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41 * Implements gmx::analysismodules::Sasa.
43 * \author Teemu Murtola <teemu.murtola@gmail.com> (C++ conversion)
44 * \ingroup module_trajectoryanalysis
54 #include "gromacs/analysisdata/analysisdata.h"
55 #include "gromacs/analysisdata/modules/average.h"
56 #include "gromacs/analysisdata/modules/plot.h"
57 #include "gromacs/fileio/confio.h"
58 #include "gromacs/fileio/pdbio.h"
59 #include "gromacs/math/units.h"
60 #include "gromacs/math/vec.h"
61 #include "gromacs/options/basicoptions.h"
62 #include "gromacs/options/filenameoption.h"
63 #include "gromacs/options/ioptionscontainer.h"
64 #include "gromacs/pbcutil/pbc.h"
65 #include "gromacs/selection/selection.h"
66 #include "gromacs/selection/selectionoption.h"
67 #include "gromacs/topology/atomprop.h"
68 #include "gromacs/topology/symtab.h"
69 #include "gromacs/topology/topology.h"
70 #include "gromacs/trajectory/trajectoryframe.h"
71 #include "gromacs/trajectoryanalysis/analysismodule.h"
72 #include "gromacs/trajectoryanalysis/analysissettings.h"
73 #include "gromacs/trajectoryanalysis/topologyinformation.h"
74 #include "gromacs/utility/exceptions.h"
75 #include "gromacs/utility/futil.h"
76 #include "gromacs/utility/pleasecite.h"
77 #include "gromacs/utility/smalloc.h"
78 #include "gromacs/utility/stringutil.h"
79 #include "gromacs/utility/unique_cptr.h"
81 #include "surfacearea.h"
86 namespace analysismodules
92 //! \addtogroup module_trajectoryanalysis
95 //! Tracks information on two nearest neighbors of a single surface dot.
98 //! Index of the second nearest neighbor dot.
100 //! Index of the nearest neighbor dot.
102 //! Squared distance to `aa`.
104 //! Squared distance to `ab`.
109 * Updates nearest neighbor information for a surface dot.
111 * \param[in,out] c Nearest neighbor information array to update.
112 * \param[in] i Index in `c` to update.
113 * \param[in] j Index of the other surface dot to add to the array.
114 * \param[in] d2 Squared distance between `i` and `j`.
116 void add_rec(t_conect c[], int i, int j, real d2)
119 { // NOLINT bugprone-branch-clone
123 else if (c[i].ab == -1)
124 { // NOLINT bugprone-branch-clone
128 else if (d2 < c[i].d2a)
133 else if (d2 < c[i].d2b)
138 /* Swap them if necessary: a must be larger than b */
139 if (c[i].d2a < c[i].d2b)
151 * Adds CONECT records for surface dots.
153 * \param[in] fn PDB file to append the CONECT records to.
154 * \param[in] n Number of dots in `x`.
155 * \param[in] x Array of surface dot positions.
157 * Adds a CONECT record that connects each surface dot to its two nearest
158 * neighbors. The function is copied verbatim from the old gmx_sas.c
161 void do_conect(const char* fn, int n, rvec x[])
163 t_conect* c = nullptr;
165 fprintf(stderr, "Building CONECT records\n");
167 for (int i = 0; (i < n); i++)
169 c[i].aa = c[i].ab = -1;
172 for (int i = 0; (i < n); i++)
174 for (int j = i + 1; (j < n); j++)
177 rvec_sub(x[i], x[j], dx);
178 const real d2 = iprod(dx, dx);
179 add_rec(c, i, j, d2);
180 add_rec(c, j, i, d2);
183 FILE* fp = gmx_ffopen(fn, "a");
184 for (int i = 0; (i < n); i++)
186 if ((c[i].aa == -1) || (c[i].ab == -1))
188 fprintf(stderr, "Warning dot %d has no connections\n", i + 1);
190 fprintf(fp, "CONECT%5d%5d%5d\n", i + 1, c[i].aa + 1, c[i].ab + 1);
197 * Plots the surface into a PDB file, optionally including the original atoms.
