src/gromacs/selection/sm_simple.cpp

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  35 /*! \internal \file
  36  * \brief
  37  * Implements simple keyword selection methods.
  38  *
  39  * \author Teemu Murtola <teemu.murtola@gmail.com>
  40  * \ingroup module_selection
  41  */
  42 #include "gmxpre.h"
  43
  44 #include <cctype>
  45
  46 #include "gromacs/selection/position.h"
  47 #include "gromacs/topology/mtop_lookup.h"
  48 #include "gromacs/topology/topology.h"
  49 #include "gromacs/utility/arraysize.h"
  50 #include "gromacs/utility/exceptions.h"
  51 #include "gromacs/utility/gmxassert.h"
  52
  53 #include "selmethod.h"
  54
  55 /** Evaluates the \p all selection keyword. */
  56 static void
  57 evaluate_all(const gmx::SelMethodEvalContext &context,
  58              gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data);
  59 /** Evaluates the \p none selection keyword. */
  60 static void
  61 evaluate_none(const gmx::SelMethodEvalContext &context,
  62               gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data);
  63 /** Evaluates the \p atomnr selection keyword. */
  64 static void
  65 evaluate_atomnr(const gmx::SelMethodEvalContext &context,
  66                 gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data);
  67 /** Evaluates the \p resnr selection keyword. */
  68 static void
  69 evaluate_resnr(const gmx::SelMethodEvalContext &context,
  70                gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data);
  71 /** Evaluates the \p resindex selection keyword. */
  72 static void
  73 evaluate_resindex(const gmx::SelMethodEvalContext &context,
  74                   gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data);
  75 /*! \brief
  76  * Checks whether molecule information is present in the topology.
  77  *
  78  * \param[in] top  Topology structure.
  79  * \param     npar Not used.
  80  * \param     param Not used.
  81  * \param     data Not used.
  82  * \returns   0 if molecule info is present in the topology, -1 otherwise.
  83  *
  84  * If molecule information is not found, also prints an error message.
  85  */
  86 static void
  87 check_molecules(const gmx_mtop_t *top, int npar, gmx_ana_selparam_t *param, void *data);
  88 /** Evaluates the \p molindex selection keyword. */
  89 static void
  90 evaluate_molindex(const gmx::SelMethodEvalContext &context,
  91                   gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data);
  92 /** Evaluates the \p atomname selection keyword. */
  93 static void
  94 evaluate_atomname(const gmx::SelMethodEvalContext &context,
  95                   gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data);
  96 /** Evaluates the \p pdbatomname selection keyword. */
  97 static void
  98 evaluate_pdbatomname(const gmx::SelMethodEvalContext &context,
  99                      gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data);
 100 /*! \brief
 101  * Checks whether atom types are present in the topology.
 102  *
 103  * \param[in] top  Topology structure.
 104  * \param     npar Not used.
 105  * \param     param Not used.
 106  * \param     data Not used.
 107  */
 108 static void
 109 check_atomtype(const gmx_mtop_t *top, int npar, gmx_ana_selparam_t *param, void *data);
 110 /** Evaluates the \p atomtype selection keyword. */
 111 static void
 112 evaluate_atomtype(const gmx::SelMethodEvalContext &context,
 113                   gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data);
 114 /** Evaluates the \p insertcode selection keyword. */
 115 static void
 116 evaluate_insertcode(const gmx::SelMethodEvalContext &context,
 117                     gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data);
 118 /** Evaluates the \p chain selection keyword. */
 119 static void
 120 evaluate_chain(const gmx::SelMethodEvalContext &context,
 121                gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data);
 122 /** Evaluates the \p mass selection keyword. */
 123 static void
 124 evaluate_mass(const gmx::SelMethodEvalContext &context,
 125               gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data);
 126 /*! \brief
 127  * Checks whether charges are present in the topology.
 128  *
 129  * \param[in] top  Topology structure.
