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39 * Implements simple keyword selection methods.
41 * \author Teemu Murtola <teemu.murtola@gmail.com>
42 * \ingroup module_selection
48 #include "gromacs/topology/mtop_lookup.h"
49 #include "gromacs/topology/topology.h"
50 #include "gromacs/utility/arraysize.h"
51 #include "gromacs/utility/exceptions.h"
52 #include "gromacs/utility/gmxassert.h"
55 #include "selmethod.h"
56 #include "selmethod_impl.h"
58 /** Evaluates the \p all selection keyword. */
59 static void evaluate_all(const gmx::SelMethodEvalContext& context,
61 gmx_ana_selvalue_t* out,
63 /** Evaluates the \p none selection keyword. */
64 static void evaluate_none(const gmx::SelMethodEvalContext& context,
66 gmx_ana_selvalue_t* out,
68 /** Evaluates the \p atomnr selection keyword. */
69 static void evaluate_atomnr(const gmx::SelMethodEvalContext& context,
71 gmx_ana_selvalue_t* out,
73 /** Evaluates the \p resnr selection keyword. */
74 static void evaluate_resnr(const gmx::SelMethodEvalContext& context,
76 gmx_ana_selvalue_t* out,
78 /** Evaluates the \p resindex selection keyword. */
79 static void evaluate_resindex(const gmx::SelMethodEvalContext& context,
81 gmx_ana_selvalue_t* out,
84 * Checks whether molecule information is present in the topology.
86 * \param[in] top Topology structure.
87 * \param npar Not used.
88 * \param param Not used.
89 * \param data Not used.
90 * \returns 0 if molecule info is present in the topology, -1 otherwise.
92 * If molecule information is not found, also prints an error message.
94 static void check_molecules(const gmx_mtop_t* top, int npar, gmx_ana_selparam_t* param, void* data);
95 /** Evaluates the \p molindex selection keyword. */
96 static void evaluate_molindex(const gmx::SelMethodEvalContext& context,
98 gmx_ana_selvalue_t* out,
100 /** Evaluates the \p atomname selection keyword. */
101 static void evaluate_atomname(const gmx::SelMethodEvalContext& context,
103 gmx_ana_selvalue_t* out,
105 /** Evaluates the \p pdbatomname selection keyword. */
106 static void evaluate_pdbatomname(const gmx::SelMethodEvalContext& context,
108 gmx_ana_selvalue_t* out,
111 * Checks whether atom types are present in the topology.
113 * \param[in] top Topology structure.
114 * \param npar Not used.
115 * \param param Not used.
116 * \param data Not used.
118 static void check_atomtype(const gmx_mtop_t* top, int npar, gmx_ana_selparam_t* param, void* data);
119 /** Evaluates the \p atomtype selection keyword. */
120 static void evaluate_atomtype(const gmx::SelMethodEvalContext& context,
122 gmx_ana_selvalue_t* out,
124 /** Evaluates the \p insertcode selection keyword. */
125 static void evaluate_insertcode(const gmx::SelMethodEvalContext& context,
127 gmx_ana_selvalue_t* out,
129 /** Evaluates the \p chain selection keyword. */
130 static void evaluate_chain(const gmx::SelMethodEvalContext& context,
132 gmx_ana_selvalue_t* out,
134 /** Evaluates the \p mass selection keyword. */
135 static void evaluate_mass(const gmx::SelMethodEvalContext& context,
137 gmx_ana_selvalue_t* out,
140 * Checks whether charges are present in the topology.
142 * \param[in] top Topology structure.
143 * \param npar Not used.
144 * \param param Not used.
145 * \param data Not used.
147 static void check_charge(const gmx_mtop_t* top, int npar, gmx_ana_selparam_t* param, void* data);
148 /** Evaluates the \p charge selection keyword. */
149 static void evaluate_charge(const gmx::SelMethodEvalContext& context,
151 gmx_ana_selvalue_t* out,
154 * Checks whether PDB info is present in the topology.
156 * \param[in] top Topology structure.
157 * \param npar Not used.
158 * \param param Not used.
159 * \param data Not used.
