
| 974 | bRet = TRUE1; |
| 975 | } |
| 976 | else |
| 977 | { |
| 978 | printf("Group %d does not exist\n", sel_nr1); |
| 979 | } |
| 980 | } |
| 981 | else if ((*string)[0] == 'a') |
| 982 | { |
| 983 | (*string)++; |
| 984 | if (check_have_atoms(atoms, ostring)) |
| 985 | { |
| 986 | if (parse_int(string, &sel_nr1)) |
| 987 | { |
| 988 | bRet = select_atomnumbers(string, atoms, sel_nr1, nr, index, gname); |
| 989 | } |
| 990 | else if (parse_names(string, &n_names, names)) |
| 991 | { |
| 992 | bRet = select_atomnames(atoms, n_names, names, nr, index, FALSE0); |
| 993 | make_gname(n_names, names, gname); |
| 994 | } |
| 995 | } |
| 996 | } |
| 997 | else if ((*string)[0] == 't') |
| 998 | { |
| 999 | (*string)++; |
| 1000 | if (check_have_atoms(atoms, ostring) && |
| 1001 | parse_names(string, &n_names, names)) |
| 1002 | { |
| 1003 | if (atoms->atomtype == NULL((void*)0)) |
| 1004 | { |
| 1005 | printf("Need a run input file to select atom types\n"); |
| 1006 | } |
| 1007 | else |
| 1008 | { |
| 1009 | bRet = select_atomnames(atoms, n_names, names, nr, index, TRUE1); |
| 1010 | make_gname(n_names, names, gname); |
| 1011 | } |
| 1012 | } |
| 1013 | } |
| 1014 | else if (strncmp(*string, "res", 3)(__extension__ (__builtin_constant_p (3) && ((__builtin_constant_p (*string) && strlen (*string) < ((size_t) (3))) || (__builtin_constant_p ("res") && strlen ("res") < ((size_t) (3)))) ? __extension__ ({ size_t __s1_len, __s2_len ; (__builtin_constant_p (*string) && __builtin_constant_p ("res") && (__s1_len = strlen (*string), __s2_len = strlen ("res"), (!((size_t)(const void *)((*string) + 1) - (size_t) (const void *)(*string) == 1) || __s1_len >= 4) && (!((size_t)(const void *)(("res") + 1) - (size_t)(const void *)("res") == 1) || __s2_len >= 4)) ? __builtin_strcmp (*string , "res") : (__builtin_constant_p (*string) && ((size_t )(const void *)((*string) + 1) - (size_t)(const void *)(*string ) == 1) && (__s1_len = strlen (*string), __s1_len < 4) ? (__builtin_constant_p ("res") && ((size_t)(const void *)(("res") + 1) - (size_t)(const void *)("res") == 1) ? __builtin_strcmp (*string, "res") : (__extension__ ({ const unsigned char *__s2 = (const unsigned char *) (const char *) ("res"); int __result = (((const unsigned char *) (const char *) (*string ))[0] - __s2[0]); if (__s1_len > 0 && __result == 0 ) { __result = (((const unsigned char *) (const char *) (*string ))[1] - __s2[1]); if (__s1_len > 1 && __result == 0 ) { __result = (((const unsigned char *) (const char *) (*string ))[2] - __s2[2]); if (__s1_len > 2 && __result == 0 ) __result = (((const unsigned char *) (const char *) (*string ))[3] - __s2[3]); } } __result; }))) : (__builtin_constant_p ( "res") && ((size_t)(const void *)(("res") + 1) - (size_t )(const void *)("res") == 1) && (__s2_len = strlen ("res" ), __s2_len < 4) ? (__builtin_constant_p (*string) && ((size_t)(const void *)((*string) + 1) - (size_t)(const void *)(*string) == 1) ? __builtin_strcmp (*string, "res") : (- ( __extension__ ({ const unsigned char *__s2 = (const unsigned char *) (const char *) (*string); int __result = (((const unsigned char *) (const char *) ("res"))[0] - __s2[0]); if (__s2_len > 0 && __result == 0) { __result = (((const unsigned char *) (const char *) ("res"))[1] - __s2[1]); if (__s2_len > 1 && __result == 0) { __result = (((const unsigned char *) (const char *) ("res"))[2] - __s2[2]); if (__s2_len > 2 && __result == 0) __result = (((const unsigned char * ) (const char *) ("res"))[3] - __s2[3]); } } __result; })))) : __builtin_strcmp (*string, "res")))); }) : strncmp (*string, "res", 3))) == 0) |
| 1015 | { |
| 1016 | (*string) += 3; |
| 1017 | if (check_have_atoms(atoms, ostring) && |
| 1018 | parse_int(string, &sel_nr1) && |
| 1019 | (sel_nr1 >= 0) && (sel_nr1 < block->nr) ) |
| 1020 | { |
| 1021 | bRet = atoms_from_residuenumbers(atoms, |
| 1022 | sel_nr1, block, nr, index, (*gn)[sel_nr1]); |
| 1023 | sprintf(gname, "atom_%s", (*gn)[sel_nr1]); |
| 1024 | } |
| 1025 | } |
| 1026 | else if (strncmp(*string, "ri", 2)(__extension__ (__builtin_constant_p (2) && ((__builtin_constant_p (*string) && strlen (*string) < ((size_t) (2))) || (__builtin_constant_p ("ri") && strlen ("ri") < ( (size_t) (2)))) ? __extension__ ({ size_t __s1_len, __s2_len; (__builtin_constant_p (*string) && __builtin_constant_p ("ri") && (__s1_len = strlen (*string), __s2_len = strlen ("ri"), (!((size_t)(const void *)((*string) + 1) - (size_t)( const void *)(*string) == 1) || __s1_len >= 4) && ( !((size_t)(const void *)(("ri") + 1) - (size_t)(const void *) ("ri") == 1) || __s2_len >= 4)) ? __builtin_strcmp (*string , "ri") : (__builtin_constant_p (*string) && ((size_t )(const void *)((*string) + 1) - (size_t)(const void *)(*string ) == 1) && (__s1_len = strlen (*string), __s1_len < 4) ? (__builtin_constant_p ("ri") && ((size_t)(const void *)(("ri") + 1) - (size_t)(const void *)("ri") == 1) ? __builtin_strcmp (*string, "ri") : (__extension__ ({ const unsigned char *__s2 = (const unsigned char *) (const char *) ("ri"); int __result = (((const unsigned char *) (const char *) (*string))[0] - __s2 [0]); if (__s1_len > 0 && __result == 0) { __result = (((const unsigned char *) (const char *) (*string))[1] - __s2 [1]); if (__s1_len > 1 && __result == 0) { __result = (((const unsigned char *) (const char *) (*string))[2] - __s2 [2]); if (__s1_len > 2 && __result == 0) __result = (((const unsigned char *) (const char *) (*string))[3] - __s2 [3]); } } __result; }))) : (__builtin_constant_p ("ri") && ((size_t)(const void *)(("ri") + 1) - (size_t)(const void *) ("ri") == 1) && (__s2_len = strlen ("ri"), __s2_len < 4) ? (__builtin_constant_p (*string) && ((size_t)(const void *)((*string) + 1) - (size_t)(const void *)(*string) == 1 ) ? __builtin_strcmp (*string, "ri") : (- (__extension__ ({ const unsigned char *__s2 = (const unsigned char *) (const char *) (*string); int __result = (((const unsigned char *) (const char *) ("ri"))[0] - __s2[0]); if (__s2_len > 0 && __result == 0) { __result = (((const unsigned char *) (const char *) ( "ri"))[1] - __s2[1]); if (__s2_len > 1 && __result == 0) { __result = (((const unsigned char *) (const char *) ( "ri"))[2] - __s2[2]); if (__s2_len > 2 && __result == 0) __result = (((const unsigned char *) (const char *) ("ri" ))[3] - __s2[3]); } } __result; })))) : __builtin_strcmp (*string , "ri")))); }) : strncmp (*string, "ri", 2))) == 0) |
| 1027 | { |
| 1028 | (*string) += 2; |
| 1029 | if (check_have_atoms(atoms, ostring) && |
| 1030 | parse_int_char(string, &sel_nr1, &c)) |
| 1031 | { |
| 1032 | bRet = select_residueindices(string, atoms, sel_nr1, c, nr, index, gname); |
| 1033 | } |
| 1034 | } |
| 1035 | else if ((*string)[0] == 'r') |
| 1036 | { |
| 1037 | (*string)++; |
| 1038 | if (check_have_atoms(atoms, ostring)) |
| 1039 | { |
| 1040 | if (parse_int_char(string, &sel_nr1, &c)) |
| 1041 | { |
| 1042 | bRet = select_residuenumbers(string, atoms, sel_nr1, c, nr, index, gname); |
| 1043 | } |
| 1044 | else if (parse_names(string, &n_names, names)) |
| 1045 | { |