 130  * \param     npar Not used.
 131  * \param     param Not used.
 132  * \param     data Not used.
 133  */
 134 static void
 135 check_charge(const gmx_mtop_t *top, int npar, gmx_ana_selparam_t *param, void *data);
 136 /** Evaluates the \p charge selection keyword. */
 137 static void
 138 evaluate_charge(const gmx::SelMethodEvalContext &context,
 139                 gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data);
 140 /*! \brief
 141  * Checks whether PDB info is present in the topology.
 142  *
 143  * \param[in] top  Topology structure.
 144  * \param     npar Not used.
 145  * \param     param Not used.
 146  * \param     data Not used.
 147  * \returns   0 if PDB info is present in the topology, -1 otherwise.
 148  *
 149  * If PDB info is not found, also prints an error message.
 150  */
 151 static void
 152 check_pdbinfo(const gmx_mtop_t *top, int npar, gmx_ana_selparam_t *param, void *data);
 153 /** Evaluates the \p altloc selection keyword. */
 154 static void
 155 evaluate_altloc(const gmx::SelMethodEvalContext &context,
 156                 gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data);
 157 /** Evaluates the \p occupancy selection keyword. */
 158 static void
 159 evaluate_occupancy(const gmx::SelMethodEvalContext &context,
 160                    gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data);
 161 /** Evaluates the \p betafactor selection keyword. */
 162 static void
 163 evaluate_betafactor(const gmx::SelMethodEvalContext &context,
 164                     gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data);
 165 /** Evaluates the \p resname selection keyword. */
 166 static void
 167 evaluate_resname(const gmx::SelMethodEvalContext &context,
 168                  gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data);
 169
 170 /** Evaluates the \p x selection keyword. */
 171 static void
 172 evaluate_x(const gmx::SelMethodEvalContext &context,
 173            gmx_ana_pos_t *pos, gmx_ana_selvalue_t *out, void *data);
 174 /** Evaluates the \p y selection keyword. */
 175 static void
 176 evaluate_y(const gmx::SelMethodEvalContext &context,
 177            gmx_ana_pos_t *pos, gmx_ana_selvalue_t *out, void *data);
 178 /** Evaluates the \p z selection keyword. */
 179 static void
 180 evaluate_z(const gmx::SelMethodEvalContext &context,
 181            gmx_ana_pos_t *pos, gmx_ana_selvalue_t *out, void *data);
 182
 183 //! Help title for atom name selection keywords.
 184 static const char        helptitle_atomname[] = "Selecting atoms by name";
 185 //! Help text for atom name selection keywords.
 186 static const char *const help_atomname[] = {
 187     "::",
 188     "",
 189     "  name",
 190     "  pdbname",
 191     "  atomname",
 192     "  pdbatomname",
 193     "",
 194     "These keywords select atoms by name. [TT]name[tt] selects atoms using",
 195     "the GROMACS atom naming convention.",
 196     "For input formats other than PDB, the atom names are matched exactly",
 197     "as they appear in the input file. For PDB files, 4 character atom names",
 198     "that start with a digit are matched after moving the digit to the end",
 199     "(e.g., to match 3HG2 from a PDB file, use [TT]name HG23[tt]).",
 200     "[TT]pdbname[tt] can only be used with a PDB input file, and selects",
 201     "atoms based on the exact name given in the input file, without the",
 202     "transformation described above.[PAR]",
 203
 204     "[TT]atomname[tt] and [TT]pdbatomname[tt] are synonyms for the above two",
 205     "keywords."