199 void connolly_plot(const char* fn,
207 gmx_bool bIncludeSolute)
209 const char* const atomnm = "DOT";
210 const char* const resnm = "DOT";
211 const char* const title = "Connolly Dot Surface Generated by gmx sasa";
213 rvec* xnew = nullptr;
218 int r0 = atoms->nres;
219 srenew(atoms->atom, atoms->nr + ndots);
220 memset(&atoms->atom[i0], 0, sizeof(*atoms->atom) * ndots);
221 srenew(atoms->atomname, atoms->nr + ndots);
222 srenew(atoms->resinfo, r0 + 1);
223 atoms->atom[i0].resind = r0;
224 t_atoms_set_resinfo(atoms, i0, symtab, resnm, r0 + 1, ' ', 0, ' ');
225 if (atoms->pdbinfo != nullptr)
227 srenew(atoms->pdbinfo, atoms->nr + ndots);
229 snew(xnew, atoms->nr + ndots);
230 for (int i = 0; (i < atoms->nr); i++)
232 copy_rvec(x[i], xnew[i]);
235 for (int i = 0; (i < ndots); i++)
238 atoms->atomname[ii0] = put_symtab(symtab, atomnm);
239 atoms->atom[ii0].resind = r0;
240 xnew[ii0][XX] = dots[k++];
241 xnew[ii0][YY] = dots[k++];
242 xnew[ii0][ZZ] = dots[k++];
243 if (atoms->pdbinfo != nullptr)
245 atoms->pdbinfo[ii0].type = PdbRecordType::Atom;
246 atoms->pdbinfo[ii0].atomnr = ii0;
247 atoms->pdbinfo[ii0].bfac = 0.0;
248 atoms->pdbinfo[ii0].occup = 0.0;
251 atoms->nr = i0 + ndots;
252 atoms->nres = r0 + 1;
253 write_sto_conf(fn, title, atoms, xnew, nullptr, pbcType, const_cast<rvec*>(box));
260 init_t_atoms(&aaa, ndots, TRUE);
261 aaa.atom[0].resind = 0;
262 t_atoms_set_resinfo(&aaa, 0, symtab, resnm, 1, ' ', 0, ' ');
265 for (int i = 0; (i < ndots); i++)
268 aaa.atomname[ii0] = put_symtab(symtab, atomnm);
269 aaa.pdbinfo[ii0].type = PdbRecordType::Atom;
270 aaa.pdbinfo[ii0].atomnr = ii0;
271 aaa.atom[ii0].resind = 0;
272 xnew[ii0][XX] = dots[k++];
273 xnew[ii0][YY] = dots[k++];
274 xnew[ii0][ZZ] = dots[k++];
275 aaa.pdbinfo[ii0].bfac = 0.0;
276 aaa.pdbinfo[ii0].occup = 0.0;
279 write_sto_conf(fn, title, &aaa, xnew, nullptr, pbcType, const_cast<rvec*>(box));
280 do_conect(fn, ndots, xnew);
286 /********************************************************************
287 * Actual analysis module
291 * Implements `gmx sas` trajectory analysis module.
293 class Sasa : public TrajectoryAnalysisModule
298 void initOptions(IOptionsContainer* options, TrajectoryAnalysisSettings* settings) override;
299 void initAnalysis(const TrajectoryAnalysisSettings& settings, const TopologyInformation& top) override;
301 TrajectoryAnalysisModuleDataPointer startFrames(const AnalysisDataParallelOptions& opt,
302 const SelectionCollection& selections) override;
303 void analyzeFrame(int frnr, const t_trxframe& fr, t_pbc* pbc, TrajectoryAnalysisModuleData* pdata) override;
305 void finishAnalysis(int nframes) override;
306 void writeOutput() override;
310 * Surface areas as a function of time.
312 * First column is for the calculation group, and the rest for the
313 * output groups. This data is always produced.
317 * Per-atom surface areas as a function of time.
319 * Contains one data set for each column in `area_`.
320 * Each column corresponds to a selection position in `surfaceSel_`.
321 * This data is only produced if atom or residue areas have been
324 AnalysisData atomArea_;
326 * Per-residue surface areas as a function of time.
