src/gromacs/selection/sm_simple.cpp

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 2009,2010,2011,2012,2013,2014,2015,2016, by the GROMACS development team, led by
   5  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
   6  * and including many others, as listed in the AUTHORS file in the
   7  * top-level source directory and at http://www.gromacs.org.
   8  *
   9  * GROMACS is free software; you can redistribute it and/or
  10  * modify it under the terms of the GNU Lesser General Public License
  11  * as published by the Free Software Foundation; either version 2.1
  12  * of the License, or (at your option) any later version.
  13  *
  14  * GROMACS is distributed in the hope that it will be useful,
  15  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  16  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  17  * Lesser General Public License for more details.
  18  *
  19  * You should have received a copy of the GNU Lesser General Public
  20  * License along with GROMACS; if not, see
  21  * http://www.gnu.org/licenses, or write to the Free Software Foundation,
  22  * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
  23  *
  24  * If you want to redistribute modifications to GROMACS, please
  25  * consider that scientific software is very special. Version
  26  * control is crucial - bugs must be traceable. We will be happy to
  27  * consider code for inclusion in the official distribution, but
  28  * derived work must not be called official GROMACS. Details are found
  29  * in the README & COPYING files - if they are missing, get the
  30  * official version at http://www.gromacs.org.
  31  *
  32  * To help us fund GROMACS development, we humbly ask that you cite
  33  * the research papers on the package. Check out http://www.gromacs.org.
  34  */
  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/topology.h"
  48 #include "gromacs/utility/arraysize.h"
  49 #include "gromacs/utility/exceptions.h"
  50
  51 #include "selmethod.h"
  52
  53 /** Evaluates the \p all selection keyword. */
  54 static void
  55 evaluate_all(t_topology *top, t_trxframe *fr, t_pbc *pbc,
  56              gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data);
  57 /** Evaluates the \p none selection keyword. */
  58 static void
  59 evaluate_none(t_topology *top, t_trxframe *fr, t_pbc *pbc,
  60               gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data);
  61 /** Evaluates the \p atomnr selection keyword. */
  62 static void
  63 evaluate_atomnr(t_topology *top, t_trxframe *fr, t_pbc *pbc,
  64                 gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data);
  65 /** Evaluates the \p resnr selection keyword. */
  66 static void
  67 evaluate_resnr(t_topology *top, t_trxframe *fr, t_pbc *pbc,
  68                gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data);
  69 /** Evaluates the \p resindex selection keyword. */
  70 static void
  71 evaluate_resindex(t_topology *top, t_trxframe *fr, t_pbc *pbc,
  72                   gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data);
  73 /*! \brief
  74  * Checks whether molecule information is present in the topology.
  75  *
  76  * \param[in] top  Topology structure.
  77  * \param     npar Not used.
  78  * \param     param Not used.
  79  * \param     data Not used.
  80  * \returns   0 if molecule info is present in the topology, -1 otherwise.
  81  *
  82  * If molecule information is not found, also prints an error message.
  83  */
  84 static void
  85 check_molecules(t_topology *top, int npar, gmx_ana_selparam_t *param, void *data);
  86 /** Evaluates the \p molindex selection keyword. */
  87 static void
  88 evaluate_molindex(t_topology *top, t_trxframe *fr, t_pbc *pbc,
  89                   gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data);
  90 /** Evaluates the \p atomname selection keyword. */
  91 static void
  92 evaluate_atomname(t_topology *top, t_trxframe *fr, t_pbc *pbc,
  93                   gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data);
  94 /** Evaluates the \p pdbatomname selection keyword. */
  95 static void
  96 evaluate_pdbatomname(t_topology *top, t_trxframe *fr, t_pbc *pbc,
  97                      gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data);
  98 /*! \brief
  99  * Checks whether atom types are present in the topology.
 100  *
 101  * \param[in] top  Topology structure.
 102  * \param     npar Not used.
 103  * \param     param Not used.
 104  * \param     data Not used.