 206 };
 207
 208 /** Selection method data for \p all selection keyword. */
 209 gmx_ana_selmethod_t sm_all = {
 210     "all", GROUP_VALUE, 0,
 211     0, NULL,
 212     NULL,
 213     NULL,
 214     NULL,
 215     NULL,
 216     NULL,
 217     NULL,
 218     &evaluate_all,
 219     NULL,
 220 };
 221
 222 /** Selection method data for \p none selection keyword. */
 223 gmx_ana_selmethod_t sm_none = {
 224     "none", GROUP_VALUE, 0,
 225     0, NULL,
 226     NULL,
 227     NULL,
 228     NULL,
 229     NULL,
 230     NULL,
 231     NULL,
 232     &evaluate_none,
 233     NULL,
 234 };
 235
 236 /** Selection method data for \p atomnr selection keyword. */
 237 gmx_ana_selmethod_t sm_atomnr = {
 238     "atomnr", INT_VALUE, 0,
 239     0, NULL,
 240     NULL,
 241     NULL,
 242     NULL,
 243     NULL,
 244     NULL,
 245     NULL,
 246     &evaluate_atomnr,
 247     NULL,
 248 };
 249
 250 /** Selection method data for \p resnr selection keyword. */
 251 gmx_ana_selmethod_t sm_resnr = {
 252     "resnr", INT_VALUE, SMETH_REQTOP,
 253     0, NULL,
 254     NULL,
 255     NULL,
 256     NULL,
 257     NULL,
 258     NULL,
 259     NULL,
 260     &evaluate_resnr,
 261     NULL,
 262 };
 263
 264 /** Selection method data for \p resindex selection keyword. */
 265 gmx_ana_selmethod_t sm_resindex = {
 266     "resindex", INT_VALUE, SMETH_REQTOP,
 267     0, NULL,
 268     NULL,
 269     NULL,
 270     NULL,
 271     NULL,
 272     NULL,
 273     NULL,
 274     &evaluate_resindex,
 275     NULL,
 276 };
 277
 278 /** Selection method data for \p molindex selection keyword. */
 279 gmx_ana_selmethod_t sm_molindex = {
 280     "molindex", INT_VALUE, SMETH_REQTOP,
 281     0, NULL,
 282     NULL,
 283     NULL,
 284     &check_molecules,
 285     NULL,
 286     NULL,
 287     NULL,
 288     &evaluate_molindex,
 289     NULL,
 290 };
 291
 292 /** Selection method data for \p atomname selection keyword. */
 293 gmx_ana_selmethod_t sm_atomname = {
 294     "atomname", STR_VALUE, SMETH_REQTOP,
 295     0, NULL,
 296     NULL,
 297     NULL,
 298     NULL,
 299     NULL,
 300     NULL,
 301     NULL,
 302     &evaluate_atomname,
 303     NULL,
 304     {NULL, helptitle_atomname, asize(help_atomname), help_atomname}
 305 };
 306
 307 /** Selection method data for \p pdbatomname selection keyword. */
 308 gmx_ana_selmethod_t sm_pdbatomname = {
 309     "pdbatomname", STR_VALUE, SMETH_REQTOP,
 310     0, NULL,
 311     NULL,
 312     NULL,
 313     &check_pdbinfo,
 314     NULL,
 315     NULL,
 316     NULL,
 317     &evaluate_pdbatomname,
 318     NULL,
 319     {NULL, helptitle_atomname, asize(help_atomname), help_atomname}
 320 };
 321
 322 /** Selection method data for \p atomtype selection keyword. */
 323 gmx_ana_selmethod_t sm_atomtype = {
 324     "atomtype", STR_VALUE, SMETH_REQTOP,
 325     0, NULL,
 326     NULL,
 327     NULL,
 328     &check_atomtype,
 329     NULL,
 330     NULL,
 331     NULL,
 332     &evaluate_atomtype,
 333     NULL,
 334 };
 335
 336 /** Selection method data for \p resname selection keyword. */
 337 gmx_ana_selmethod_t sm_resname = {
 338     "resname", STR_VALUE, SMETH_REQTOP,
 339     0, NULL,
 340     NULL,
 341     NULL,
 342     NULL,
 343     NULL,
 344     NULL,
 345     NULL,