328 * Contains one data set for each column in `area_`.
329 * Each column corresponds to a distinct residue `surfaceSel_`.
330 * For example, if `surfaceSel_` selects residues 2, 5, and 7, there
331 * will be three columns here.
332 * This data is only produced if atom or residue areas have been
335 AnalysisData residueArea_;
337 * Free energy estimates as a function of time.
339 * Column layout is the same as for `area_`.
340 * This data is only produced if the output is requested.
342 AnalysisData dgSolv_;
344 * Total volume and density of the calculation group as a function of
347 * The first column is the volume and the second column is the density.
348 * This data is only produced if the output is requested.
350 AnalysisData volume_;
353 * The selection to calculate the surface for.
355 * Selection::originalId() and Selection::mappedId() store the mapping
356 * from the positions to the columns of `residueArea_`.
357 * The selection is computed with SelectionOption::dynamicMask(), i.e.,
358 * even in the presence of a dynamic selection, the number of returned
359 * positions is fixed, and SelectionPosition::selected() is used.
361 Selection surfaceSel_;
363 * List of optional additional output groups.
365 * Each of these must be a subset of the `surfaceSel_`.
366 * Selection::originalId() and Selection::mappedId() store the mapping
367 * from the positions to the corresponsing positions in `surfaceSel_`.
369 SelectionList outputSel_;
372 std::string fnAtomArea_;
373 std::string fnResidueArea_;
374 std::string fnDGSolv_;
375 std::string fnVolume_;
376 std::string fnConnolly_;
382 bool bIncludeSolute_;
384 //! Global topology corresponding to the input.
386 //! Per-atom data corresponding to the input.
388 //! Combined VdW and probe radii for each atom in the calculation group.
389 std::vector<real> radii_;
391 * Solvation free energy coefficients for each atom in the calculation
394 * Empty if the free energy output has not been requested.
396 std::vector<real> dgsFactor_;
397 //! Calculation algorithm.
398 SurfaceAreaCalculator calculator_;
400 // Copy and assign disallowed by base.
407 bIncludeSolute_(true),
412 registerAnalysisDataset(&area_, "area");
413 registerAnalysisDataset(&atomArea_, "atomarea");
414 registerAnalysisDataset(&residueArea_, "resarea");
415 registerAnalysisDataset(&dgSolv_, "dgsolv");
416 registerAnalysisDataset(&volume_, "volume");
419 void Sasa::initOptions(IOptionsContainer* options, TrajectoryAnalysisSettings* settings)
421 static const char* const desc[] = {
422 "[THISMODULE] computes solvent accessible surface areas.",
423 "See Eisenhaber F, Lijnzaad P, Argos P, Sander C, & Scharf M",
424 "(1995) J. Comput. Chem. 16, 273-284 for the algorithm used.",
425 "With [TT]-q[tt], the Connolly surface can be generated as well",
426 "in a [REF].pdb[ref] file where the nodes are represented as atoms",
427 "and the edges connecting the nearest nodes as CONECT records.",
428 "[TT]-odg[tt] allows for estimation of solvation free energies",
429 "from per-atom solvation energies per exposed surface area.[PAR]",
431 "The program requires a selection for the surface calculation to be",
432 "specified with [TT]-surface[tt]. This should always consist of all",
433 "non-solvent atoms in the system. The area of this group is always",
434 "calculated. Optionally, [TT]-output[tt] can specify additional",
435 "selections, which should be subsets of the calculation group.",
436 "The solvent-accessible areas for these groups are also extracted",
437 "from the full surface.[PAR]",
439 "The average and standard deviation of the area over the trajectory",
440 "can be calculated per residue and atom (options [TT]-or[tt] and",
441 "[TT]-oa[tt]).[PAR]",
442 //"In combination with the latter option an [REF].itp[ref] file can be",
443 //"generated (option [TT]-i[tt])",
444 //"which can be used to restrain surface atoms.[PAR]",
446 "With the [TT]-tv[tt] option the total volume and density of the",
447 "molecule can be computed. With [TT]-pbc[tt] (the default), you",
448 "must ensure that your molecule/surface group is not split across PBC.",
449 "Otherwise, you will get non-sensical results.",
450 "Please also consider whether the normal probe radius is appropriate",
451 "in this case or whether you would rather use, e.g., 0. It is good",
452 "to keep in mind that the results for volume and density are very",
453 "approximate. For example, in ice Ih, one can easily fit water molecules in the",
454 "pores which would yield a volume that is too low, and surface area and density",
455 "that are both too high."