 105  * \returns   0 if atom types are present in the topology, -1 otherwise.
 106  *
 107  * If the atom types are not found, also prints an error message.
 108  */
 109 static void
 110 check_atomtype(t_topology *top, int npar, gmx_ana_selparam_t *param, void *data);
 111 /** Evaluates the \p atomtype selection keyword. */
 112 static void
 113 evaluate_atomtype(t_topology *top, t_trxframe *fr, t_pbc *pbc,
 114                   gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data);
 115 /** Evaluates the \p insertcode selection keyword. */
 116 static void
 117 evaluate_insertcode(t_topology *top, t_trxframe *fr, t_pbc *pbc,
 118                     gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data);
 119 /** Evaluates the \p chain selection keyword. */
 120 static void
 121 evaluate_chain(t_topology *top, t_trxframe *fr, t_pbc *pbc,
 122                gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data);
 123 /** Evaluates the \p mass selection keyword. */
 124 static void
 125 evaluate_mass(t_topology *top, t_trxframe *fr, t_pbc *pbc,
 126               gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data);
 127 /** Evaluates the \p charge selection keyword. */
 128 static void
 129 evaluate_charge(t_topology *top, t_trxframe *fr, t_pbc *pbc,
 130                 gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data);
 131 /*! \brief
 132  * Checks whether PDB info is present in the topology.
 133  *
 134  * \param[in] top  Topology structure.
 135  * \param     npar Not used.
 136  * \param     param Not used.
 137  * \param     data Not used.
 138  * \returns   0 if PDB info is present in the topology, -1 otherwise.
 139  *
 140  * If PDB info is not found, also prints an error message.
 141  */
 142 static void
 143 check_pdbinfo(t_topology *top, int npar, gmx_ana_selparam_t *param, void *data);
 144 /** Evaluates the \p altloc selection keyword. */
 145 static void
 146 evaluate_altloc(t_topology *top, t_trxframe *fr, t_pbc *pbc,
 147                 gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data);
 148 /** Evaluates the \p occupancy selection keyword. */
 149 static void
 150 evaluate_occupancy(t_topology *top, t_trxframe *fr, t_pbc *pbc,
 151                    gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data);
 152 /** Evaluates the \p betafactor selection keyword. */
 153 static void
 154 evaluate_betafactor(t_topology *top, t_trxframe *fr, t_pbc *pbc,
 155                     gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data);
 156 /** Evaluates the \p resname selection keyword. */
 157 static void
 158 evaluate_resname(t_topology *top, t_trxframe *fr, t_pbc *pbc,
 159                  gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data);
 160
 161 /** Evaluates the \p x selection keyword. */
 162 static void
 163 evaluate_x(t_topology *top, t_trxframe *fr, t_pbc *pbc,
 164            gmx_ana_pos_t *pos, gmx_ana_selvalue_t *out, void *data);
 165 /** Evaluates the \p y selection keyword. */
 166 static void
 167 evaluate_y(t_topology *top, t_trxframe *fr, t_pbc *pbc,
 168            gmx_ana_pos_t *pos, gmx_ana_selvalue_t *out, void *data);
 169 /** Evaluates the \p z selection keyword. */
 170 static void
 171 evaluate_z(t_topology *top, t_trxframe *fr, t_pbc *pbc,
 172            gmx_ana_pos_t *pos, gmx_ana_selvalue_t *out, void *data);
 173
 174 //! Help title for atom name selection keywords.
 175 static const char        helptitle_atomname[] = "Selecting atoms by name";
 176 //! Help text for atom name selection keywords.