 346     &evaluate_resname,
 347     NULL,
 348 };
 349
 350 /** Selection method data for \p chain selection keyword. */
 351 gmx_ana_selmethod_t sm_insertcode = {
 352     "insertcode", STR_VALUE, SMETH_REQTOP | SMETH_CHARVAL,
 353     0, NULL,
 354     NULL,
 355     NULL,
 356     NULL,
 357     NULL,
 358     NULL,
 359     NULL,
 360     &evaluate_insertcode,
 361     NULL,
 362 };
 363
 364 /** Selection method data for \p chain selection keyword. */
 365 gmx_ana_selmethod_t sm_chain = {
 366     "chain", STR_VALUE, SMETH_REQTOP | SMETH_CHARVAL,
 367     0, NULL,
 368     NULL,
 369     NULL,
 370     NULL,
 371     NULL,
 372     NULL,
 373     NULL,
 374     &evaluate_chain,
 375     NULL,
 376 };
 377
 378 /** Selection method data for \p mass selection keyword. */
 379 gmx_ana_selmethod_t sm_mass = {
 380     "mass", REAL_VALUE, SMETH_REQMASS,
 381     0, NULL,
 382     NULL,
 383     NULL,
 384     NULL,
 385     NULL,
 386     NULL,
 387     NULL,
 388     &evaluate_mass,
 389     NULL,
 390 };
 391
 392 /** Selection method data for \p charge selection keyword. */
 393 gmx_ana_selmethod_t sm_charge = {
 394     "charge", REAL_VALUE, SMETH_REQTOP,
 395     0, NULL,
 396     NULL,
 397     NULL,
 398     &check_charge,
 399     NULL,
 400     NULL,
 401     NULL,
 402     &evaluate_charge,
 403     NULL,
 404 };
 405
 406 /** Selection method data for \p chain selection keyword. */
 407 gmx_ana_selmethod_t sm_altloc = {
 408     "altloc", STR_VALUE, SMETH_REQTOP | SMETH_CHARVAL,
 409     0, NULL,
 410     NULL,
 411     NULL,
 412     &check_pdbinfo,
 413     NULL,
 414     NULL,
 415     NULL,
 416     &evaluate_altloc,
 417     NULL,
 418 };
 419
 420 /** Selection method data for \p occupancy selection keyword. */
 421 gmx_ana_selmethod_t sm_occupancy = {
 422     "occupancy", REAL_VALUE, SMETH_REQTOP,
 423     0, NULL,
 424     NULL,
 425     NULL,
 426     &check_pdbinfo,
 427     NULL,
 428     NULL,
 429     NULL,
 430     &evaluate_occupancy,
 431     NULL,
 432 };
 433
 434 /** Selection method data for \p betafactor selection keyword. */
 435 gmx_ana_selmethod_t sm_betafactor = {
 436     "betafactor", REAL_VALUE, SMETH_REQTOP,
 437     0, NULL,
 438     NULL,
 439     NULL,
 440     &check_pdbinfo,
 441     NULL,
 442     NULL,
 443     NULL,
 444     &evaluate_betafactor,
 445     NULL,
 446 };
 447
 448 /** Selection method data for \p x selection keyword. */
 449 gmx_ana_selmethod_t sm_x = {
 450     "x", REAL_VALUE, SMETH_DYNAMIC,
 451     0, NULL,
 452     NULL,
 453     NULL,
 454     NULL,
 455     NULL,
 456     NULL,
 457     NULL,
 458     NULL,
 459     &evaluate_x,
 460 };
 461
 462 /** Selection method data for \p y selection keyword. */
 463 gmx_ana_selmethod_t sm_y = {
 464     "y", REAL_VALUE, SMETH_DYNAMIC,
 465     0, NULL,
 466     NULL,
 467     NULL,
 468     NULL,
 469     NULL,
 470     NULL,
 471     NULL,
 472     NULL,
 473     &evaluate_y,
 474 };
 475
 476 /** Selection method data for \p z selection keyword. */
 477 gmx_ana_selmethod_t sm_z = {
 478     "z", REAL_VALUE, SMETH_DYNAMIC,
 479     0, NULL,
 480     NULL,
 481     NULL,
 482     NULL,
 483     NULL,
 484     NULL,
 485     NULL,
 486     NULL,
 487     &evaluate_z,
 488 };
 489
 490 /*!