458 settings->setHelpText(desc);
460 options->addOption(FileNameOption("o")
465 .defaultBasename("area")
466 .description("Total area as a function of time"));
468 FileNameOption("odg")
472 .defaultBasename("dgsolv")
473 .description("Estimated solvation free energy as a function of time"));
474 options->addOption(FileNameOption("or")
477 .store(&fnResidueArea_)
478 .defaultBasename("resarea")
479 .description("Average area per residue"));
480 options->addOption(FileNameOption("oa")
484 .defaultBasename("atomarea")
485 .description("Average area per atom"));
486 options->addOption(FileNameOption("tv")
490 .defaultBasename("volume")
491 .description("Total volume and density as a function of time"));
492 options->addOption(FileNameOption("q")
496 .defaultBasename("connolly")
497 .description("PDB file for Connolly surface"));
498 // options->addOption(FileNameOption("i").filetype(eftITP).outputFile()
499 // .store(&fnRestraints_).defaultBasename("surfat")
500 // .description("Topology file for position restraings on surface atoms"));
504 DoubleOption("probe").store(&solsize_).description("Radius of the solvent probe (nm)"));
505 options->addOption(IntegerOption("ndots").store(&ndots_).description(
506 "Number of dots per sphere, more dots means more accuracy"));
507 // options->addOption(DoubleOption("minarea").store(&minarea_)
508 // .description("The minimum area (nm^2) to count an atom as a surface atom when writing a position restraint file (see help)"));
510 BooleanOption("prot").store(&bIncludeSolute_).description("Output the protein to the Connolly [REF].pdb[ref] file too"));
512 DoubleOption("dgs").store(&dgsDefault_).description("Default value for solvation free energy per area (kJ/mol/nm^2)"));
514 // Selections must select atoms for the VdW radii lookup to work.
515 // The calculation group uses dynamicMask() so that the coordinates
516 // match a static array of VdW radii.
517 options->addOption(SelectionOption("surface")
522 .description("Surface calculation selection"));
524 SelectionOption("output").storeVector(&outputSel_).onlySortedAtoms().multiValue().description("Output selection(s)"));
526 // Atom names etc. are required for the VdW radii lookup.
527 settings->setFlag(TrajectoryAnalysisSettings::efRequireTop);
530 void Sasa::initAnalysis(const TrajectoryAnalysisSettings& settings, const TopologyInformation& top)
533 atoms_ = top.copyAtoms();
535 // bITP = opt2bSet("-i", nfile, fnm);
536 const bool bResAt = !fnResidueArea_.empty() || !fnAtomArea_.empty(); // || bITP;
537 const bool bDGsol = !fnDGSolv_.empty();
542 fprintf(stderr, "Probe size too small, setting it to %g\n", solsize_);
547 fprintf(stderr, "Ndots too small, setting it to %d\n", ndots_);
550 please_cite(stderr, "Eisenhaber95");
551 // if ((top.pbcType() != PbcType::Xyz) || (TRICLINIC(fr.box)))
553 // fprintf(stderr, "\n\nWARNING: non-rectangular boxes may give erroneous results or crashes.\n"
554 // "Analysis based on vacuum simulations (with the possibility of evaporation)\n"
555 // "will certainly crash the analysis.\n\n");
560 if (!top.hasFullTopology())
562 GMX_THROW(InconsistentInputError(
563 "Cannot compute Delta G of solvation without a tpr file"));
567 if (strcmp(*(atoms_->atomtype[0]), "?") == 0)
569 GMX_THROW(InconsistentInputError(
570 "Your input tpr file is too old (does not contain atom types). Cannot not "
571 "compute Delta G of solvation"));
575 printf("Free energy of solvation predictions:\n");
576 please_cite(stdout, "Eisenberg86a");
581 // Now compute atomic radii including solvent probe size.