| 1046 | bRet = select_residuenames(atoms, n_names, names, nr, index); |
| 1047 | make_gname(n_names, names, gname); |
| 1048 | } |
| 1049 | } |
| 1050 | } |
| 1051 | else if (strncmp(*string, "chain", 5)(__extension__ (__builtin_constant_p (5) && ((__builtin_constant_p (*string) && strlen (*string) < ((size_t) (5))) || (__builtin_constant_p ("chain") && strlen ("chain") < ((size_t) (5)))) ? __extension__ ({ size_t __s1_len, __s2_len ; (__builtin_constant_p (*string) && __builtin_constant_p ("chain") && (__s1_len = strlen (*string), __s2_len = strlen ("chain"), (!((size_t)(const void *)((*string) + 1) - (size_t)(const void *)(*string) == 1) || __s1_len >= 4) && (!((size_t)(const void *)(("chain") + 1) - (size_t)(const void *)("chain") == 1) || __s2_len >= 4)) ? __builtin_strcmp ( *string, "chain") : (__builtin_constant_p (*string) && ((size_t)(const void *)((*string) + 1) - (size_t)(const void *)(*string) == 1) && (__s1_len = strlen (*string), __s1_len < 4) ? (__builtin_constant_p ("chain") && ((size_t )(const void *)(("chain") + 1) - (size_t)(const void *)("chain" ) == 1) ? __builtin_strcmp (*string, "chain") : (__extension__ ({ const unsigned char *__s2 = (const unsigned char *) (const char *) ("chain"); int __result = (((const unsigned char *) ( const char *) (*string))[0] - __s2[0]); if (__s1_len > 0 && __result == 0) { __result = (((const unsigned char *) (const char *) (*string))[1] - __s2[1]); if (__s1_len > 1 && __result == 0) { __result = (((const unsigned char *) (const char *) (*string))[2] - __s2[2]); if (__s1_len > 2 && __result == 0) __result = (((const unsigned char *) (const char *) (*string))[3] - __s2[3]); } } __result; }))) : (__builtin_constant_p ("chain") && ((size_t)(const void *)(("chain") + 1) - (size_t)(const void *)("chain") == 1) && (__s2_len = strlen ("chain"), __s2_len < 4) ? (__builtin_constant_p ( *string) && ((size_t)(const void *)((*string) + 1) - ( size_t)(const void *)(*string) == 1) ? __builtin_strcmp (*string , "chain") : (- (__extension__ ({ const unsigned char *__s2 = (const unsigned char *) (const char *) (*string); int __result = (((const unsigned char *) (const char *) ("chain"))[0] - __s2 [0]); if (__s2_len > 0 && __result == 0) { __result = (((const unsigned char *) (const char *) ("chain"))[1] - __s2 [1]); if (__s2_len > 1 && __result == 0) { __result = (((const unsigned char *) (const char *) ("chain"))[2] - __s2 [2]); if (__s2_len > 2 && __result == 0) __result = (((const unsigned char *) (const char *) ("chain"))[3] - __s2 [3]); } } __result; })))) : __builtin_strcmp (*string, "chain" )))); }) : strncmp (*string, "chain", 5))) == 0) |
| 1052 | { |
| 1053 | (*string) += 5; |
| 1054 | if (check_have_atoms(atoms, ostring) && |
| 1055 | parse_names(string, &n_names, names)) |
| 1056 | { |
| 1057 | bRet = select_chainnames(atoms, n_names, names, nr, index); |
| 1058 | sprintf(gname, "ch%s", names[0]); |
| 1059 | for (i = 1; i < n_names; i++) |
| 1060 | { |
| 1061 | strcat(gname, names[i]); |
| 1062 | } |
| 1063 | } |
| 1064 | } |
| 1065 | if (bRet && bCompl) |
| 1066 | { |
| 1067 | snew(index1, natoms-*nr)(index1) = save_calloc("index1", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_make_ndx.c" , 1067, (natoms-*nr), sizeof(*(index1))); |
| 1068 | nr1 = 0; |
| 1069 | for (i = 0; i < natoms; i++) |
| 1070 | { |
| 1071 | j = 0; |
| 1072 | while ((j < *nr) && (index[j] != i)) |
| 1073 | { |
| 1074 | j++; |
| 1075 | } |
| 1076 | if (j == *nr) |
| 1077 | { |
| 1078 | if (nr1 >= natoms-*nr) |
| 1079 | { |
| 1080 | printf("There are double atoms in your index group\n"); |
| 1081 | break; |
| 1082 | } |
| 1083 | index1[nr1] = i; |
| 1084 | nr1++; |
| 1085 | } |
| 1086 | } |
| 1087 | *nr = nr1; |
| 1088 | for (i = 0; i < nr1; i++) |
| 1089 | { |
| 1090 | index[i] = index1[i]; |
| 1091 | } |
| 1092 | sfree(index1)save_free("index1", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_make_ndx.c" , 1092, (index1)); |
| 1093 | |
| 1094 | for (i = strlen(gname)+1; i > 0; i--) |
| 1095 | { |
| 1096 | gname[i] = gname[i-1]; |
| 1097 | } |
| 1098 | gname[0] = '!'; |
| 1099 | printf("Complemented group: %d atoms\n", *nr); |
| 1100 | } |
| 1101 | |
| 1102 | return bRet; |
| 1103 | } |
| 1104 | |
| 1105 | static void list_residues(t_atoms *atoms) |
| 1106 | { |
| 1107 | int i, j, start, end, prev_resind, resind; |
| 1108 | gmx_bool bDiff; |
| 1109 | |
| 1110 | /* Print all the residues, assuming continuous resnr count */ |
| 1111 | start = atoms->atom[0].resind; |
| 1112 | prev_resind = start; |
| 1113 | for (i = 0; i < atoms->nr; i++) |
| 1114 | { |
| 1115 | resind = atoms->atom[i].resind; |
| 1116 | if ((resind != prev_resind) || (i == atoms->nr-1)) |
| 1117 | { |
| 1118 | if ((bDiff = strcmp(*atoms->resinfo[resind].name,__extension__ ({ size_t __s1_len, __s2_len; (__builtin_constant_p (*atoms->resinfo[resind].name) && __builtin_constant_p (*atoms->resinfo[start].name) && (__s1_len = strlen (*atoms->resinfo[resind].name), __s2_len = strlen (*atoms ->resinfo[start].name), (!((size_t)(const void *)((*atoms-> resinfo[resind].name) + 1) - (size_t)(const void *)(*atoms-> resinfo[resind].name) == 1) || __s1_len >= 4) && ( !((size_t)(const void *)((*atoms->resinfo[start].name) + 1 ) - (size_t)(const void *)(*atoms->resinfo[start].name) == 1) || __s2_len >= 4)) ? __builtin_strcmp (*atoms->resinfo [resind].name, *atoms->resinfo[start].name) : (__builtin_constant_p (*atoms->resinfo[resind].name) && ((size_t)(const void *)((*atoms->resinfo[resind].name) + 1) - (size_t)(const void *)(*atoms->resinfo[resind].name) == 1) && (__s1_len = strlen (*atoms->resinfo[resind].name), __s1_len < 4) ? (__builtin_constant_p (*atoms->resinfo[start].name) && ((size_t)(const void *)((*atoms->resinfo[start].name) + 1 ) - (size_t)(const void *)(*atoms->resinfo[start].name) == 1) ? __builtin_strcmp (*atoms->resinfo[resind].name, *atoms ->resinfo[start].name) : (__extension__ ({ const unsigned char *__s2 = (const unsigned char *) (const char *) (*atoms->resinfo [start].name); int __result = (((const unsigned char *) (const char *) (*atoms->resinfo[resind].name))[0] - __s2[0]); if (__s1_len > 0 && __result == 0) { __result = (((const unsigned char *) (const char *) (*atoms->resinfo[resind]. name))[1] - __s2[1]); if (__s1_len > 1 && __result == 0) { __result = (((const unsigned char *) (const char *) ( *atoms->resinfo[resind].name))[2] - __s2[2]); if (__s1_len > 2 && __result == 0) __result = (((const unsigned char *) (const char *) (*atoms->resinfo[resind].name))[3] - __s2[3]); } } __result; }))) : (__builtin_constant_p (*atoms ->resinfo[start].name) && ((size_t)(const void *)( (*atoms->resinfo[start].name) + 1) - (size_t)(const void * )(*atoms->resinfo[start].name) == 1) && (__s2_len = strlen (*atoms->resinfo[start].name), __s2_len < 4) ? ( __builtin_constant_p (*atoms->resinfo[resind].name) && ((size_t)(const void *)((*atoms->resinfo[resind].name) + 1 ) - (size_t)(const void *)(*atoms->resinfo[resind].name) == 1) ? __builtin_strcmp (*atoms->resinfo[resind].name, *atoms ->resinfo[start].name) : (- (__extension__ ({ const unsigned char *__s2 = (const unsigned char *) (const char *) (*atoms-> resinfo[resind].name); int __result = (((const unsigned char * ) (const char *) (*atoms->resinfo[start].name))[0] - __s2[ 0]); if (__s2_len > 0 && __result == 0) { __result = (((const unsigned char *) (const char *) (*atoms->resinfo [start].name))[1] - __s2[1]); if (__s2_len > 1 && __result == 0) { __result = (((const unsigned char *) (const char *) ( *atoms->resinfo[start].name))[2] - __s2[2]); if (__s2_len > 2 && __result == 0) __result = (((const unsigned char *) (const char *) (*atoms->resinfo[start].name))[3] - __s2 [3]); } } __result; })))) : __builtin_strcmp (*atoms->resinfo [resind].name, *atoms->resinfo[start].name)))); }) |