 491  * See sel_updatefunc() for description of the parameters.
 492  * \p data is not used.
 493  *
 494  * Copies \p g to \p out->u.g.
 495  */
 496 static void
 497 evaluate_all(const gmx::SelMethodEvalContext & /*context*/,
 498              gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void * /* data */)
 499 {
 500     gmx_ana_index_copy(out->u.g, g, false);
 501 }
 502
 503 /*!
 504  * See sel_updatefunc() for description of the parameters.
 505  * \p data is not used.
 506  *
 507  * Returns an empty \p out->u.g.
 508  */
 509 static void
 510 evaluate_none(const gmx::SelMethodEvalContext & /*context*/,
 511               gmx_ana_index_t * /* g */, gmx_ana_selvalue_t *out, void * /* data */)
 512 {
 513     out->u.g->isize = 0;
 514 }
 515
 516 /*!
 517  * See sel_updatefunc() for description of the parameters.
 518  * \p data is not used.
 519  *
 520  * Returns the indices for each atom in \p out->u.i.
 521  */
 522 static void
 523 evaluate_atomnr(const gmx::SelMethodEvalContext & /*context*/,
 524                 gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void * /* data */)
 525 {
 526     int  i;
 527
 528     out->nr = g->isize;
 529     for (i = 0; i < g->isize; ++i)
 530     {
 531         out->u.i[i] = g->index[i] + 1;
 532     }
 533 }
 534
 535 /*!
 536  * See sel_updatefunc() for description of the parameters.
 537  * \p data is not used.
 538  *
 539  * Returns the residue numbers for each atom in \p out->u.i.
 540  */
 541 static void
 542 evaluate_resnr(const gmx::SelMethodEvalContext &context,
 543                gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void * /* data */)
 544 {
 545     out->nr  = g->isize;
 546     int molb = 0;
 547     for (int i = 0; i < g->isize; ++i)
 548     {
 549         mtopGetAtomAndResidueName(context.top, g->index[i], &molb,
 550                                   nullptr, &out->u.i[i], nullptr, nullptr);
 551     }
 552 }
 553
 554 /*!
 555  * See sel_updatefunc() for description of the parameters.
 556  * \p data is not used.
 557  *
 558  * Returns the residue indices for each atom in \p out->u.i.
 559  */
 560 static void
 561 evaluate_resindex(const gmx::SelMethodEvalContext &context,
 562                   gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void * /* data */)
 563 {
 564     out->nr  = g->isize;
 565     int molb = 0;
 566     for (int i = 0; i < g->isize; ++i)
 567     {
 568         int resind;
 569         mtopGetAtomAndResidueName(context.top, g->index[i], &molb,
 570                                   nullptr, nullptr, nullptr, &resind);
 571         out->u.i[i] = resind + 1;
 572     }
 573 }
 574
 575 static void
 576 check_molecules(const gmx_mtop_t *top, int /* npar */, gmx_ana_selparam_t * /* param */, void * /* data */)
 577 {
 578     bool bOk;
 579
 580     bOk = (top != NULL && top->mols.nr > 0);
 581     if (!bOk)
 582     {
 583         GMX_THROW(gmx::InconsistentInputError("Molecule information not available in topology"));
 584     }
 585 }
 586
 587 /*!
 588  * See sel_updatefunc() for description of the parameters.
 589  * \p data is not used.
 590  *
 591  * Returns the molecule indices for each atom in \p out->u.i.