582 // Also, fetch solvation free energy coefficients and
583 // compute the residue indices that map the calculation atoms
584 // to the columns of residueArea_.
585 radii_.reserve(surfaceSel_.posCount());
588 dgsFactor_.reserve(surfaceSel_.posCount());
591 const int resCount = surfaceSel_.initOriginalIdsToGroup(top.mtop(), INDEX_RES);
593 // TODO: Not exception-safe, but nice solution would be to have a C++
594 // atom properties class...
597 ArrayRef<const int> atomIndices = surfaceSel_.atomIndices();
599 for (int i = 0; i < surfaceSel_.posCount(); i++)
601 const int ii = atomIndices[i];
602 const int resind = atoms_->atom[ii].resind;
604 if (!aps.setAtomProperty(epropVDW, *(atoms_->resinfo[resind].name), *(atoms_->atomname[ii]), &radius))
608 radii_.push_back(radius + solsize_);
612 if (!aps.setAtomProperty(
613 epropDGsol, *(atoms_->resinfo[resind].name), *(atoms_->atomtype[ii]), &dgsFactor))
615 dgsFactor = dgsDefault_;
617 dgsFactor_.push_back(dgsFactor);
622 fprintf(stderr, "WARNING: could not find a Van der Waals radius for %d atoms\n", ndefault);
625 // Pre-compute mapping from the output groups to the calculation group,
626 // and store it in the selection ID map for easy lookup.
627 for (size_t g = 0; g < outputSel_.size(); ++g)
629 ArrayRef<const int> outputIndices = outputSel_[g].atomIndices();
630 for (int i = 0, j = 0; i < outputSel_[g].posCount(); ++i)
632 while (j < surfaceSel_.posCount() && outputIndices[i] > atomIndices[j])
636 if (j == surfaceSel_.posCount() || outputIndices[i] != atomIndices[j])
638 const std::string message = formatString(
639 "Output selection '%s' is not a subset of "
640 "the surface selection (atom %d is the first "
641 "atom not in the surface selection)",
642 outputSel_[g].name(),
643 outputIndices[i] + 1);
644 GMX_THROW(InconsistentInputError(message));
646 outputSel_[g].setOriginalId(i, j);
650 calculator_.setDotCount(ndots_);
651 calculator_.setRadii(radii_);
653 // Initialize all the output data objects and initialize the output plotters.
655 area_.setColumnCount(0, 1 + outputSel_.size());
657 AnalysisDataPlotModulePointer plotm(new AnalysisDataPlotModule(settings.plotSettings()));
658 plotm->setFileName(fnArea_);
659 plotm->setTitle("Solvent Accessible Surface");
660 plotm->setXAxisIsTime();
661 plotm->setYLabel("Area (nm\\S2\\N)");
662 plotm->appendLegend("Total");
663 for (size_t i = 0; i < outputSel_.size(); ++i)
665 plotm->appendLegend(outputSel_[i].name());
667 area_.addModule(plotm);
672 atomArea_.setDataSetCount(1 + outputSel_.size());
673 residueArea_.setDataSetCount(1 + outputSel_.size());
674 for (size_t i = 0; i <= outputSel_.size(); ++i)
676 atomArea_.setColumnCount(i, surfaceSel_.posCount());
677 residueArea_.setColumnCount(i, resCount);
680 AnalysisDataAverageModulePointer avem(new AnalysisDataAverageModule);
681 for (int i = 0; i < surfaceSel_.posCount(); ++i)
683 avem->setXAxisValue(i, surfaceSel_.position(i).atomIndices()[0] + 1);
685 atomArea_.addModule(avem);
686 if (!fnAtomArea_.empty())
688 AnalysisDataPlotModulePointer plotm(new AnalysisDataPlotModule(settings.plotSettings()));
689 plotm->setFileName(fnAtomArea_);
690 plotm->setTitle("Area per atom over the trajectory");
691 plotm->setXLabel("Atom");
692 plotm->setXFormat(8, 0);
693 plotm->setYLabel("Area (nm\\S2\\N)");
694 plotm->setErrorsAsSeparateColumn(true);