 177 static const char *const help_atomname[] = {
 178     "::",
 179     "",
 180     "  name",
 181     "  pdbname",
 182     "  atomname",
 183     "  pdbatomname",
 184     "",
 185     "These keywords select atoms by name. [TT]name[tt] selects atoms using",
 186     "the GROMACS atom naming convention.",
 187     "For input formats other than PDB, the atom names are matched exactly",
 188     "as they appear in the input file. For PDB files, 4 character atom names",
 189     "that start with a digit are matched after moving the digit to the end",
 190     "(e.g., to match 3HG2 from a PDB file, use [TT]name HG23[tt]).",
 191     "[TT]pdbname[tt] can only be used with a PDB input file, and selects",
 192     "atoms based on the exact name given in the input file, without the",
 193     "transformation described above.[PAR]",
 194
 195     "[TT]atomname[tt] and [TT]pdbatomname[tt] are synonyms for the above two",
 196     "keywords."
 197 };
 198
 199 /** Selection method data for \p all selection keyword. */
 200 gmx_ana_selmethod_t sm_all = {
 201     "all", GROUP_VALUE, 0,
 202     0, NULL,
 203     NULL,
 204     NULL,
 205     NULL,
 206     NULL,
 207     NULL,
 208     NULL,
 209     &evaluate_all,
 210     NULL,
 211 };
 212
 213 /** Selection method data for \p none selection keyword. */
 214 gmx_ana_selmethod_t sm_none = {
 215     "none", GROUP_VALUE, 0,
 216     0, NULL,
 217     NULL,
 218     NULL,
 219     NULL,
 220     NULL,
 221     NULL,
 222     NULL,
 223     &evaluate_none,
 224     NULL,
 225 };
 226
 227 /** Selection method data for \p atomnr selection keyword. */
 228 gmx_ana_selmethod_t sm_atomnr = {
 229     "atomnr", INT_VALUE, 0,
 230     0, NULL,
 231     NULL,
 232     NULL,
 233     NULL,
 234     NULL,
 235     NULL,
 236     NULL,
 237     &evaluate_atomnr,
 238     NULL,
 239 };
 240
 241 /** Selection method data for \p resnr selection keyword. */
 242 gmx_ana_selmethod_t sm_resnr = {
 243     "resnr", INT_VALUE, SMETH_REQTOP,
 244     0, NULL,
 245     NULL,
 246     NULL,
 247     NULL,
 248     NULL,
 249     NULL,
 250     NULL,
 251     &evaluate_resnr,
 252     NULL,
 253 };
 254
 255 /** Selection method data for \p resindex selection keyword. */
 256 gmx_ana_selmethod_t sm_resindex = {
 257     "resindex", INT_VALUE, SMETH_REQTOP,
 258     0, NULL,
 259     NULL,
 260     NULL,
 261     NULL,
 262     NULL,
 263     NULL,
 264     NULL,
 265     &evaluate_resindex,
 266     NULL,
 267 };
 268
 269 /** Selection method data for \p molindex selection keyword. */
 270 gmx_ana_selmethod_t sm_molindex = {
 271     "molindex", INT_VALUE, SMETH_REQTOP,
 272     0, NULL,
 273     NULL,
 274     NULL,
 275     &check_molecules,
 276     NULL,
 277     NULL,
 278     NULL,
 279     &evaluate_molindex,
 280     NULL,
 281 };
 282
 283 /** Selection method data for \p atomname selection keyword. */
 284 gmx_ana_selmethod_t sm_atomname = {
 285     "atomname", STR_VALUE, SMETH_REQTOP,
 286     0, NULL,
 287     NULL,
 288     NULL,
 289     NULL,
 290     NULL,
 291     NULL,
 292     NULL,
 293     &evaluate_atomname,
 294     NULL,
 295     {NULL, helptitle_atomname, asize(help_atomname), help_atomname}
 296 };
 297
 298 /** Selection method data for \p pdbatomname selection keyword. */
 299 gmx_ana_selmethod_t sm_pdbatomname = {
 300     "pdbatomname", STR_VALUE, SMETH_REQTOP,
 301     0, NULL,
 302     NULL,
 303     NULL,
 304     &check_pdbinfo,
 305     NULL,
 306     NULL,
 307     NULL,
 308     &evaluate_pdbatomname,
 309     NULL,
 310     {NULL, helptitle_atomname, asize(help_atomname), help_atomname}
 311 };
 312
 313 /** Selection method data for \p atomtype selection keyword. */
 314 gmx_ana_selmethod_t sm_atomtype = {