160 * \returns 0 if PDB info is present in the topology, -1 otherwise.
162 * If PDB info is not found, also prints an error message.
164 static void check_pdbinfo(const gmx_mtop_t* top, int npar, gmx_ana_selparam_t* param, void* data);
165 /** Evaluates the \p altloc selection keyword. */
166 static void evaluate_altloc(const gmx::SelMethodEvalContext& context,
168 gmx_ana_selvalue_t* out,
170 /** Evaluates the \p occupancy selection keyword. */
171 static void evaluate_occupancy(const gmx::SelMethodEvalContext& context,
173 gmx_ana_selvalue_t* out,
175 /** Evaluates the \p betafactor selection keyword. */
176 static void evaluate_betafactor(const gmx::SelMethodEvalContext& context,
178 gmx_ana_selvalue_t* out,
180 /** Evaluates the \p resname selection keyword. */
181 static void evaluate_resname(const gmx::SelMethodEvalContext& context,
183 gmx_ana_selvalue_t* out,
186 /** Evaluates the \p x selection keyword. */
187 static void evaluate_x(const gmx::SelMethodEvalContext& context,
189 gmx_ana_selvalue_t* out,
191 /** Evaluates the \p y selection keyword. */
192 static void evaluate_y(const gmx::SelMethodEvalContext& context,
194 gmx_ana_selvalue_t* out,
196 /** Evaluates the \p z selection keyword. */
197 static void evaluate_z(const gmx::SelMethodEvalContext& context,
199 gmx_ana_selvalue_t* out,
202 //! Help title for atom name selection keywords.
203 static const char helptitle_atomname[] = "Selecting atoms by name";
204 //! Help text for atom name selection keywords.
205 static const char* const help_atomname[] = {
213 "These keywords select atoms by name. [TT]name[tt] selects atoms using",
214 "the GROMACS atom naming convention.",
215 "For input formats other than PDB, the atom names are matched exactly",
216 "as they appear in the input file. For PDB files, 4 character atom names",
217 "that start with a digit are matched after moving the digit to the end",
218 "(e.g., to match 3HG2 from a PDB file, use [TT]name HG23[tt]).",
219 "[TT]pdbname[tt] can only be used with a PDB input file, and selects",
220 "atoms based on the exact name given in the input file, without the",
221 "transformation described above.[PAR]",
223 "[TT]atomname[tt] and [TT]pdbatomname[tt] are synonyms for the above two",
227 //! Help title for residue index selection keywords.
228 static const char helptitle_resindex[] = "Selecting atoms by residue number";
229 //! Help text for residue index selection keywords.
230 static const char* const help_resindex[] = {
238 "[TT]resnr[tt] selects atoms using the residue numbering in the input",
239 "file. [TT]resid[tt] is synonym for this keyword for VMD compatibility.",
241 "[TT]resindex N[tt] selects the [TT]N[tt] th residue starting from the",
242 "beginning of the input file. This is useful for uniquely identifying",
243 "residues if there are duplicate numbers in the input file (e.g., in",
245 "[TT]residue[tt] is a synonym for [TT]resindex[tt]. This allows",
246 "[TT]same residue as[tt] to work as expected."