695 plotm->appendLegend("Average (nm\\S2\\N)");
696 plotm->appendLegend("Standard deviation (nm\\S2\\N)");
697 avem->addModule(plotm);
701 AnalysisDataAverageModulePointer avem(new AnalysisDataAverageModule);
703 for (int i = 0; i < surfaceSel_.posCount(); ++i)
705 const int residueGroup = surfaceSel_.position(i).mappedId();
706 if (residueGroup >= nextRow)
708 GMX_ASSERT(residueGroup == nextRow,
709 "Inconsistent (non-uniformly increasing) residue grouping");
710 const int atomIndex = surfaceSel_.position(i).atomIndices()[0];
711 const int residueIndex = atoms_->atom[atomIndex].resind;
712 avem->setXAxisValue(nextRow, atoms_->resinfo[residueIndex].nr);
716 residueArea_.addModule(avem);
717 if (!fnResidueArea_.empty())
719 AnalysisDataPlotModulePointer plotm(new AnalysisDataPlotModule(settings.plotSettings()));
720 plotm->setFileName(fnResidueArea_);
721 plotm->setTitle("Area per residue over the trajectory");
722 plotm->setXLabel("Residue");
723 plotm->setXFormat(8, 0);
724 plotm->setYLabel("Area (nm\\S2\\N)");
725 plotm->setErrorsAsSeparateColumn(true);
726 plotm->appendLegend("Average (nm\\S2\\N)");
727 plotm->appendLegend("Standard deviation (nm\\S2\\N)");
728 avem->addModule(plotm);
733 if (!fnDGSolv_.empty())
735 dgSolv_.setColumnCount(0, 1 + outputSel_.size());
736 AnalysisDataPlotModulePointer plotm(new AnalysisDataPlotModule(settings.plotSettings()));
737 plotm->setFileName(fnDGSolv_);
738 plotm->setTitle("Free Energy of Solvation");
739 plotm->setXAxisIsTime();
740 plotm->setYLabel("D Gsolv");
741 plotm->appendLegend("Total");
742 for (size_t i = 0; i < outputSel_.size(); ++i)
744 plotm->appendLegend(outputSel_[i].name());
746 dgSolv_.addModule(plotm);
749 if (!fnVolume_.empty())
751 volume_.setColumnCount(0, 2);
752 AnalysisDataPlotModulePointer plotm(new AnalysisDataPlotModule(settings.plotSettings()));
753 plotm->setFileName(fnVolume_);
754 plotm->setTitle("Volume and Density");
755 plotm->setXAxisIsTime();
756 plotm->appendLegend("Volume (nm\\S3\\N)");
757 plotm->appendLegend("Density (g/l)");
758 volume_.addModule(plotm);
763 * Temporary memory for use within a single-frame calculation.
765 class SasaModuleData : public TrajectoryAnalysisModuleData
769 * Reserves memory for the frame-local data.
771 * `residueCount` will be zero if per-residue data is not being
774 SasaModuleData(TrajectoryAnalysisModule* module,
775 const AnalysisDataParallelOptions& opt,
776 const SelectionCollection& selections,
779 TrajectoryAnalysisModuleData(module, opt, selections)
781 index_.reserve(atomCount);
782 // If the calculation group is not dynamic, pre-calculate
783 // the index, since it is not going to change.
784 for (int i = 0; i < atomCount; ++i)
788 atomAreas_.resize(atomCount);
789 res_a_.resize(residueCount);
792 void finish() override { finishDataHandles(); }
794 //! Indices of the calculation selection positions selected for the frame.
795 std::vector<int> index_;
797 * Atom areas for each calculation selection position for the frame.
799 * One entry for each position in the calculation group.
800 * Values for atoms not selected are set to zero.
802 std::vector<real> atomAreas_;
804 * Working array to accumulate areas for each residue.
806 * One entry for each distinct residue in the calculation group;
807 * indices are not directly residue numbers or residue indices.