 592  */
 593 static void
 594 evaluate_molindex(const gmx::SelMethodEvalContext &context,
 595                   gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void * /* data */)
 596 {
 597     int  i, j;
 598
 599     out->nr = g->isize;
 600     for (i = j = 0; i < g->isize; ++i)
 601     {
 602         while (context.top->mols.index[j + 1] <= g->index[i])
 603         {
 604             ++j;
 605         }
 606         out->u.i[i] = j + 1;
 607     }
 608 }
 609
 610 /*!
 611  * See sel_updatefunc() for description of the parameters.
 612  * \p data is not used.
 613  *
 614  * Returns the atom name for each atom in \p out->u.s.
 615  */
 616 static void
 617 evaluate_atomname(const gmx::SelMethodEvalContext &context,
 618                   gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void * /* data */)
 619 {
 620     out->nr = g->isize;
 621     int molb = 0;
 622     for (int i = 0; i < g->isize; ++i)
 623     {
 624         const char *atom_name;
 625         mtopGetAtomAndResidueName(context.top, g->index[i], &molb,
 626                                   &atom_name, nullptr, nullptr, nullptr);
 627         out->u.s[i] = const_cast<char *>(atom_name);
 628     }
 629 }
 630
 631 /*!
 632  * See sel_updatefunc() for description of the parameters.
 633  * \p data is not used.
 634  *
 635  * Returns the PDB atom name for each atom in \p out->u.s.
 636  */
 637 static void
 638 evaluate_pdbatomname(const gmx::SelMethodEvalContext &context,
 639                      gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void * /* data */)
 640 {
 641     out->nr = g->isize;
 642     int molb = 0;
 643     for (int i = 0; i < g->isize; ++i)
 644     {
 645         const char *s = mtopGetAtomPdbInfo(context.top, g->index[i], &molb).atomnm;
 646         while (std::isspace(*s))
 647         {
 648             ++s;
 649         }
 650         out->u.s[i] = const_cast<char *>(s);
 651     }
 652 }
 653
 654 static void
 655 check_atomtype(const gmx_mtop_t *top, int /* npar */, gmx_ana_selparam_t * /* param */, void * /* data */)
 656 {
 657     if (!gmx_mtop_has_atomtypes(top))
 658     {
 659         GMX_THROW(gmx::InconsistentInputError("Atom types not available in topology"));
 660     }
 661 }
 662
 663 /*!
 664  * See sel_updatefunc() for description of the parameters.
 665  * \p data is not used.
 666  *
 667  * Returns the atom type for each atom in \p out->u.s.
 668  * Segfaults if atom types are not found in the topology.
 669  */
 670 static void
 671 evaluate_atomtype(const gmx::SelMethodEvalContext &context,
 672                   gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void * /* data */)
 673 {
 674     out->nr = g->isize;
 675     int molb = 0;
 676     for (int i = 0; i < g->isize; ++i)
 677     {
 678         int atomIndexInMolecule;
 679         mtopGetMolblockIndex(context.top, g->index[i], &molb,
 680                              nullptr, &atomIndexInMolecule);
 681         const gmx_moltype_t &moltype = context.top->moltype[context.top->molblock[molb].type];
 682         out->u.s[i] = *moltype.atoms.atomtype[atomIndexInMolecule];
 683     }
 684 }
 685
 686 /*!
 687  * See sel_updatefunc() for description of the parameters.
 688  * \p data is not used.
 689  *
 690  * Returns the residue name for each atom in \p out->u.s.
 691  */
 692 static void
 693 evaluate_resname(const gmx::SelMethodEvalContext &context,
 694                  gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void * /* data */)
 695 {
 696     out->nr = g->isize;
 697     int molb = 0;
 698     for (int i = 0; i < g->isize; ++i)
 699     {
 700         out->u.s[i] = *mtopGetResidueInfo(context.top, g->index[i], &molb).name;
 701     }
 702 }
 703
 704 /*!