249 /** Selection method data for \p all selection keyword. */
250 gmx_ana_selmethod_t sm_all = {
251 "all", GROUP_VALUE, 0, 0, nullptr, nullptr, nullptr,
252 nullptr, nullptr, nullptr, nullptr, &evaluate_all, nullptr,
255 /** Selection method data for \p none selection keyword. */
256 gmx_ana_selmethod_t sm_none = {
257 "none", GROUP_VALUE, 0, 0, nullptr, nullptr, nullptr,
258 nullptr, nullptr, nullptr, nullptr, &evaluate_none, nullptr,
261 /** Selection method data for \p atomnr selection keyword. */
262 gmx_ana_selmethod_t sm_atomnr = {
263 "atomnr", INT_VALUE, 0, 0, nullptr, nullptr, nullptr,
264 nullptr, nullptr, nullptr, nullptr, &evaluate_atomnr, nullptr,
267 /** Selection method data for \p resnr selection keyword. */
268 gmx_ana_selmethod_t sm_resnr = {
274 nullptr, &evaluate_resnr,
275 nullptr, { nullptr, helptitle_resindex, asize(help_resindex), help_resindex }
278 /** Selection method data for \p resindex selection keyword. */
279 gmx_ana_selmethod_t sm_resindex = {
280 "resindex", INT_VALUE,
285 nullptr, &evaluate_resindex,
286 nullptr, { nullptr, helptitle_resindex, asize(help_resindex), help_resindex }
289 /** Selection method data for \p molindex selection keyword. */
290 gmx_ana_selmethod_t sm_molindex = {
291 "molindex", INT_VALUE, SMETH_REQTOP, 0, nullptr, nullptr,
292 nullptr, &check_molecules, nullptr, nullptr, nullptr, &evaluate_molindex,
296 /** Selection method data for \p atomname selection keyword. */
297 gmx_ana_selmethod_t sm_atomname = {
298 "atomname", STR_VALUE,
303 nullptr, &evaluate_atomname,
304 nullptr, { nullptr, helptitle_atomname, asize(help_atomname), help_atomname }
307 /** Selection method data for \p pdbatomname selection keyword. */
308 gmx_ana_selmethod_t sm_pdbatomname = {
309 "pdbatomname", STR_VALUE,
312 nullptr, &check_pdbinfo,
314 nullptr, &evaluate_pdbatomname,
315 nullptr, { nullptr, helptitle_atomname, asize(help_atomname), help_atomname }
318 /** Selection method data for \p atomtype selection keyword. */
319 gmx_ana_selmethod_t sm_atomtype = {
320 "atomtype", STR_VALUE, SMETH_REQTOP, 0, nullptr, nullptr,
321 nullptr, &check_atomtype, nullptr, nullptr, nullptr, &evaluate_atomtype,
325 /** Selection method data for \p resname selection keyword. */
326 gmx_ana_selmethod_t sm_resname = {
327 "resname", STR_VALUE, SMETH_REQTOP, 0, nullptr, nullptr, nullptr,
328 nullptr, nullptr, nullptr, nullptr, &evaluate_resname, nullptr,
331 /** Selection method data for \p chain selection keyword. */
332 gmx_ana_selmethod_t sm_insertcode = {
335 SMETH_REQTOP | SMETH_CHARVAL,
344 &evaluate_insertcode,
348 /** Selection method data for \p chain selection keyword. */
349 gmx_ana_selmethod_t sm_chain = {
350 "chain", STR_VALUE, SMETH_REQTOP | SMETH_CHARVAL,
352 nullptr, nullptr, nullptr,
353 nullptr, nullptr, &evaluate_chain,
357 /** Selection method data for \p mass selection keyword. */
358 gmx_ana_selmethod_t sm_mass = {
359 "mass", REAL_VALUE, SMETH_REQMASS, 0, nullptr, nullptr, nullptr,
360 nullptr, nullptr, nullptr, nullptr, &evaluate_mass, nullptr,
363 /** Selection method data for \p charge selection keyword. */
364 gmx_ana_selmethod_t sm_charge = {
365 "charge", REAL_VALUE, SMETH_REQTOP, 0, nullptr, nullptr, nullptr,
366 &check_charge, nullptr, nullptr, nullptr, &evaluate_charge, nullptr,
369 /** Selection method data for \p chain selection keyword. */
370 gmx_ana_selmethod_t sm_altloc = {
371 "altloc", STR_VALUE, SMETH_REQTOP | SMETH_CHARVAL,
373 nullptr, &check_pdbinfo, nullptr,
374 nullptr, nullptr, &evaluate_altloc,
378 /** Selection method data for \p occupancy selection keyword. */