809 * This vector is empty if residue area calculations are not being
812 std::vector<real> res_a_;
815 TrajectoryAnalysisModuleDataPointer Sasa::startFrames(const AnalysisDataParallelOptions& opt,
816 const SelectionCollection& selections)
818 return TrajectoryAnalysisModuleDataPointer(new SasaModuleData(
819 this, opt, selections, surfaceSel_.posCount(), residueArea_.columnCount(0)));
823 * Helper method to compute the areas for a single selection.
825 * \param[in] surfaceSel The calculation selection.
826 * \param[in] sel The selection to compute the areas for (can be
827 * `surfaceSel` or one of the output selections).
828 * \param[in] atomAreas Atom areas for each position in `surfaceSel`.
829 * \param[in] dgsFactor Free energy coefficients for each position in
830 * `surfaceSel`. If empty, free energies are not calculated.
831 * \param[out] totalAreaOut Total area of `sel` (sum of atom areas it selects).
832 * \param[out] dgsolvOut Solvation free energy.
833 * Will be zero of `dgsFactor` is empty.
834 * \param atomAreaHandle Data handle to use for storing atom areas for `sel`.
835 * \param resAreaHandle Data handle to use for storing residue areas for `sel`.
836 * \param resAreaWork Work array for accumulating the residue areas.
837 * If empty, atom and residue areas are not calculated.
839 * `atomAreaHandle` and `resAreaHandle` are not used if `resAreaWork` is empty.
841 void computeAreas(const Selection& surfaceSel,
842 const Selection& sel,
843 const std::vector<real>& atomAreas,
844 const std::vector<real>& dgsFactor,
847 AnalysisDataHandle atomAreaHandle,
848 AnalysisDataHandle resAreaHandle,
849 std::vector<real>* resAreaWork)
851 const bool bResAt = !resAreaWork->empty();
852 const bool bDGsolv = !dgsFactor.empty();
858 std::fill(resAreaWork->begin(), resAreaWork->end(), 0.0_real);
860 for (int i = 0; i < sel.posCount(); ++i)
862 // Get the index of the atom in the calculation group.
863 // For the output groups, the mapping has been precalculated in
865 const int ii = (sel != surfaceSel ? sel.position(i).mappedId() : i);
866 if (!surfaceSel.position(ii).selected())
868 // For the calculation group, skip unselected atoms.
869 if (sel == surfaceSel)
873 GMX_THROW(InconsistentInputError(
874 "Output selection is not a subset of the surface selection"));
876 // Get the internal index of the matching residue.
877 // These have been precalculated in initAnalysis().
878 const int ri = surfaceSel.position(ii).mappedId();
879 const real atomArea = atomAreas[ii];
880 totalArea += atomArea;
883 atomAreaHandle.setPoint(ii, atomArea);
884 (*resAreaWork)[ri] += atomArea;
888 dgsolv += atomArea * dgsFactor[ii];
893 for (size_t i = 0; i < (*resAreaWork).size(); ++i)
895 resAreaHandle.setPoint(i, (*resAreaWork)[i]);
898 *totalAreaOut = totalArea;
902 void Sasa::analyzeFrame(int frnr, const t_trxframe& fr, t_pbc* pbc, TrajectoryAnalysisModuleData* pdata)
904 AnalysisDataHandle ah = pdata->dataHandle(area_);
905 AnalysisDataHandle dgh = pdata->dataHandle(dgSolv_);
906 AnalysisDataHandle aah = pdata->dataHandle(atomArea_);
907 AnalysisDataHandle rah = pdata->dataHandle(residueArea_);
908 AnalysisDataHandle vh = pdata->dataHandle(volume_);
909 const Selection& surfaceSel = TrajectoryAnalysisModuleData::parallelSelection(surfaceSel_);
910 const SelectionList& outputSel = TrajectoryAnalysisModuleData::parallelSelections(outputSel_);
911 SasaModuleData& frameData = *static_cast<SasaModuleData*>(pdata);
913 const bool bResAt = !frameData.res_a_.empty();
914 const bool bDGsol = !dgsFactor_.empty();
915 const bool bConnolly = (frnr == 0 && !fnConnolly_.empty());
917 // Update indices of selected atoms in the work array.