 315     "atomtype", STR_VALUE, SMETH_REQTOP,
 316     0, NULL,
 317     NULL,
 318     NULL,
 319     &check_atomtype,
 320     NULL,
 321     NULL,
 322     NULL,
 323     &evaluate_atomtype,
 324     NULL,
 325 };
 326
 327 /** Selection method data for \p resname selection keyword. */
 328 gmx_ana_selmethod_t sm_resname = {
 329     "resname", STR_VALUE, SMETH_REQTOP,
 330     0, NULL,
 331     NULL,
 332     NULL,
 333     NULL,
 334     NULL,
 335     NULL,
 336     NULL,
 337     &evaluate_resname,
 338     NULL,
 339 };
 340
 341 /** Selection method data for \p chain selection keyword. */
 342 gmx_ana_selmethod_t sm_insertcode = {
 343     "insertcode", STR_VALUE, SMETH_REQTOP | SMETH_CHARVAL,
 344     0, NULL,
 345     NULL,
 346     NULL,
 347     NULL,
 348     NULL,
 349     NULL,
 350     NULL,
 351     &evaluate_insertcode,
 352     NULL,
 353 };
 354
 355 /** Selection method data for \p chain selection keyword. */
 356 gmx_ana_selmethod_t sm_chain = {
 357     "chain", STR_VALUE, SMETH_REQTOP | SMETH_CHARVAL,
 358     0, NULL,
 359     NULL,
 360     NULL,
 361     NULL,
 362     NULL,
 363     NULL,
 364     NULL,
 365     &evaluate_chain,
 366     NULL,
 367 };
 368
 369 /** Selection method data for \p mass selection keyword. */
 370 gmx_ana_selmethod_t sm_mass = {
 371     "mass", REAL_VALUE, SMETH_REQTOP,
 372     0, NULL,
 373     NULL,
 374     NULL,
 375     NULL,
 376     NULL,
 377     NULL,
 378     NULL,
 379     &evaluate_mass,
 380     NULL,
 381 };
 382
 383 /** Selection method data for \p charge selection keyword. */
 384 gmx_ana_selmethod_t sm_charge = {
 385     "charge", REAL_VALUE, SMETH_REQTOP,
 386     0, NULL,
 387     NULL,
 388     NULL,
 389     NULL,
 390     NULL,
 391     NULL,
 392     NULL,
 393     &evaluate_charge,
 394     NULL,
 395 };
 396
 397 /** Selection method data for \p chain selection keyword. */
 398 gmx_ana_selmethod_t sm_altloc = {
 399     "altloc", STR_VALUE, SMETH_REQTOP | SMETH_CHARVAL,
 400     0, NULL,
 401     NULL,
 402     NULL,
 403     &check_pdbinfo,
 404     NULL,
 405     NULL,
 406     NULL,
 407     &evaluate_altloc,
 408     NULL,
 409 };
 410
 411 /** Selection method data for \p occupancy selection keyword. */
 412 gmx_ana_selmethod_t sm_occupancy = {
 413     "occupancy", REAL_VALUE, SMETH_REQTOP,
 414     0, NULL,
 415     NULL,
 416     NULL,
 417     &check_pdbinfo,
 418     NULL,
 419     NULL,
 420     NULL,
 421     &evaluate_occupancy,
 422     NULL,
 423 };
 424
 425 /** Selection method data for \p betafactor selection keyword. */
 426 gmx_ana_selmethod_t sm_betafactor = {
 427     "betafactor", REAL_VALUE, SMETH_REQTOP,
 428     0, NULL,
 429     NULL,
 430     NULL,
 431     &check_pdbinfo,
 432     NULL,
 433     NULL,
 434     NULL,
 435     &evaluate_betafactor,
 436     NULL,
 437 };
 438
 439 /** Selection method data for \p x selection keyword. */
 440 gmx_ana_selmethod_t sm_x = {
 441     "x", REAL_VALUE, SMETH_DYNAMIC,
 442     0, NULL,
 443     NULL,
 444     NULL,
 445     NULL,
 446     NULL,
 447     NULL,
 448     NULL,
 449     NULL,
 450     &evaluate_x,
 451 };
 452
 453 /** Selection method data for \p y selection keyword. */
 454 gmx_ana_selmethod_t sm_y = {
 455     "y", REAL_VALUE, SMETH_DYNAMIC,
 456     0, NULL,
 457     NULL,
 458     NULL,
 459     NULL,
 460     NULL,
 461     NULL,
 462     NULL,
 463     NULL,
 464     &evaluate_y,
 465 };
 466
 467 /** Selection method data for \p z selection keyword. */
 468 gmx_ana_selmethod_t sm_z = {
 469     "z", REAL_VALUE, SMETH_DYNAMIC,
 470     0, NULL,
 471     NULL,
 472     NULL,
 473     NULL,
 474     NULL,
 475     NULL,
 476     NULL,
 477     NULL,
 478     &evaluate_z,
 479 };
 480
 481 /*!