379 gmx_ana_selmethod_t sm_occupancy = {
380 "occupancy", REAL_VALUE, SMETH_REQTOP, 0, nullptr, nullptr,
381 nullptr, &check_pdbinfo, nullptr, nullptr, nullptr, &evaluate_occupancy,
385 /** Selection method data for \p betafactor selection keyword. */
386 gmx_ana_selmethod_t sm_betafactor = {
387 "betafactor", REAL_VALUE, SMETH_REQTOP, 0, nullptr, nullptr,
388 nullptr, &check_pdbinfo, nullptr, nullptr, nullptr, &evaluate_betafactor,
392 /** Selection method data for \p x selection keyword. */
393 gmx_ana_selmethod_t sm_x = {
394 "x", REAL_VALUE, SMETH_DYNAMIC, 0, nullptr, nullptr, nullptr,
395 nullptr, nullptr, nullptr, nullptr, nullptr, &evaluate_x,
398 /** Selection method data for \p y selection keyword. */
399 gmx_ana_selmethod_t sm_y = {
400 "y", REAL_VALUE, SMETH_DYNAMIC, 0, nullptr, nullptr, nullptr,
401 nullptr, nullptr, nullptr, nullptr, nullptr, &evaluate_y,
404 /** Selection method data for \p z selection keyword. */
405 gmx_ana_selmethod_t sm_z = {
406 "z", REAL_VALUE, SMETH_DYNAMIC, 0, nullptr, nullptr, nullptr,
407 nullptr, nullptr, nullptr, nullptr, nullptr, &evaluate_z,
411 * See sel_updatefunc() for description of the parameters.
412 * \p data is not used.
414 * Copies \p g to \p out->u.g.
416 static void evaluate_all(const gmx::SelMethodEvalContext& /*context*/,
418 gmx_ana_selvalue_t* out,
421 gmx_ana_index_copy(out->u.g, g, false);
425 * See sel_updatefunc() for description of the parameters.
426 * \p data is not used.
428 * Returns an empty \p out->u.g.
430 static void evaluate_none(const gmx::SelMethodEvalContext& /*context*/,
431 gmx_ana_index_t* /* g */,
432 gmx_ana_selvalue_t* out,
439 * See sel_updatefunc() for description of the parameters.
440 * \p data is not used.
442 * Returns the indices for each atom in \p out->u.i.
444 static void evaluate_atomnr(const gmx::SelMethodEvalContext& /*context*/,
446 gmx_ana_selvalue_t* out,
452 for (i = 0; i < g->isize; ++i)
454 out->u.i[i] = g->index[i] + 1;
459 * See sel_updatefunc() for description of the parameters.
460 * \p data is not used.
462 * Returns the residue numbers for each atom in \p out->u.i.
464 static void evaluate_resnr(const gmx::SelMethodEvalContext& context,
466 gmx_ana_selvalue_t* out,
471 for (int i = 0; i < g->isize; ++i)
473 mtopGetAtomAndResidueName(*context.top, g->index[i], &molb, nullptr, &out->u.i[i], nullptr, nullptr);
478 * See sel_updatefunc() for description of the parameters.
479 * \p data is not used.
481 * Returns the residue indices for each atom in \p out->u.i.
483 static void evaluate_resindex(const gmx::SelMethodEvalContext& context,
485 gmx_ana_selvalue_t* out,
490 for (int i = 0; i < g->isize; ++i)
493 mtopGetAtomAndResidueName(*context.top, g->index[i], &molb, nullptr, nullptr, nullptr, &resind);
494 out->u.i[i] = resind + 1;
498 static void check_molecules(const gmx_mtop_t* top, int /* npar */, gmx_ana_selparam_t* /* param */, void* /* data */)
502 bOk = (top != nullptr && top->haveMoleculeIndices);
505 GMX_THROW(gmx::InconsistentInputError("Molecule information not available in topology"));
510 * See sel_updatefunc() for description of the parameters.
511 * \p data is not used.
513 * Returns the molecule indices for each atom in \p out->u.i.
515 static void evaluate_molindex(const gmx::SelMethodEvalContext& context,
517 gmx_ana_selvalue_t* out,
522 for (int i = 0; i < g->isize; ++i)
524 out->u.i[i] = mtopGetMoleculeIndex(*context.top, g->index[i], &molb) + 1;
529 * See sel_updatefunc() for description of the parameters.
530 * \p data is not used.
532 * Returns the atom name for each atom in \p out->u.s.