| 1119 | *atoms->resinfo[start].name)__extension__ ({ size_t __s1_len, __s2_len; (__builtin_constant_p (*atoms->resinfo[resind].name) && __builtin_constant_p (*atoms->resinfo[start].name) && (__s1_len = strlen (*atoms->resinfo[resind].name), __s2_len = strlen (*atoms ->resinfo[start].name), (!((size_t)(const void *)((*atoms-> resinfo[resind].name) + 1) - (size_t)(const void *)(*atoms-> resinfo[resind].name) == 1) || __s1_len >= 4) && ( !((size_t)(const void *)((*atoms->resinfo[start].name) + 1 ) - (size_t)(const void *)(*atoms->resinfo[start].name) == 1) || __s2_len >= 4)) ? __builtin_strcmp (*atoms->resinfo [resind].name, *atoms->resinfo[start].name) : (__builtin_constant_p (*atoms->resinfo[resind].name) && ((size_t)(const void *)((*atoms->resinfo[resind].name) + 1) - (size_t)(const void *)(*atoms->resinfo[resind].name) == 1) && (__s1_len = strlen (*atoms->resinfo[resind].name), __s1_len < 4) ? (__builtin_constant_p (*atoms->resinfo[start].name) && ((size_t)(const void *)((*atoms->resinfo[start].name) + 1 ) - (size_t)(const void *)(*atoms->resinfo[start].name) == 1) ? __builtin_strcmp (*atoms->resinfo[resind].name, *atoms ->resinfo[start].name) : (__extension__ ({ const unsigned char *__s2 = (const unsigned char *) (const char *) (*atoms->resinfo [start].name); int __result = (((const unsigned char *) (const char *) (*atoms->resinfo[resind].name))[0] - __s2[0]); if (__s1_len > 0 && __result == 0) { __result = (((const unsigned char *) (const char *) (*atoms->resinfo[resind]. name))[1] - __s2[1]); if (__s1_len > 1 && __result == 0) { __result = (((const unsigned char *) (const char *) ( *atoms->resinfo[resind].name))[2] - __s2[2]); if (__s1_len > 2 && __result == 0) __result = (((const unsigned char *) (const char *) (*atoms->resinfo[resind].name))[3] - __s2[3]); } } __result; }))) : (__builtin_constant_p (*atoms ->resinfo[start].name) && ((size_t)(const void *)( (*atoms->resinfo[start].name) + 1) - (size_t)(const void * )(*atoms->resinfo[start].name) == 1) && (__s2_len = strlen (*atoms->resinfo[start].name), __s2_len < 4) ? ( __builtin_constant_p (*atoms->resinfo[resind].name) && ((size_t)(const void *)((*atoms->resinfo[resind].name) + 1 ) - (size_t)(const void *)(*atoms->resinfo[resind].name) == 1) ? __builtin_strcmp (*atoms->resinfo[resind].name, *atoms ->resinfo[start].name) : (- (__extension__ ({ const unsigned char *__s2 = (const unsigned char *) (const char *) (*atoms-> resinfo[resind].name); int __result = (((const unsigned char * ) (const char *) (*atoms->resinfo[start].name))[0] - __s2[ 0]); if (__s2_len > 0 && __result == 0) { __result = (((const unsigned char *) (const char *) (*atoms->resinfo [start].name))[1] - __s2[1]); if (__s2_len > 1 && __result == 0) { __result = (((const unsigned char *) (const char *) ( *atoms->resinfo[start].name))[2] - __s2[2]); if (__s2_len > 2 && __result == 0) __result = (((const unsigned char *) (const char *) (*atoms->resinfo[start].name))[3] - __s2 [3]); } } __result; })))) : __builtin_strcmp (*atoms->resinfo [resind].name, *atoms->resinfo[start].name)))); })) || |
| 1120 | (i == atoms->nr-1)) |
| 1121 | { |
| 1122 | if (bDiff) |
| 1123 | { |
| 1124 | end = prev_resind; |
| 1125 | } |
| 1126 | else |
| 1127 | { |
| 1128 | end = resind; |
| 1129 | } |
| 1130 | if (end < start+3) |
| 1131 | { |
| 1132 | for (j = start; j <= end; j++) |
| 1133 | { |
| 1134 | printf("%4d %-5s", |
| 1135 | j+1, *(atoms->resinfo[j].name)); |
| 1136 | } |
| 1137 | } |
| 1138 | else |
| 1139 | { |
| 1140 | printf(" %4d - %4d %-5s ", |
| 1141 | start+1, end+1, *(atoms->resinfo[start].name)); |
| 1142 | } |
| 1143 | start = resind; |
| 1144 | } |
| 1145 | } |
| 1146 | prev_resind = resind; |
| 1147 | } |
| 1148 | printf("\n"); |
| 1149 | } |
| 1150 | |
| 1151 | static void edit_index(int natoms, t_atoms *atoms, rvec *x, t_blocka *block, char ***gn, gmx_bool bVerbose) |
| 1152 | { |
| 1153 | static char **atnames, *ostring; |
| 1154 | static gmx_bool bFirst = TRUE1; |
| 1155 | char inp_string[STRLEN4096], *string; |
| 1156 | char gname[STRLEN4096], gname1[STRLEN4096], gname2[STRLEN4096]; |
| 1157 | int i, i0, i1, sel_nr, sel_nr2, newgroup; |
| 1158 | atom_id nr, nr1, nr2, *index, *index1, *index2; |
| 1159 | gmx_bool bAnd, bOr, bPrintOnce; |
| 1160 | |
| 1161 | if (bFirst) |
| 1162 | { |
| 1163 | bFirst = FALSE0; |
| 1164 | snew(atnames, MAXNAMES)(atnames) = save_calloc("atnames", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_make_ndx.c" , 1164, (30), sizeof(*(atnames))); |
| 1165 | for (i = 0; i < MAXNAMES30; i++) |
| 1166 | { |
| 1167 | snew(atnames[i], NAME_LEN+1)(atnames[i]) = save_calloc("atnames[i]", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_make_ndx.c" , 1167, (30 +1), sizeof(*(atnames[i]))); |
| 1168 | } |
| 1169 | } |
| 1170 | |
| 1171 | string = NULL((void*)0); |
| 1172 | |
| 1173 | snew(index, natoms)(index) = save_calloc("index", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_make_ndx.c" , 1173, (natoms), sizeof(*(index))); |
| 1174 | snew(index1, natoms)(index1) = save_calloc("index1", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_make_ndx.c" , 1174, (natoms), sizeof(*(index1))); |
| 1175 | snew(index2, natoms)(index2) = save_calloc("index2", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_make_ndx.c" , 1175, (natoms), sizeof(*(index2))); |
| 1176 | |
| 1177 | newgroup = NOTSET-12345; |
| 1178 | bPrintOnce = TRUE1; |
| 1179 | do |
| 1180 | { |
| 1181 | gname1[0] = '\0'; |
| 1182 | if (bVerbose || bPrintOnce || newgroup != NOTSET-12345) |
| 1183 | { |
| 1184 | printf("\n"); |
| 1185 | if (bVerbose || bPrintOnce || newgroup == NOTSET-12345) |
| 1186 | { |
| 1187 | i0 = 0; |
| 1188 | i1 = block->nr; |
| 1189 | } |
| 1190 | else |
| 1191 | { |
| 1192 | i0 = newgroup; |
| 1193 | i1 = newgroup+1; |
| 1194 | } |
| 1195 | for (i = i0; i < i1; i++) |
| 1196 | { |
| 1197 | printf("%3d %-20s: %5d atoms\n", i, (*gn)[i], |
| 1198 | block->index[i+1]-block->index[i]); |
| 1199 | } |
| 1200 | newgroup = NOTSET-12345; |
| 1201 | } |
| 1202 | if (bVerbose || bPrintOnce) |
| 1203 | { |
| 1204 | printf("\n"); |
| 1205 | printf(" nr : group ! 'name' nr name 'splitch' nr Enter: list groups\n"); |
| 1206 | printf(" 'a': atom & 'del' nr 'splitres' nr 'l': list residues\n"); |
| 1207 | printf(" 't': atom type | 'keep' nr 'splitat' nr 'h': help\n"); |