 705  * See sel_updatefunc() for description of the parameters.
 706  * \p data is not used.
 707  *
 708  * Returns the insertion code for each atom in \p out->u.s.
 709  */
 710 static void
 711 evaluate_insertcode(const gmx::SelMethodEvalContext &context,
 712                     gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void * /* data */)
 713 {
 714     out->nr = g->isize;
 715     int molb = 0;
 716     for (int i = 0; i < g->isize; ++i)
 717     {
 718         out->u.s[i][0] = mtopGetResidueInfo(context.top, g->index[i], &molb).ic;
 719     }
 720 }
 721
 722 /*!
 723  * See sel_updatefunc() for description of the parameters.
 724  * \p data is not used.
 725  *
 726  * Returns the chain for each atom in \p out->u.s.
 727  */
 728 static void
 729 evaluate_chain(const gmx::SelMethodEvalContext &context,
 730                gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void * /* data */)
 731 {
 732     out->nr = g->isize;
 733     int molb = 0;
 734     for (int i = 0; i < g->isize; ++i)
 735     {
 736         out->u.s[i][0] = mtopGetResidueInfo(context.top, g->index[i], &molb).chainid;
 737     }
 738 }
 739
 740 /*!
 741  * See sel_updatefunc() for description of the parameters.
 742  * \p data is not used.
 743  *
 744  * Returns the mass for each atom in \p out->u.r.
 745  */
 746 static void
 747 evaluate_mass(const gmx::SelMethodEvalContext &context,
 748               gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void * /* data */)
 749 {
 750     GMX_RELEASE_ASSERT(gmx_mtop_has_masses(context.top),
 751                        "Masses not available for evaluation");
 752     out->nr = g->isize;
 753     int molb = 0;
 754     for (int i = 0; i < g->isize; ++i)
 755     {
 756         out->u.r[i] = mtopGetAtomMass(context.top, g->index[i], &molb);
 757     }
 758 }
 759
 760
 761 static void
 762 check_charge(const gmx_mtop_t *top, int /* npar */, gmx_ana_selparam_t * /* param */, void * /* data */)
 763 {
 764     if (!gmx_mtop_has_charges(top))
 765     {
 766         GMX_THROW(gmx::InconsistentInputError("Charges not available in topology"));
 767     }
 768 }
 769
 770 /*!
 771  * See sel_updatefunc() for description of the parameters.
 772  * \p data is not used.
 773  *
 774  * Returns the charge for each atom in \p out->u.r.
 775  */
 776 static void
 777 evaluate_charge(const gmx::SelMethodEvalContext &context,
 778                 gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void * /* data */)
 779 {
 780     out->nr = g->isize;
 781     int molb = 0;
 782     for (int i = 0; i < g->isize; ++i)
 783     {
 784         out->u.r[i] = mtopGetAtomParameters(context.top, g->index[i], &molb).q;
 785     }
 786 }
 787
 788 static void
 789 check_pdbinfo(const gmx_mtop_t *top, int /* npar */, gmx_ana_selparam_t * /* param */, void * /* data */)
 790 {
 791     if (!gmx_mtop_has_pdbinfo(top))
 792     {
 793         GMX_THROW(gmx::InconsistentInputError("PDB info not available in topology"));
 794     }
 795 }
 796
 797 /*!
 798  * See sel_updatefunc() for description of the parameters.
 799  * \p data is not used.
 800  *
 801  * Returns the alternate location identifier for each atom in \p out->u.s.
 802  */
 803 static void
 804 evaluate_altloc(const gmx::SelMethodEvalContext &context,
 805                 gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void * /* data */)
 806 {
 807     out->nr = g->isize;
 808     int molb = 0;
 809     for (int i = 0; i < g->isize; ++i)
 810     {
 811         out->u.s[i][0] = mtopGetAtomPdbInfo(context.top, g->index[i], &molb).altloc;
 812     }
 813 }
 814
 815 /*!