534 static void evaluate_atomname(const gmx::SelMethodEvalContext& context,
536 gmx_ana_selvalue_t* out,
541 for (int i = 0; i < g->isize; ++i)
543 const char* atom_name;
544 mtopGetAtomAndResidueName(*context.top, g->index[i], &molb, &atom_name, nullptr, nullptr, nullptr);
545 out->u.s[i] = const_cast<char*>(atom_name);
550 * See sel_updatefunc() for description of the parameters.
551 * \p data is not used.
553 * Returns the PDB atom name for each atom in \p out->u.s.
555 static void evaluate_pdbatomname(const gmx::SelMethodEvalContext& context,
557 gmx_ana_selvalue_t* out,
562 for (int i = 0; i < g->isize; ++i)
564 const char* s = mtopGetAtomPdbInfo(*context.top, g->index[i], &molb).atomnm;
565 while (std::isspace(*s))
569 out->u.s[i] = const_cast<char*>(s);
573 static void check_atomtype(const gmx_mtop_t* top, int /* npar */, gmx_ana_selparam_t* /* param */, void* /* data */)
575 if (!gmx_mtop_has_atomtypes(top))
577 GMX_THROW(gmx::InconsistentInputError("Atom types not available in topology"));
582 * See sel_updatefunc() for description of the parameters.
583 * \p data is not used.
585 * Returns the atom type for each atom in \p out->u.s.
586 * Segfaults if atom types are not found in the topology.
588 static void evaluate_atomtype(const gmx::SelMethodEvalContext& context,
590 gmx_ana_selvalue_t* out,
595 for (int i = 0; i < g->isize; ++i)
597 int atomIndexInMolecule;
598 mtopGetMolblockIndex(*context.top, g->index[i], &molb, nullptr, &atomIndexInMolecule);
599 const gmx_moltype_t& moltype = context.top->moltype[context.top->molblock[molb].type];
600 out->u.s[i] = *moltype.atoms.atomtype[atomIndexInMolecule];
605 * See sel_updatefunc() for description of the parameters.
606 * \p data is not used.
608 * Returns the residue name for each atom in \p out->u.s.
610 static void evaluate_resname(const gmx::SelMethodEvalContext& context,
612 gmx_ana_selvalue_t* out,
617 for (int i = 0; i < g->isize; ++i)
619 out->u.s[i] = *mtopGetResidueInfo(*context.top, g->index[i], &molb).name;
624 * See sel_updatefunc() for description of the parameters.
625 * \p data is not used.
627 * Returns the insertion code for each atom in \p out->u.s.
629 static void evaluate_insertcode(const gmx::SelMethodEvalContext& context,
631 gmx_ana_selvalue_t* out,
636 for (int i = 0; i < g->isize; ++i)
638 out->u.s[i][0] = mtopGetResidueInfo(*context.top, g->index[i], &molb).ic;
643 * See sel_updatefunc() for description of the parameters.
644 * \p data is not used.
646 * Returns the chain for each atom in \p out->u.s.
648 static void evaluate_chain(const gmx::SelMethodEvalContext& context,
650 gmx_ana_selvalue_t* out,
655 for (int i = 0; i < g->isize; ++i)
657 out->u.s[i][0] = mtopGetResidueInfo(*context.top, g->index[i], &molb).chainid;
662 * See sel_updatefunc() for description of the parameters.
663 * \p data is not used.
665 * Returns the mass for each atom in \p out->u.r.
667 static void evaluate_mass(const gmx::SelMethodEvalContext& context,
669 gmx_ana_selvalue_t* out,
672 GMX_RELEASE_ASSERT(gmx_mtop_has_masses(context.top), "Masses not available for evaluation");
675 for (int i = 0; i < g->isize; ++i)
677 out->u.r[i] = mtopGetAtomMass(*context.top, g->index[i], &molb);
682 static void check_charge(const gmx_mtop_t* top, int /* npar */, gmx_ana_selparam_t* /* param */, void* /* data */)
684 if (!gmx_mtop_has_charges(top))
686 GMX_THROW(gmx::InconsistentInputError("Charges not available in topology"));
691 * See sel_updatefunc() for description of the parameters.