| 1208 | printf(" 'r': residue 'res' nr 'chain' char\n"); |
| 1209 | printf(" \"name\": group 'case': case %s 'q': save and quit\n", |
| 1210 | bCase ? "insensitive" : "sensitive "); |
| 1211 | printf(" 'ri': residue index\n"); |
| 1212 | bPrintOnce = FALSE0; |
| 1213 | } |
| 1214 | printf("\n"); |
| 1215 | printf("> "); |
| 1216 | if (NULL((void*)0) == fgets(inp_string, STRLEN4096, stdinstdin)) |
| 1217 | { |
| 1218 | gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_make_ndx.c" , 1218, "Error reading user input"); |
| 1219 | } |
| 1220 | inp_string[strlen(inp_string)-1] = 0; |
| 1221 | printf("\n"); |
| 1222 | string = inp_string; |
| 1223 | while (string[0] == ' ') |
| 1224 | { |
| 1225 | string++; |
| 1226 | } |
| 1227 | |
| 1228 | ostring = string; |
| 1229 | nr = 0; |
| 1230 | if (string[0] == 'h') |
| 1231 | { |
| 1232 | printf(" nr : selects an index group by number or quoted string.\n"); |
| 1233 | printf(" The string is first matched against the whole group name,\n"); |
| 1234 | printf(" then against the beginning and finally against an\n"); |
| 1235 | printf(" arbitrary substring. A multiple match is an error.\n"); |
| 1236 | |
| 1237 | printf(" 'a' nr1 [nr2 ...] : selects atoms, atom numbering starts at 1.\n"); |
| 1238 | printf(" 'a' nr1 - nr2 : selects atoms in the range from nr1 to nr2.\n"); |
| 1239 | printf(" 'a' name1[*] [name2[*] ...] : selects atoms by name(s), '?' matches any char,\n"); |
| 1240 | printf(" wildcard '*' allowed at the end of a name.\n"); |
| 1241 | printf(" 't' type1[*] [type2[*] ...] : as 'a', but for type, run input file required.\n"); |
| 1242 | printf(" 'r' nr1[ic1] [nr2[ic2] ...] : selects residues by number and insertion code.\n"); |
| 1243 | printf(" 'r' nr1 - nr2 : selects residues in the range from nr1 to nr2.\n"); |
| 1244 | printf(" 'r' name1[*] [name2[*] ...] : as 'a', but for residue names.\n"); |
| 1245 | printf(" 'ri' nr1 - nr2 : selects residue indices, 1-indexed, (as opposed to numbers) in the range from nr1 to nr2.\n"); |
| 1246 | printf(" 'chain' ch1 [ch2 ...] : selects atoms by chain identifier(s),\n"); |
| 1247 | printf(" not available with a .gro file as input.\n"); |
| 1248 | printf(" ! : takes the complement of a group with respect to all\n"); |
| 1249 | printf(" the atoms in the input file.\n"); |
| 1250 | printf(" & | : AND and OR, can be placed between any of the options\n"); |
| 1251 | printf(" above, the input is processed from left to right.\n"); |
| 1252 | printf(" 'name' nr name : rename group nr to name.\n"); |
| 1253 | printf(" 'del' nr1 [- nr2] : deletes one group or groups in the range from nr1 to nr2.\n"); |
| 1254 | printf(" 'keep' nr : deletes all groups except nr.\n"); |
| 1255 | printf(" 'case' : make all name compares case (in)sensitive.\n"); |
| 1256 | printf(" 'splitch' nr : split group into chains using CA distances.\n"); |
| 1257 | printf(" 'splitres' nr : split group into residues.\n"); |
| 1258 | printf(" 'splitat' nr : split group into atoms.\n"); |
| 1259 | printf(" 'res' nr : interpret numbers in group as residue numbers\n"); |
| 1260 | printf(" Enter : list the currently defined groups and commands\n"); |
| 1261 | printf(" 'l' : list the residues.\n"); |
| 1262 | printf(" 'h' : show this help.\n"); |
| 1263 | printf(" 'q' : save and quit.\n"); |
| 1264 | printf("\n"); |
| 1265 | printf(" Examples:\n"); |
| 1266 | printf(" > 2 | 4 & r 3-5\n"); |
| 1267 | printf(" selects all atoms from group 2 and 4 that have residue numbers 3, 4 or 5\n"); |
| 1268 | printf(" > a C* & !a C CA\n"); |
| 1269 | printf(" selects all atoms starting with 'C' but not the atoms 'C' and 'CA'\n"); |
| 1270 | printf(" > \"protein\" & ! \"backb\"\n"); |
| 1271 | printf(" selects all atoms that are in group 'protein' and not in group 'backbone'\n"); |
| 1272 | if (bVerbose) |
| 1273 | { |
| 1274 | printf("\npress Enter "); |
| 1275 | getchar(); |
| 1276 | } |
| 1277 | } |
| 1278 | else if (strncmp(string, "del", 3)(__extension__ (__builtin_constant_p (3) && ((__builtin_constant_p (string) && strlen (string) < ((size_t) (3))) || ( __builtin_constant_p ("del") && strlen ("del") < ( (size_t) (3)))) ? __extension__ ({ size_t __s1_len, __s2_len; (__builtin_constant_p (string) && __builtin_constant_p ("del") && (__s1_len = strlen (string), __s2_len = strlen ("del"), (!((size_t)(const void *)((string) + 1) - (size_t)( const void *)(string) == 1) || __s1_len >= 4) && ( !((size_t)(const void *)(("del") + 1) - (size_t)(const void * )("del") == 1) || __s2_len >= 4)) ? __builtin_strcmp (string , "del") : (__builtin_constant_p (string) && ((size_t )(const void *)((string) + 1) - (size_t)(const void *)(string ) == 1) && (__s1_len = strlen (string), __s1_len < 4) ? (__builtin_constant_p ("del") && ((size_t)(const void *)(("del") + 1) - (size_t)(const void *)("del") == 1) ? __builtin_strcmp (string, "del") : (__extension__ ({ const unsigned char *__s2 = (const unsigned char *) (const char *) ("del"); int __result = (((const unsigned char *) (const char *) (string ))[0] - __s2[0]); if (__s1_len > 0 && __result == 0 ) { __result = (((const unsigned char *) (const char *) (string ))[1] - __s2[1]); if (__s1_len > 1 && __result == 0 ) { __result = (((const unsigned char *) (const char *) (string ))[2] - __s2[2]); if (__s1_len > 2 && __result == 0 ) __result = (((const unsigned char *) (const char *) (string ))[3] - __s2[3]); } } __result; }))) : (__builtin_constant_p ( "del") && ((size_t)(const void *)(("del") + 1) - (size_t )(const void *)("del") == 1) && (__s2_len = strlen ("del" ), __s2_len < 4) ? (__builtin_constant_p (string) && ((size_t)(const void *)((string) + 1) - (size_t)(const void * )(string) == 1) ? __builtin_strcmp (string, "del") : (- (__extension__ ({ const unsigned char *__s2 = (const unsigned char *) (const char *) (string); int __result = (((const unsigned char *) ( const char *) ("del"))[0] - __s2[0]); if (__s2_len > 0 && __result == 0) { __result = (((const unsigned char *) (const char *) ("del"))[1] - __s2[1]); if (__s2_len > 1 && __result == 0) { __result = (((const unsigned char *) (const char *) ("del"))[2] - __s2[2]); if (__s2_len > 2 && __result == 0) __result = (((const unsigned char *) (const char *) ("del"))[3] - __s2[3]); } } __result; })))) : __builtin_strcmp (string, "del")))); }) : strncmp (string, "del", 3))) == 0) |
| 1279 | { |
| 1280 | string += 3; |
| 1281 | if (parse_int(&string, &sel_nr)) |
| 1282 | { |
| 1283 | while (string[0] == ' ') |
| 1284 | { |
| 1285 | string++; |
| 1286 | } |
| 1287 | if (string[0] == '-') |
| 1288 | { |
| 1289 | string++; |
| 1290 | parse_int(&string, &sel_nr2); |
| 1291 | } |
| 1292 | else |
| 1293 | { |
| 1294 | sel_nr2 = NOTSET-12345; |
| 1295 | } |
| 1296 | while (string[0] == ' ') |
| 1297 | { |
| 1298 | string++; |
| 1299 | } |
| 1300 | if (string[0] == '\0') |
| 1301 | { |
| 1302 | remove_group(sel_nr, sel_nr2, block, gn); |
| 1303 | } |
| 1304 | else |
| 1305 | { |
| 1306 | printf("\nSyntax error: \"%s\"\n", string); |
| 1307 | } |
| 1308 | } |
| 1309 | } |