918 if (surfaceSel.isDynamic())
920 frameData.index_.clear();
921 for (int i = 0; i < surfaceSel.posCount(); ++i)
923 if (surfaceSel.position(i).selected())
925 frameData.index_.push_back(i);
930 // Determine what needs to be calculated.
932 if (bResAt || bDGsol || !outputSel.empty())
934 flag |= FLAG_ATOM_AREA;
940 if (volume_.columnCount() > 0)
945 // Do the low-level calculation.
946 // totarea and totvolume receive the values for the calculation group.
947 // area array contains the per-atom areas for the selected positions.
948 // surfacedots contains nsurfacedots entries, and contains the actual
952 real *area = nullptr, *surfacedots = nullptr;
953 int nsurfacedots = 0;
954 calculator_.calculate(surfaceSel.coordinates().data(),
956 frameData.index_.size(),
957 frameData.index_.data(),
964 // Unpack the atomwise areas into the frameData.atomAreas_ array for easier
965 // indexing in the case of dynamic surfaceSel.
968 if (surfaceSel.isDynamic())
970 std::fill(frameData.atomAreas_.begin(), frameData.atomAreas_.end(), 0.0_real);
971 for (size_t i = 0; i < frameData.index_.size(); ++i)
973 frameData.atomAreas_[frameData.index_[i]] = area[i];
978 std::copy(area, area + surfaceSel.posCount(), frameData.atomAreas_.begin());
982 const sfree_guard dotsGuard(surfacedots);
986 if (fr.natoms != mtop_->natoms)
989 InconsistentInputError("Connolly plot (-q) is only supported for trajectories "
990 "that contain all the atoms"));
992 // This is somewhat nasty, as it modifies the atoms and symtab
993 // structures. But since it is only used in the first frame, and no
994 // one else uses the topology after initialization, it may just work
995 // even with future parallelization.
996 connolly_plot(fnConnolly_.c_str(),
1007 ah.startFrame(frnr, fr.time);
1010 aah.startFrame(frnr, fr.time);
1011 rah.startFrame(frnr, fr.time);
1015 dgh.startFrame(frnr, fr.time);
1018 ah.setPoint(0, totarea);
1022 if (bResAt || bDGsol)
1024 computeAreas(surfaceSel,
1026 frameData.atomAreas_,
1035 dgh.setPoint(0, dgsolv);
1038 for (size_t g = 0; g < outputSel.size(); ++g)
1042 aah.selectDataSet(g + 1);
1043 rah.selectDataSet(g + 1);
1045 computeAreas(surfaceSel,
1047 frameData.atomAreas_,
1054 ah.setPoint(g + 1, totalArea);
1057 dgh.setPoint(g + 1, dgsolv);
1075 for (int i = 0; i < surfaceSel.posCount(); ++i)
1077 totmass += surfaceSel.position(i).mass();
1079 const real density = totmass * AMU / (totvolume * NANO * NANO * NANO);
1080 vh.startFrame(frnr, fr.time);
1081 vh.setPoint(0, totvolume);
1082 vh.setPoint(1, density);
1087 void Sasa::finishAnalysis(int /*nframes*/)
1091 // fp3 = ftp2FILE(efITP, nfile, fnm, "w");
1092 // fprintf(fp3, "[ position_restraints ]\n"
1093 // "#define FCX 1000\n"
1094 // "#define FCY 1000\n"
1095 // "#define FCZ 1000\n"
1096 // "; Atom Type fx fy fz\n");
1097 // for (i = 0; i < nx[0]; i++)
1099 // if (atom_area[i] > minarea)
1101 // fprintf(fp3, "%5d 1 FCX FCX FCZ\n", ii+1);
1108 void Sasa::writeOutput() {}
1114 const char SasaInfo::name[] = "sasa";
1115 const char SasaInfo::shortDescription[] = "Compute solvent accessible surface area";
1117 TrajectoryAnalysisModulePointer SasaInfo::create()
1119 return TrajectoryAnalysisModulePointer(new Sasa);
1122 } // namespace analysismodules