 482  * See sel_updatefunc() for description of the parameters.
 483  * \p data is not used.
 484  *
 485  * Copies \p g to \p out->u.g.
 486  */
 487 static void
 488 evaluate_all(t_topology * /* top */, t_trxframe * /* fr */, t_pbc * /* pbc */,
 489              gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void * /* data */)
 490 {
 491     gmx_ana_index_copy(out->u.g, g, false);
 492 }
 493
 494 /*!
 495  * See sel_updatefunc() for description of the parameters.
 496  * \p data is not used.
 497  *
 498  * Returns an empty \p out->u.g.
 499  */
 500 static void
 501 evaluate_none(t_topology * /* top */, t_trxframe * /* fr */, t_pbc * /* pbc */,
 502               gmx_ana_index_t * /* g */, gmx_ana_selvalue_t *out, void * /* data */)
 503 {
 504     out->u.g->isize = 0;
 505 }
 506
 507 /*!
 508  * See sel_updatefunc() for description of the parameters.
 509  * \p data is not used.
 510  *
 511  * Returns the indices for each atom in \p out->u.i.
 512  */
 513 static void
 514 evaluate_atomnr(t_topology * /* top */, t_trxframe * /* fr */, t_pbc * /* pbc */,
 515                 gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void * /* data */)
 516 {
 517     int  i;
 518
 519     out->nr = g->isize;
 520     for (i = 0; i < g->isize; ++i)
 521     {
 522         out->u.i[i] = g->index[i] + 1;
 523     }
 524 }
 525
 526 /*!
 527  * See sel_updatefunc() for description of the parameters.
 528  * \p data is not used.
 529  *
 530  * Returns the residue numbers for each atom in \p out->u.i.
 531  */
 532 static void
 533 evaluate_resnr(t_topology *top, t_trxframe * /* fr */, t_pbc * /* pbc */,
 534                gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void * /* data */)
 535 {
 536     int  i;
 537     int  resind;
 538
 539     out->nr = g->isize;
 540     for (i = 0; i < g->isize; ++i)
 541     {
 542         resind      = top->atoms.atom[g->index[i]].resind;
 543         out->u.i[i] = top->atoms.resinfo[resind].nr;
 544     }
 545 }
 546
 547 /*!
 548  * See sel_updatefunc() for description of the parameters.
 549  * \p data is not used.
 550  *
 551  * Returns the residue indices for each atom in \p out->u.i.
 552  */
 553 static void
 554 evaluate_resindex(t_topology *top, t_trxframe * /* fr */, t_pbc * /* pbc */,
 555                   gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void * /* data */)
 556 {
 557     int  i;
 558
 559     out->nr = g->isize;
 560     for (i = 0; i < g->isize; ++i)
 561     {
 562         out->u.i[i] = top->atoms.atom[g->index[i]].resind + 1;
 563     }
 564 }
 565
 566 static void
 567 check_molecules(t_topology *top, int /* npar */, gmx_ana_selparam_t * /* param */, void * /* data */)
 568 {
 569     bool bOk;
 570
 571     bOk = (top != NULL && top->mols.nr > 0);
 572     if (!bOk)
 573     {
 574         GMX_THROW(gmx::InconsistentInputError("Molecule information not available in topology"));
 575     }
 576 }
 577
 578 /*!