 816  * See sel_updatefunc() for description of the parameters.
 817  * \p data is not used.
 818  *
 819  * Returns the occupancy numbers for each atom in \p out->u.r.
 820  * Segfaults if PDB info is not found in the topology.
 821  */
 822 static void
 823 evaluate_occupancy(const gmx::SelMethodEvalContext &context,
 824                    gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void * /* data */)
 825 {
 826     out->nr = g->isize;
 827     int molb = 0;
 828     for (int i = 0; i < g->isize; ++i)
 829     {
 830         out->u.r[i] = mtopGetAtomPdbInfo(context.top, g->index[i], &molb).occup;
 831     }
 832 }
 833
 834 /*!
 835  * See sel_updatefunc() for description of the parameters.
 836  * \p data is not used.
 837  *
 838  * Returns the B-factors for each atom in \p out->u.r.
 839  * Segfaults if PDB info is not found in the topology.
 840  */
 841 static void
 842 evaluate_betafactor(const gmx::SelMethodEvalContext &context,
 843                     gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void * /* data */)
 844 {
 845     out->nr = g->isize;
 846     int molb = 0;
 847     for (int i = 0; i < g->isize; ++i)
 848     {
 849         out->u.r[i] = mtopGetAtomPdbInfo(context.top, g->index[i], &molb).bfac;
 850     }
 851 }
 852
 853 /*! \brief
 854  * Internal utility function for position keyword evaluation.
 855  *
 856  * \param[out] out  Output array.
 857  * \param[in]  pos  Position data to use instead of atomic coordinates.
 858  * \param[in]  d    Coordinate index to evaluate (\p XX, \p YY or \p ZZ).
 859  *
 860  * This function is used internally by evaluate_x(), evaluate_y() and
 861  * evaluate_z() to do the actual evaluation.
 862  */
 863 static void
 864 evaluate_coord(real out[], gmx_ana_pos_t *pos, int d)
 865 {
 866     for (int i = 0; i < pos->count(); ++i)
 867     {
 868         out[i] = pos->x[i][d];
 869     }
 870     // TODO: Make this more efficient by directly extracting the coordinates
 871     // from the frame coordinates for atomic positions instead of going through
 872     // a position calculation.
 873 }
 874
 875 /*!
 876  * See sel_updatefunc_pos() for description of the parameters.
 877  * \p data is not used.
 878  *
 879  * Returns the \p x coordinate for each position in \p out->u.r.
 880  */
 881 static void
 882 evaluate_x(const gmx::SelMethodEvalContext & /*context*/,
 883            gmx_ana_pos_t *pos, gmx_ana_selvalue_t *out, void * /*data*/)
 884 {
 885     out->nr = pos->count();
 886     evaluate_coord(out->u.r, pos, XX);
 887 }
 888
 889 /*!
 890  * See sel_updatefunc() for description of the parameters.
 891  * \p data is not used.
 892  *
 893  * Returns the \p y coordinate for each position in \p out->u.r.
 894  */
 895 static void
 896 evaluate_y(const gmx::SelMethodEvalContext & /*context*/,
 897            gmx_ana_pos_t *pos, gmx_ana_selvalue_t *out, void * /*data*/)
 898 {
 899     out->nr = pos->count();
 900     evaluate_coord(out->u.r, pos, YY);
 901 }
 902
 903 /*!
 904  * See sel_updatefunc() for description of the parameters.
 905  * \p data is not used.
 906  *
 907  * Returns the \p z coordinate for each position in \p out->u.r.
 908  */
 909 static void
 910 evaluate_z(const gmx::SelMethodEvalContext & /*context*/,
 911            gmx_ana_pos_t *pos, gmx_ana_selvalue_t *out, void * /*data*/)
 912 {
 913     out->nr = pos->count();
 914     evaluate_coord(out->u.r, pos, ZZ);
 915 }