| 1310 | else if (strncmp(string, "keep", 4)(__extension__ (__builtin_constant_p (4) && ((__builtin_constant_p (string) && strlen (string) < ((size_t) (4))) || ( __builtin_constant_p ("keep") && strlen ("keep") < ((size_t) (4)))) ? __extension__ ({ size_t __s1_len, __s2_len ; (__builtin_constant_p (string) && __builtin_constant_p ("keep") && (__s1_len = strlen (string), __s2_len = strlen ("keep"), (!((size_t)(const void *)((string) + 1) - (size_t) (const void *)(string) == 1) || __s1_len >= 4) && ( !((size_t)(const void *)(("keep") + 1) - (size_t)(const void * )("keep") == 1) || __s2_len >= 4)) ? __builtin_strcmp (string , "keep") : (__builtin_constant_p (string) && ((size_t )(const void *)((string) + 1) - (size_t)(const void *)(string ) == 1) && (__s1_len = strlen (string), __s1_len < 4) ? (__builtin_constant_p ("keep") && ((size_t)(const void *)(("keep") + 1) - (size_t)(const void *)("keep") == 1) ? __builtin_strcmp (string, "keep") : (__extension__ ({ const unsigned char *__s2 = (const unsigned char *) (const char *) ("keep"); int __result = (((const unsigned char *) (const char *) (string))[0] - __s2[0]); if (__s1_len > 0 && __result == 0) { __result = (((const unsigned char *) (const char *) ( string))[1] - __s2[1]); if (__s1_len > 1 && __result == 0) { __result = (((const unsigned char *) (const char *) ( string))[2] - __s2[2]); if (__s1_len > 2 && __result == 0) __result = (((const unsigned char *) (const char *) (string ))[3] - __s2[3]); } } __result; }))) : (__builtin_constant_p ( "keep") && ((size_t)(const void *)(("keep") + 1) - (size_t )(const void *)("keep") == 1) && (__s2_len = strlen ( "keep"), __s2_len < 4) ? (__builtin_constant_p (string) && ((size_t)(const void *)((string) + 1) - (size_t)(const void * )(string) == 1) ? __builtin_strcmp (string, "keep") : (- (__extension__ ({ const unsigned char *__s2 = (const unsigned char *) (const char *) (string); int __result = (((const unsigned char *) ( const char *) ("keep"))[0] - __s2[0]); if (__s2_len > 0 && __result == 0) { __result = (((const unsigned char *) (const char *) ("keep"))[1] - __s2[1]); if (__s2_len > 1 && __result == 0) { __result = (((const unsigned char *) (const char *) ("keep"))[2] - __s2[2]); if (__s2_len > 2 && __result == 0) __result = (((const unsigned char *) (const char *) ("keep"))[3] - __s2[3]); } } __result; })))) : __builtin_strcmp (string, "keep")))); }) : strncmp (string, "keep", 4))) == 0) |
| 1311 | { |
| 1312 | string += 4; |
| 1313 | if (parse_int(&string, &sel_nr)) |
| 1314 | { |
| 1315 | remove_group(sel_nr+1, block->nr-1, block, gn); |
| 1316 | remove_group(0, sel_nr-1, block, gn); |
| 1317 | } |
| 1318 | } |
| 1319 | else if (strncmp(string, "name", 4)(__extension__ (__builtin_constant_p (4) && ((__builtin_constant_p (string) && strlen (string) < ((size_t) (4))) || ( __builtin_constant_p ("name") && strlen ("name") < ((size_t) (4)))) ? __extension__ ({ size_t __s1_len, __s2_len ; (__builtin_constant_p (string) && __builtin_constant_p ("name") && (__s1_len = strlen (string), __s2_len = strlen ("name"), (!((size_t)(const void *)((string) + 1) - (size_t) (const void *)(string) == 1) || __s1_len >= 4) && ( !((size_t)(const void *)(("name") + 1) - (size_t)(const void * )("name") == 1) || __s2_len >= 4)) ? __builtin_strcmp (string , "name") : (__builtin_constant_p (string) && ((size_t )(const void *)((string) + 1) - (size_t)(const void *)(string ) == 1) && (__s1_len = strlen (string), __s1_len < 4) ? (__builtin_constant_p ("name") && ((size_t)(const void *)(("name") + 1) - (size_t)(const void *)("name") == 1) ? __builtin_strcmp (string, "name") : (__extension__ ({ const unsigned char *__s2 = (const unsigned char *) (const char *) ("name"); int __result = (((const unsigned char *) (const char *) (string))[0] - __s2[0]); if (__s1_len > 0 && __result == 0) { __result = (((const unsigned char *) (const char *) ( string))[1] - __s2[1]); if (__s1_len > 1 && __result == 0) { __result = (((const unsigned char *) (const char *) ( string))[2] - __s2[2]); if (__s1_len > 2 && __result == 0) __result = (((const unsigned char *) (const char *) (string ))[3] - __s2[3]); } } __result; }))) : (__builtin_constant_p ( "name") && ((size_t)(const void *)(("name") + 1) - (size_t )(const void *)("name") == 1) && (__s2_len = strlen ( "name"), __s2_len < 4) ? (__builtin_constant_p (string) && ((size_t)(const void *)((string) + 1) - (size_t)(const void * )(string) == 1) ? __builtin_strcmp (string, "name") : (- (__extension__ ({ const unsigned char *__s2 = (const unsigned char *) (const char *) (string); int __result = (((const unsigned char *) ( const char *) ("name"))[0] - __s2[0]); if (__s2_len > 0 && __result == 0) { __result = (((const unsigned char *) (const char *) ("name"))[1] - __s2[1]); if (__s2_len > 1 && __result == 0) { __result = (((const unsigned char *) (const char *) ("name"))[2] - __s2[2]); if (__s2_len > 2 && __result == 0) __result = (((const unsigned char *) (const char *) ("name"))[3] - __s2[3]); } } __result; })))) : __builtin_strcmp (string, "name")))); }) : strncmp (string, "name", 4))) == 0) |
| 1320 | { |
| 1321 | string += 4; |
| 1322 | if (parse_int(&string, &sel_nr)) |
| 1323 | { |
| 1324 | if ((sel_nr >= 0) && (sel_nr < block->nr)) |
| 1325 | { |
| 1326 | sscanf(string, "%s", gname); |
| 1327 | sfree((*gn)[sel_nr])save_free("(*gn)[sel_nr]", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_make_ndx.c" , 1327, ((*gn)[sel_nr])); |
| 1328 | (*gn)[sel_nr] = strdup(gname)(__extension__ (__builtin_constant_p (gname) && ((size_t )(const void *)((gname) + 1) - (size_t)(const void *)(gname) == 1) ? (((const char *) (gname))[0] == '\0' ? (char *) calloc ( (size_t) 1, (size_t) 1) : ({ size_t __len = strlen (gname) + 1 ; char *__retval = (char *) malloc (__len); if (__retval != ( (void*)0)) __retval = (char *) memcpy (__retval, gname, __len ); __retval; })) : __strdup (gname))); |
| 1329 | } |
| 1330 | } |
| 1331 | } |
| 1332 | else if (strncmp(string, "case", 4)(__extension__ (__builtin_constant_p (4) && ((__builtin_constant_p (string) && strlen (string) < ((size_t) (4))) || ( __builtin_constant_p ("case") && strlen ("case") < ((size_t) (4)))) ? __extension__ ({ size_t __s1_len, __s2_len ; (__builtin_constant_p (string) && __builtin_constant_p ("case") && (__s1_len = strlen (string), __s2_len = strlen ("case"), (!((size_t)(const void *)((string) + 1) - (size_t) (const void *)(string) == 1) || __s1_len >= 4) && ( !