 579  * See sel_updatefunc() for description of the parameters.
 580  * \p data is not used.
 581  *
 582  * Returns the molecule indices for each atom in \p out->u.i.
 583  */
 584 static void
 585 evaluate_molindex(t_topology *top, t_trxframe * /* fr */, t_pbc * /* pbc */,
 586                   gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void * /* data */)
 587 {
 588     int  i, j;
 589
 590     out->nr = g->isize;
 591     for (i = j = 0; i < g->isize; ++i)
 592     {
 593         while (top->mols.index[j + 1] <= g->index[i])
 594         {
 595             ++j;
 596         }
 597         out->u.i[i] = j + 1;
 598     }
 599 }
 600
 601 /*!
 602  * See sel_updatefunc() for description of the parameters.
 603  * \p data is not used.
 604  *
 605  * Returns the atom name for each atom in \p out->u.s.
 606  */
 607 static void
 608 evaluate_atomname(t_topology *top, t_trxframe * /* fr */, t_pbc * /* pbc */,
 609                   gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void * /* data */)
 610 {
 611     int  i;
 612
 613     out->nr = g->isize;
 614     for (i = 0; i < g->isize; ++i)
 615     {
 616         out->u.s[i] = *top->atoms.atomname[g->index[i]];
 617     }
 618 }
 619
 620 /*!
 621  * See sel_updatefunc() for description of the parameters.
 622  * \p data is not used.
 623  *
 624  * Returns the PDB atom name for each atom in \p out->u.s.
 625  */
 626 static void
 627 evaluate_pdbatomname(t_topology *top, t_trxframe * /* fr */, t_pbc * /* pbc */,
 628                      gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void * /* data */)
 629 {
 630     int  i;
 631
 632     out->nr = g->isize;
 633     for (i = 0; i < g->isize; ++i)
 634     {
 635         char *s = top->atoms.pdbinfo[g->index[i]].atomnm;
 636         while (std::isspace(*s))
 637         {
 638             ++s;
 639         }
 640         out->u.s[i] = s;
 641     }
 642 }
 643
 644 static void
 645 check_atomtype(t_topology *top, int /* npar */, gmx_ana_selparam_t * /* param */, void * /* data */)
 646 {
 647     bool bOk;
 648
 649     bOk = (top != NULL && (top->atoms.haveType));
 650     if (!bOk)
 651     {
 652         GMX_THROW(gmx::InconsistentInputError("Atom types not available in topology"));
 653     }
 654 }
 655
 656 /*!
 657  * See sel_updatefunc() for description of the parameters.
 658  * \p data is not used.
 659  *
 660  * Returns the atom type for each atom in \p out->u.s.
 661  * Segfaults if atom types are not found in the topology.
 662  */
 663 static void
 664 evaluate_atomtype(t_topology *top, t_trxframe * /* fr */, t_pbc * /* pbc */,
 665                   gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void * /* data */)
 666 {
 667     int  i;
 668
 669     out->nr = g->isize;
 670     for (i = 0; i < g->isize; ++i)
 671     {
 672         out->u.s[i] = *top->atoms.atomtype[g->index[i]];
 673     }
 674 }
 675
 676 /*!
 677  * See sel_updatefunc() for description of the parameters.
 678  * \p data is not used.
 679  *
 680  * Returns the residue name for each atom in \p out->u.s.