692 * \p data is not used.
694 * Returns the charge for each atom in \p out->u.r.
696 static void evaluate_charge(const gmx::SelMethodEvalContext& context,
698 gmx_ana_selvalue_t* out,
703 for (int i = 0; i < g->isize; ++i)
705 out->u.r[i] = mtopGetAtomParameters(*context.top, g->index[i], &molb).q;
709 static void check_pdbinfo(const gmx_mtop_t* top, int /* npar */, gmx_ana_selparam_t* /* param */, void* /* data */)
711 if (!gmx_mtop_has_pdbinfo(top))
713 GMX_THROW(gmx::InconsistentInputError("PDB info not available in topology"));
718 * See sel_updatefunc() for description of the parameters.
719 * \p data is not used.
721 * Returns the alternate location identifier for each atom in \p out->u.s.
723 static void evaluate_altloc(const gmx::SelMethodEvalContext& context,
725 gmx_ana_selvalue_t* out,
730 for (int i = 0; i < g->isize; ++i)
732 out->u.s[i][0] = mtopGetAtomPdbInfo(*context.top, g->index[i], &molb).altloc;
737 * See sel_updatefunc() for description of the parameters.
738 * \p data is not used.
740 * Returns the occupancy numbers for each atom in \p out->u.r.
741 * Segfaults if PDB info is not found in the topology.
743 static void evaluate_occupancy(const gmx::SelMethodEvalContext& context,
745 gmx_ana_selvalue_t* out,
750 for (int i = 0; i < g->isize; ++i)
752 out->u.r[i] = mtopGetAtomPdbInfo(*context.top, g->index[i], &molb).occup;
757 * See sel_updatefunc() for description of the parameters.
758 * \p data is not used.
760 * Returns the B-factors for each atom in \p out->u.r.
761 * Segfaults if PDB info is not found in the topology.
763 static void evaluate_betafactor(const gmx::SelMethodEvalContext& context,
765 gmx_ana_selvalue_t* out,
770 for (int i = 0; i < g->isize; ++i)
772 out->u.r[i] = mtopGetAtomPdbInfo(*context.top, g->index[i], &molb).bfac;
777 * Internal utility function for position keyword evaluation.
779 * \param[out] out Output array.
780 * \param[in] pos Position data to use instead of atomic coordinates.
781 * \param[in] d Coordinate index to evaluate (\p XX, \p YY or \p ZZ).
783 * This function is used internally by evaluate_x(), evaluate_y() and
784 * evaluate_z() to do the actual evaluation.
786 static void evaluate_coord(real out[], gmx_ana_pos_t* pos, int d)
788 for (int i = 0; i < pos->count(); ++i)
790 out[i] = pos->x[i][d];
792 // TODO: Make this more efficient by directly extracting the coordinates
793 // from the frame coordinates for atomic positions instead of going through
794 // a position calculation.
798 * See sel_updatefunc_pos() for description of the parameters.
799 * \p data is not used.
801 * Returns the \p x coordinate for each position in \p out->u.r.
803 static void evaluate_x(const gmx::SelMethodEvalContext& /*context*/,
805 gmx_ana_selvalue_t* out,
808 out->nr = pos->count();
809 evaluate_coord(out->u.r, pos, XX);
813 * See sel_updatefunc() for description of the parameters.
814 * \p data is not used.
816 * Returns the \p y coordinate for each position in \p out->u.r.
818 static void evaluate_y(const gmx::SelMethodEvalContext& /*context*/,
820 gmx_ana_selvalue_t* out,
823 out->nr = pos->count();
824 evaluate_coord(out->u.r, pos, YY);
828 * See sel_updatefunc() for description of the parameters.
829 * \p data is not used.
831 * Returns the \p z coordinate for each position in \p out->u.r.
833 static void evaluate_z(const gmx::SelMethodEvalContext& /*context*/,
835 gmx_ana_selvalue_t* out,
838 out->nr = pos->count();
839 evaluate_coord(out->u.r, pos, ZZ);