((size_t)(const void *)(("case") + 1) - (size_t)(const void * )("case") == 1) || __s2_len >= 4)) ? __builtin_strcmp (string , "case") : (__builtin_constant_p (string) && ((size_t )(const void *)((string) + 1) - (size_t)(const void *)(string ) == 1) && (__s1_len = strlen (string), __s1_len < 4) ? (__builtin_constant_p ("case") && ((size_t)(const void *)(("case") + 1) - (size_t)(const void *)("case") == 1) ? __builtin_strcmp (string, "case") : (__extension__ ({ const unsigned char *__s2 = (const unsigned char *) (const char *) ("case"); int __result = (((const unsigned char *) (const char *) (string))[0] - __s2[0]); if (__s1_len > 0 && __result == 0) { __result = (((const unsigned char *) (const char *) ( string))[1] - __s2[1]); if (__s1_len > 1 && __result == 0) { __result = (((const unsigned char *) (const char *) ( string))[2] - __s2[2]); if (__s1_len > 2 && __result == 0) __result = (((const unsigned char *) (const char *) (string ))[3] - __s2[3]); } } __result; }))) : (__builtin_constant_p ( "case") && ((size_t)(const void *)(("case") + 1) - (size_t )(const void *)("case") == 1) && (__s2_len = strlen ( "case"), __s2_len < 4) ? (__builtin_constant_p (string) && ((size_t)(const void *)((string) + 1) - (size_t)(const void * )(string) == 1) ? __builtin_strcmp (string, "case") : (- (__extension__ ({ const unsigned char *__s2 = (const unsigned char *) (const char *) (string); int __result = (((const unsigned char *) ( const char *) ("case"))[0] - __s2[0]); if (__s2_len > 0 && __result == 0) { __result = (((const unsigned char *) (const char *) ("case"))[1] - __s2[1]); if (__s2_len > 1 && __result == 0) { __result = (((const unsigned char *) (const char *) ("case"))[2] - __s2[2]); if (__s2_len > 2 && __result == 0) __result = (((const unsigned char *) (const char *) ("case"))[3] - __s2[3]); } } __result; })))) : __builtin_strcmp (string, "case")))); }) : strncmp (string, "case", 4))) == 0) |
| 1333 | { |
| 1334 | bCase = !bCase; |
| 1335 | printf("Switched to case %s\n", bCase ? "sensitive" : "insensitive"); |
| 1336 | } |
| 1337 | else if (string[0] == 'v') |
| 1338 | { |
| 1339 | bVerbose = !bVerbose; |
| 1340 | printf("Turned verbose %s\n", bVerbose ? "on" : "off"); |
| 1341 | } |
| 1342 | else if (string[0] == 'l') |
| 1343 | { |
| 1344 | if (check_have_atoms(atoms, ostring) ) |
| 1345 | { |
| 1346 | list_residues(atoms); |
| 1347 | } |
| 1348 | } |
| 1349 | else if (strncmp(string, "splitch", 7)(__extension__ (__builtin_constant_p (7) && ((__builtin_constant_p (string) && strlen (string) < ((size_t) (7))) || ( __builtin_constant_p ("splitch") && strlen ("splitch" ) < ((size_t) (7)))) ? __extension__ ({ size_t __s1_len, __s2_len ; (__builtin_constant_p (string) && __builtin_constant_p ("splitch") && (__s1_len = strlen (string), __s2_len = strlen ("splitch"), (!((size_t)(const void *)((string) + 1 ) - (size_t)(const void *)(string) == 1) || __s1_len >= 4) && (!((size_t)(const void *)(("splitch") + 1) - (size_t )(const void *)("splitch") == 1) || __s2_len >= 4)) ? __builtin_strcmp (string, "splitch") : (__builtin_constant_p (string) && ((size_t)(const void *)((string) + 1) - (size_t)(const void * )(string) == 1) && (__s1_len = strlen (string), __s1_len < 4) ? (__builtin_constant_p ("splitch") && ((size_t )(const void *)(("splitch") + 1) - (size_t)(const void *)("splitch" ) == 1) ? __builtin_strcmp (string, "splitch") : (__extension__ ({ const unsigned char *__s2 = (const unsigned char *) (const char *) ("splitch"); int __result = (((const unsigned char * ) (const char *) (string))[0] - __s2[0]); if (__s1_len > 0 && __result == 0) { __result = (((const unsigned char *) (const char *) (string))[1] - __s2[1]); if (__s1_len > 1 && __result == 0) { __result = (((const unsigned char *) (const char *) (string))[2] - __s2[2]); if (__s1_len > 2 && __result == 0) __result = (((const unsigned char *) (const char *) (string))[3] - __s2[3]); } } __result; })) ) : (__builtin_constant_p ("splitch") && ((size_t)(const void *)(("splitch") + 1) - (size_t)(const void *)("splitch") == 1) && (__s2_len = strlen ("splitch"), __s2_len < 4) ? (__builtin_constant_p (string) && ((size_t)(const void *)((string) + 1) - (size_t)(const void *)(string) == 1) ? __builtin_strcmp (string, "splitch") : (- (__extension__ ( { const unsigned char *__s2 = (const unsigned char *) (const char *) (string); int __result = (((const unsigned char *) (const char *) ("splitch"))[0] - __s2[0]); if (__s2_len > 0 && __result == 0) { __result = (((const unsigned char *) (const char *) ("splitch"))[1] - __s2[1]); if (__s2_len > 1 && __result == 0) { __result = (((const unsigned char *) (const char *) ("splitch"))[2] - __s2[2]); if (__s2_len > 2 && __result == 0) __result = (((const unsigned char *) (const char *) ("splitch"))[3] - __s2[3]); } } __result; })))) : __builtin_strcmp (string, "splitch")))); }) : strncmp (string, "splitch", 7)) ) == 0) |
| 1350 | { |
| 1351 | string += 7; |
| 1352 | if (check_have_atoms(atoms, ostring) && |
| 1353 | parse_int(&string, &sel_nr) && |
| 1354 | (sel_nr >= 0) && (sel_nr < block->nr)) |
| 1355 | { |
| 1356 | split_chain(atoms, x, sel_nr, block, gn); |
| 1357 | } |
| 1358 | } |
| 1359 | else if (strncmp(string, "splitres", 8)(__extension__ (__builtin_constant_p (8) && ((__builtin_constant_p (string) && strlen (string) < ((size_t) (8))) || ( __builtin_constant_p ("splitres") && strlen ("splitres" ) < ((size_t) (8)))) ? __extension__ ({ size_t __s1_len, __s2_len ; (__builtin_constant_p (string) && __builtin_constant_p ("splitres") && (__s1_len = strlen (string), __s2_len = strlen ("splitres"), (!((size_t)(const void *)((string) + 1 ) - (size_t)(const void *)(string) == 1) || __s1_len >= 4) && (!((size_t)(const void *)(("splitres") + 1) - (size_t )(const void *)("splitres") == 1) || __s2_len >= 4)) ? __builtin_strcmp (string, "splitres") : (__builtin_constant_p (string) && ((size_t)(const void *)((string) + 1) - (size_t)(const void * )(string) == 1) && (__s1_len = strlen (string), __s1_len < 4) ? (__builtin_constant_p ("splitres") && ((size_t )(const void *)(("splitres") + 1) - (size_t)(const void *)("splitres" ) == 1) ? __builtin_strcmp (string, "splitres") : (__extension__ ({ const unsigned char *__s2 = (const unsigned char *) (const char *) ("splitres"); int __result = (((const unsigned char * ) (const char *) (string))[0] - __s2[0]); if (__s1_len > 0 && __result == 0) { __result = (((const unsigned char *) (const char *) (string))[1] - __s2[1]); if (__s1_len > 1 && __result == 0) { __result = (((const unsigned char *) (const char *) (string))[2] - __s2[2]); if (__s1_len > 2 && __result == 0) __result = (((const unsigned char *) (const char *) (string))[3] - __s2[3]); } } __result; })) ) : (__builtin_constant_p ("splitres") && ((size_t)(const void *)(("splitres") + 1) - (size_t)(const void *)("splitres" ) == 1) && (__s2_len = strlen ("splitres"), __s2_len < 4) ? (__builtin_constant_p (string) && ((size_t)(const void *)((string) + 1) - (size_t)(const void *)(string) == 1) ? __builtin_strcmp (string, "splitres") : (- (__extension__ ( { const unsigned char *__s2 = (const unsigned char *) (const char *) (string); int __result = (((const unsigned char *) (const char *) ("splitres"))[0] - __s2[0]); if (__s2_len > 0 && __result == 0) { __result = (((const unsigned char *) (const char *) ("splitres"))[1] - __s2[1]); if (__s2_len > 1 && __result == 0) { __result = (((const unsigned char *) (const char *) ("splitres"))[2] - __s2[2]); if (__s2_len > 2 && __result == 0) __result = (((const unsigned char *) (const char *) ("splitres"))[3] - __s2[3]); } } __result; })))) : __builtin_strcmp (string, "splitres")))); }) : strncmp (string, "splitres", 8 ))) == 0) |