 681  */
 682 static void
 683 evaluate_resname(t_topology *top, t_trxframe * /* fr */, t_pbc * /* pbc */,
 684                  gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void * /* data */)
 685 {
 686     int  i;
 687     int  resind;
 688
 689     out->nr = g->isize;
 690     for (i = 0; i < g->isize; ++i)
 691     {
 692         resind      = top->atoms.atom[g->index[i]].resind;
 693         out->u.s[i] = *top->atoms.resinfo[resind].name;
 694     }
 695 }
 696
 697 /*!
 698  * See sel_updatefunc() for description of the parameters.
 699  * \p data is not used.
 700  *
 701  * Returns the insertion code for each atom in \p out->u.s.
 702  */
 703 static void
 704 evaluate_insertcode(t_topology *top, t_trxframe * /* fr */, t_pbc * /* pbc */,
 705                     gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void * /* data */)
 706 {
 707     int  i;
 708     int  resind;
 709
 710     out->nr = g->isize;
 711     for (i = 0; i < g->isize; ++i)
 712     {
 713         resind         = top->atoms.atom[g->index[i]].resind;
 714         out->u.s[i][0] = top->atoms.resinfo[resind].ic;
 715     }
 716 }
 717
 718 /*!
 719  * See sel_updatefunc() for description of the parameters.
 720  * \p data is not used.
 721  *
 722  * Returns the chain for each atom in \p out->u.s.
 723  */
 724 static void
 725 evaluate_chain(t_topology *top, t_trxframe * /* fr */, t_pbc * /* pbc */,
 726                gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void * /* data */)
 727 {
 728     int  i;
 729     int  resind;
 730
 731     out->nr = g->isize;
 732     for (i = 0; i < g->isize; ++i)
 733     {
 734         resind         = top->atoms.atom[g->index[i]].resind;
 735         out->u.s[i][0] = top->atoms.resinfo[resind].chainid;
 736     }
 737 }
 738
 739 /*!
 740  * See sel_updatefunc() for description of the parameters.
 741  * \p data is not used.
 742  *
 743  * Returns the mass for each atom in \p out->u.r.
 744  */
 745 static void
 746 evaluate_mass(t_topology *top, t_trxframe * /* fr */, t_pbc * /* pbc */,
 747               gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void * /* data */)
 748 {
 749     int  i;
 750
 751     out->nr = g->isize;
 752     for (i = 0; i < g->isize; ++i)
 753     {
 754         out->u.r[i] = top->atoms.atom[g->index[i]].m;
 755     }
 756 }
 757
 758 /*!
 759  * See sel_updatefunc() for description of the parameters.
 760  * \p data is not used.
 761  *
 762  * Returns the charge for each atom in \p out->u.r.
 763  */
 764 static void
 765 evaluate_charge(t_topology *top, t_trxframe * /* fr */, t_pbc * /* pbc */,
 766                 gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void * /* data */)
 767 {
 768     int  i;
 769
 770     out->nr = g->isize;
 771     for (i = 0; i < g->isize; ++i)
 772     {
 773         out->u.r[i] = top->atoms.atom[g->index[i]].q;
 774     }
 775 }
 776
 777 static void
 778 check_pdbinfo(t_topology *top, int /* npar */, gmx_ana_selparam_t * /* param */, void * /* data */)
 779 {
 780     bool bOk;
 781
 782     bOk = (top != NULL && top->atoms.havePdbInfo);
 783     if (!bOk)
 784     {
 785         GMX_THROW(gmx::InconsistentInputError("PDB info not available in topology"));
 786     }
 787 }
 788
 789 /*!
 790  * See sel_updatefunc() for description of the parameters.
 791  * \p data is not used.
 792  *
 793  * Returns the alternate location identifier for each atom in \p out->u.s.
 794  */
 795 static void
 796 evaluate_altloc(t_topology *top, t_trxframe * /* fr */, t_pbc * /* pbc */,
 797                 gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void * /* data */)
 798 {
 799     int  i;
 800
 801     out->nr = g->isize;
 802     for (i = 0; i < g->isize; ++i)
 803     {
 804         out->u.s[i][0] = top->atoms.pdbinfo[g->index[i]].altloc;
 805     }
 806 }
 807
 808 /*!