| 1360 | { |
| 1361 | string += 8; |
| 1362 | if (check_have_atoms(atoms, ostring) && |
| 1363 | parse_int(&string, &sel_nr) && |
| 1364 | (sel_nr >= 0) && (sel_nr < block->nr)) |
| 1365 | { |
| 1366 | split_group(atoms, sel_nr, block, gn, FALSE0); |
| 1367 | } |
| 1368 | } |
| 1369 | else if (strncmp(string, "splitat", 7)(__extension__ (__builtin_constant_p (7) && ((__builtin_constant_p (string) && strlen (string) < ((size_t) (7))) || ( __builtin_constant_p ("splitat") && strlen ("splitat" ) < ((size_t) (7)))) ? __extension__ ({ size_t __s1_len, __s2_len ; (__builtin_constant_p (string) && __builtin_constant_p ("splitat") && (__s1_len = strlen (string), __s2_len = strlen ("splitat"), (!((size_t)(const void *)((string) + 1 ) - (size_t)(const void *)(string) == 1) || __s1_len >= 4) && (!((size_t)(const void *)(("splitat") + 1) - (size_t )(const void *)("splitat") == 1) || __s2_len >= 4)) ? __builtin_strcmp (string, "splitat") : (__builtin_constant_p (string) && ((size_t)(const void *)((string) + 1) - (size_t)(const void * )(string) == 1) && (__s1_len = strlen (string), __s1_len < 4) ? (__builtin_constant_p ("splitat") && ((size_t )(const void *)(("splitat") + 1) - (size_t)(const void *)("splitat" ) == 1) ? __builtin_strcmp (string, "splitat") : (__extension__ ({ const unsigned char *__s2 = (const unsigned char *) (const char *) ("splitat"); int __result = (((const unsigned char * ) (const char *) (string))[0] - __s2[0]); if (__s1_len > 0 && __result == 0) { __result = (((const unsigned char *) (const char *) (string))[1] - __s2[1]); if (__s1_len > 1 && __result == 0) { __result = (((const unsigned char *) (const char *) (string))[2] - __s2[2]); if (__s1_len > 2 && __result == 0) __result = (((const unsigned char *) (const char *) (string))[3] - __s2[3]); } } __result; })) ) : (__builtin_constant_p ("splitat") && ((size_t)(const void *)(("splitat") + 1) - (size_t)(const void *)("splitat") == 1) && (__s2_len = strlen ("splitat"), __s2_len < 4) ? (__builtin_constant_p (string) && ((size_t)(const void *)((string) + 1) - (size_t)(const void *)(string) == 1) ? __builtin_strcmp (string, "splitat") : (- (__extension__ ( { const unsigned char *__s2 = (const unsigned char *) (const char *) (string); int __result = (((const unsigned char *) (const char *) ("splitat"))[0] - __s2[0]); if (__s2_len > 0 && __result == 0) { __result = (((const unsigned char *) (const char *) ("splitat"))[1] - __s2[1]); if (__s2_len > 1 && __result == 0) { __result = (((const unsigned char *) (const char *) ("splitat"))[2] - __s2[2]); if (__s2_len > 2 && __result == 0) __result = (((const unsigned char *) (const char *) ("splitat"))[3] - __s2[3]); } } __result; })))) : __builtin_strcmp (string, "splitat")))); }) : strncmp (string, "splitat", 7)) ) == 0) |
| 1370 | { |
| 1371 | string += 7; |
| 1372 | if (check_have_atoms(atoms, ostring) && |
| 1373 | parse_int(&string, &sel_nr) && |
| 1374 | (sel_nr >= 0) && (sel_nr < block->nr)) |
| 1375 | { |
| 1376 | split_group(atoms, sel_nr, block, gn, TRUE1); |
| 1377 | } |
| 1378 | } |
| 1379 | else if (string[0] == '\0') |
| 1380 | { |
| 1381 | bPrintOnce = TRUE1; |
| 1382 | } |
| 1383 | else if (string[0] != 'q') |
| 1384 | { |
| 1385 | nr1 = -1; |
Value stored to 'nr1' is never read | |
| 1386 | nr2 = -1; |
| 1387 | if (parse_entry(&string, natoms, atoms, block, gn, &nr, index, gname)) |
| 1388 | { |
| 1389 | do |
| 1390 | { |
| 1391 | while (string[0] == ' ') |
| 1392 | { |
| 1393 | string++; |
| 1394 | } |
| 1395 | |
| 1396 | bAnd = FALSE0; |
| 1397 | bOr = FALSE0; |
| 1398 | if (string[0] == '&') |
| 1399 | { |
| 1400 | bAnd = TRUE1; |
| 1401 | } |
| 1402 | else if (string[0] == '|') |
| 1403 | { |
| 1404 | bOr = TRUE1; |
| 1405 | } |
| 1406 | |
| 1407 | if (bAnd || bOr) |
| 1408 | { |
| 1409 | string++; |
| 1410 | nr1 = nr; |
| 1411 | for (i = 0; i < nr; i++) |
| 1412 | { |
| 1413 | index1[i] = index[i]; |
| 1414 | } |
| 1415 | strcpy(gname1, gname); |
| 1416 | if (parse_entry(&string, natoms, atoms, block, gn, &nr2, index2, gname2)) |
| 1417 | { |
| 1418 | if (bOr) |
| 1419 | { |
| 1420 | or_groups(nr1, index1, nr2, index2, &nr, index); |
| 1421 | sprintf(gname, "%s_%s", gname1, gname2); |
| 1422 | } |
| 1423 | else |
| 1424 | { |
| 1425 | and_groups(nr1, index1, nr2, index2, &nr, index); |
| 1426 | sprintf(gname, "%s_&_%s", gname1, gname2); |
| 1427 | } |
| 1428 | } |
| 1429 | } |
| 1430 | } |
| 1431 | while (bAnd || bOr); |
| 1432 | } |
| 1433 | while (string[0] == ' ') |
| 1434 | { |
| 1435 | string++; |
| 1436 | } |
| 1437 | if (string[0]) |
| 1438 | { |
| 1439 | printf("\nSyntax error: \"%s\"\n", string); |
| 1440 | } |
| 1441 | else if (nr > 0) |
| 1442 | { |
| 1443 | copy2block(nr, index, block); |
| 1444 | srenew(*gn, block->nr)(*gn) = save_realloc("*gn", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_make_ndx.c" , 1444, (*gn), (block->nr), sizeof(*(*gn))); |
| 1445 | newgroup = block->nr-1; |
| 1446 | (*gn)[newgroup] = strdup(gname)(__extension__ (__builtin_constant_p (gname) && ((size_t )(const void *)((gname) + 1) - (size_t)(const void *)(gname) == 1) ? (((const char *) (gname))[0] == '\0' ? (char *) calloc ( (size_t) 1, (size_t) 1) : ({ size_t __len = strlen (gname) + 1 ; char *__retval = (char *) malloc (__len); if (__retval != ( (void*)0)) __retval = (char *) memcpy (__retval, gname, __len ); __retval; })) : __strdup (gname))); |
| 1447 | } |
| 1448 | else |
| 1449 | { |
| 1450 | printf("Group is empty\n"); |
| 1451 | } |
| 1452 | } |
| 1453 | } |
| 1454 | while (string[0] != 'q'); |
| 1455 | |
| 1456 | sfree(index)save_free("index", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_make_ndx.c" , 1456, (index)); |
| 1457 | sfree(index1)save_free("index1", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_make_ndx.c" , 1457, (index1)); |
| 1458 | sfree(index2)save_free("index2", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_make_ndx.c" , 1458, (index2)); |
| 1459 | } |
| 1460 | |
| 1461 | static int block2natoms(t_blocka *block) |
| 1462 | { |
| 1463 | int i, natoms; |
| 1464 | |
| 1465 | natoms = 0; |
| 1466 | for (i = 0; i < block->nra; i++) |
| 1467 | { |
| 1468 | natoms = max(natoms, block->a[i])(((natoms) > (block->a[i])) ? (natoms) : (block->a[i ]) ); |
| 1469 | } |
| 1470 | natoms++; |
| 1471 | |
| 1472 | return natoms; |
| 1473 | } |
| 1474 | |
| 1475 | void merge_blocks(t_blocka *dest, t_blocka *source) |
| 1476 | { |
| 1477 | int i, nra0, i0; |
| 1478 | |
| 1479 | /* count groups, srenew and fill */ |
| 1480 | i0 = dest->nr; |
| 1481 | nra0 = dest->nra; |
| 1482 | dest->nr += source->nr; |
| 1483 | srenew(dest->index, dest->nr+1)(dest->index) = save_realloc("dest->index", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_make_ndx.c" , 1483, (dest->index), (dest->nr+1), sizeof(*(dest-> index))); |
| 1484 | for (i = 0; i < source->nr; i++) |
| 1485 | { |
| 1486 | dest->index[i0+i] = nra0 + source->index[i]; |
| 1487 | } |
| 1488 | /* count atoms, srenew and fill */ |
| 1489 | dest->nra += source->nra; |