 809  * See sel_updatefunc() for description of the parameters.
 810  * \p data is not used.
 811  *
 812  * Returns the occupancy numbers for each atom in \p out->u.r.
 813  * Segfaults if PDB info is not found in the topology.
 814  */
 815 static void
 816 evaluate_occupancy(t_topology *top, t_trxframe * /* fr */, t_pbc * /* pbc */,
 817                    gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void * /* data */)
 818 {
 819     int  i;
 820
 821     out->nr = g->isize;
 822     for (i = 0; i < g->isize; ++i)
 823     {
 824         out->u.r[i] = top->atoms.pdbinfo[g->index[i]].occup;
 825     }
 826 }
 827
 828 /*!
 829  * See sel_updatefunc() for description of the parameters.
 830  * \p data is not used.
 831  *
 832  * Returns the B-factors for each atom in \p out->u.r.
 833  * Segfaults if PDB info is not found in the topology.
 834  */
 835 static void
 836 evaluate_betafactor(t_topology *top, t_trxframe * /* fr */, t_pbc * /* pbc */,
 837                     gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void * /* data */)
 838 {
 839     int  i;
 840
 841     out->nr = g->isize;
 842     for (i = 0; i < g->isize; ++i)
 843     {
 844         out->u.r[i] = top->atoms.pdbinfo[g->index[i]].bfac;
 845     }
 846 }
 847
 848 /*! \brief
 849  * Internal utility function for position keyword evaluation.
 850  *
 851  * \param[out] out  Output array.
 852  * \param[in]  pos  Position data to use instead of atomic coordinates.
 853  * \param[in]  d    Coordinate index to evaluate (\p XX, \p YY or \p ZZ).
 854  *
 855  * This function is used internally by evaluate_x(), evaluate_y() and
 856  * evaluate_z() to do the actual evaluation.
 857  */
 858 static void
 859 evaluate_coord(real out[], gmx_ana_pos_t *pos, int d)
 860 {
 861     for (int i = 0; i < pos->count(); ++i)
 862     {
 863         out[i] = pos->x[i][d];
 864     }
 865     // TODO: Make this more efficient by directly extracting the coordinates
 866     // from the frame coordinates for atomic positions instead of going through
 867     // a position calculation.
 868 }
 869
 870 /*!
 871  * See sel_updatefunc_pos() for description of the parameters.
 872  * \p data is not used.
 873  *
 874  * Returns the \p x coordinate for each position in \p out->u.r.
 875  */
 876 static void
 877 evaluate_x(t_topology * /*top*/, t_trxframe * /*fr*/, t_pbc * /*pbc*/,
 878            gmx_ana_pos_t *pos, gmx_ana_selvalue_t *out, void * /*data*/)
 879 {
 880     out->nr = pos->count();
 881     evaluate_coord(out->u.r, pos, XX);
 882 }
 883
 884 /*!
 885  * See sel_updatefunc() for description of the parameters.
 886  * \p data is not used.
 887  *
 888  * Returns the \p y coordinate for each position in \p out->u.r.
 889  */
 890 static void
 891 evaluate_y(t_topology * /*top*/, t_trxframe * /*fr*/, t_pbc * /*pbc*/,
 892            gmx_ana_pos_t *pos, gmx_ana_selvalue_t *out, void * /*data*/)
 893 {
 894     out->nr = pos->count();
 895     evaluate_coord(out->u.r, pos, YY);
 896 }
 897
 898 /*!
 899  * See sel_updatefunc() for description of the parameters.
 900  * \p data is not used.
 901  *
 902  * Returns the \p z coordinate for each position in \p out->u.r.
 903  */
 904 static void
 905 evaluate_z(t_topology * /*top*/, t_trxframe * /*fr*/, t_pbc * /*pbc*/,
 906            gmx_ana_pos_t *pos, gmx_ana_selvalue_t *out, void * /*data*/)
 907 {
 908     out->nr = pos->count();
 909     evaluate_coord(out->u.r, pos, ZZ);
 910 }