| 1490 | srenew(dest->a, dest->nra)(dest->a) = save_realloc("dest->a", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_make_ndx.c" , 1490, (dest->a), (dest->nra), sizeof(*(dest->a))); |
| 1491 | for (i = 0; i < source->nra; i++) |
| 1492 | { |
| 1493 | dest->a[nra0+i] = source->a[i]; |
| 1494 | } |
| 1495 | |
| 1496 | /* terminate list */ |
| 1497 | dest->index[dest->nr] = dest->nra; |
| 1498 | |
| 1499 | } |
| 1500 | |
| 1501 | int gmx_make_ndx(int argc, char *argv[]) |
| 1502 | { |
| 1503 | const char *desc[] = { |
| 1504 | "Index groups are necessary for almost every GROMACS program.", |
| 1505 | "All these programs can generate default index groups. You ONLY", |
| 1506 | "have to use [THISMODULE] when you need SPECIAL index groups.", |
| 1507 | "There is a default index group for the whole system, 9 default", |
| 1508 | "index groups for proteins, and a default index group", |
| 1509 | "is generated for every other residue name.[PAR]", |
| 1510 | "When no index file is supplied, also [THISMODULE] will generate the", |
| 1511 | "default groups.", |
| 1512 | "With the index editor you can select on atom, residue and chain names", |
| 1513 | "and numbers.", |
| 1514 | "When a run input file is supplied you can also select on atom type.", |
| 1515 | "You can use NOT, AND and OR, you can split groups", |
| 1516 | "into chains, residues or atoms. You can delete and rename groups.[PAR]", |
| 1517 | "The atom numbering in the editor and the index file starts at 1.[PAR]", |
| 1518 | "The [TT]-twin[tt] switch duplicates all index groups with an offset of", |
| 1519 | "[TT]-natoms[tt], which is useful for Computational Electrophysiology", |
| 1520 | "double-layer membrane setups." |
| 1521 | }; |
| 1522 | |
| 1523 | static int natoms = 0; |
| 1524 | static gmx_bool bVerbose = FALSE0; |
| 1525 | static gmx_bool bDuplicate = FALSE0; |
| 1526 | t_pargs pa[] = { |
| 1527 | { "-natoms", FALSE0, etINT, {&natoms}, |
| 1528 | "set number of atoms (default: read from coordinate or index file)" }, |
| 1529 | { "-twin", FALSE0, etBOOL, {&bDuplicate}, |
| 1530 | "Duplicate all index groups with an offset of -natoms" }, |
| 1531 | { "-verbose", FALSE0, etBOOL, {&bVerbose}, |
| 1532 | "HIDDENVerbose output" } |
| 1533 | }; |
| 1534 | #define NPA((int)(sizeof(pa)/sizeof((pa)[0]))) asize(pa)((int)(sizeof(pa)/sizeof((pa)[0]))) |
| 1535 | |
| 1536 | output_env_t oenv; |
| 1537 | char title[STRLEN4096]; |
| 1538 | int nndxin; |
| 1539 | const char *stxfile; |
| 1540 | char **ndxinfiles; |
| 1541 | const char *ndxoutfile; |
| 1542 | gmx_bool bNatoms; |
| 1543 | int i, j; |
| 1544 | t_atoms *atoms; |
| 1545 | rvec *x, *v; |
| 1546 | int ePBC; |
| 1547 | matrix box; |
| 1548 | t_blocka *block, *block2; |
| 1549 | char **gnames, **gnames2; |
| 1550 | t_filenm fnm[] = { |
| 1551 | { efSTX, "-f", NULL((void*)0), ffOPTRD(1<<1 | 1<<3) }, |
| 1552 | { efNDX, "-n", NULL((void*)0), ffOPTRDMULT((1<<1 | 1<<5) | 1<<3) }, |
| 1553 | { efNDX, "-o", NULL((void*)0), ffWRITE1<<2 } |
| 1554 | }; |
| 1555 | #define NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))) asize(fnm)((int)(sizeof(fnm)/sizeof((fnm)[0]))) |
| 1556 | |
| 1557 | if (!parse_common_args(&argc, argv, 0, NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm, NPA((int)(sizeof(pa)/sizeof((pa)[0]))), pa, asize(desc)((int)(sizeof(desc)/sizeof((desc)[0]))), desc, |
| 1558 | 0, NULL((void*)0), &oenv)) |
| 1559 | { |
| 1560 | return 0; |
| 1561 | } |
| 1562 | |
| 1563 | stxfile = ftp2fn_null(efSTX, NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm); |
| 1564 | if (opt2bSet("-n", NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm)) |
| 1565 | { |
| 1566 | nndxin = opt2fns(&ndxinfiles, "-n", NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm); |
| 1567 | } |
| 1568 | else |
| 1569 | { |
| 1570 | nndxin = 0; |
| 1571 | } |
| 1572 | ndxoutfile = opt2fn("-o", NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm); |
| 1573 | bNatoms = opt2parg_bSet("-natoms", NPA((int)(sizeof(pa)/sizeof((pa)[0]))), pa); |
| 1574 | |
| 1575 | if (!stxfile && !nndxin) |
| 1576 | { |
| 1577 | gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_make_ndx.c" , 1577, "No input files (structure or index)"); |
| 1578 | } |
| 1579 | |
| 1580 | if (stxfile) |
| 1581 | { |
| 1582 | snew(atoms, 1)(atoms) = save_calloc("atoms", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_make_ndx.c" , 1582, (1), sizeof(*(atoms))); |
| 1583 | get_stx_coordnum(stxfile, &(atoms->nr)); |
| 1584 | init_t_atoms(atoms, atoms->nr, TRUE1); |
| 1585 | snew(x, atoms->nr)(x) = save_calloc("x", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_make_ndx.c" , 1585, (atoms->nr), sizeof(*(x))); |
| 1586 | snew(v, atoms->nr)(v) = save_calloc("v", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_make_ndx.c" , 1586, (atoms->nr), sizeof(*(v))); |
| 1587 | fprintf(stderrstderr, "\nReading structure file\n"); |
| 1588 | read_stx_conf(stxfile, title, atoms, x, v, &ePBC, box); |
| 1589 | natoms = atoms->nr; |
| 1590 | bNatoms = TRUE1; |
| 1591 | } |
| 1592 | else |
| 1593 | { |
| 1594 | atoms = NULL((void*)0); |
| 1595 | x = NULL((void*)0); |
| 1596 | } |
| 1597 | |
| 1598 | /* read input file(s) */ |
| 1599 | block = new_blocka(); |
| 1600 | gnames = NULL((void*)0); |
| 1601 | printf("Going to read %d old index file(s)\n", nndxin); |
| 1602 | if (nndxin) |
| 1603 | { |
| 1604 | for (i = 0; i < nndxin; i++) |
| 1605 | { |
| 1606 | block2 = init_index(ndxinfiles[i], &gnames2); |
| 1607 | srenew(gnames, block->nr+block2->nr)(gnames) = save_realloc("gnames", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_make_ndx.c" , 1607, (gnames), (block->nr+block2->nr), sizeof(*(gnames ))); |
| 1608 | for (j = 0; j < block2->nr; j++) |
| 1609 | { |
| 1610 | gnames[block->nr+j] = gnames2[j]; |
| 1611 | } |
| 1612 | sfree(gnames2)save_free("gnames2", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_make_ndx.c" , 1612, (gnames2)); |
| 1613 | merge_blocks(block, block2); |
| 1614 | sfree(block2->a)save_free("block2->a", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_make_ndx.c" , 1614, (block2->a)); |
| 1615 | sfree(block2->index)save_free("block2->index", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_make_ndx.c" , 1615, (block2->index)); |
| 1616 | /* done_block(block2); */ |
| 1617 | sfree(block2)save_free("block2", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_make_ndx.c" , 1617, (block2)); |
| 1618 | } |
| 1619 | } |
| 1620 | else |
| 1621 | { |
| 1622 | snew(gnames, 1)(gnames) = save_calloc("gnames", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_make_ndx.c" , 1622, (1), sizeof(*(gnames))); |
| 1623 | analyse(atoms, block, &gnames, FALSE0, TRUE1); |
| 1624 | } |
| 1625 | |
| 1626 | if (!bNatoms) |
| 1627 | { |
| 1628 | natoms = block2natoms(block); |
| 1629 | printf("Counted atom numbers up to %d in index file\n", natoms); |
| 1630 | } |
| 1631 | |
| 1632 | edit_index(natoms, atoms, x, block, &gnames, bVerbose); |
| 1633 | |
| 1634 | write_index(ndxoutfile, block, gnames, bDuplicate, natoms); |
| 1635 | |
| 1636 | return 0; |
| 1637 | } |