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39 * Implements gmx::analysismodules::Sasa.
41 * \author Teemu Murtola <teemu.murtola@gmail.com> (C++ conversion)
42 * \ingroup module_trajectoryanalysis
52 #include "gromacs/analysisdata/analysisdata.h"
53 #include "gromacs/analysisdata/modules/average.h"
54 #include "gromacs/analysisdata/modules/plot.h"
55 #include "gromacs/fileio/confio.h"
56 #include "gromacs/fileio/pdbio.h"
57 #include "gromacs/fileio/trx.h"
58 #include "gromacs/legacyheaders/copyrite.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/options.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/trajectoryanalysis/analysismodule.h"
71 #include "gromacs/trajectoryanalysis/analysissettings.h"
72 #include "gromacs/utility/exceptions.h"
73 #include "gromacs/utility/futil.h"
74 #include "gromacs/utility/scoped_cptr.h"
75 #include "gromacs/utility/smalloc.h"
76 #include "gromacs/utility/stringutil.h"
78 #include "surfacearea.h"
83 namespace analysismodules
89 //! \addtogroup module_trajectoryanalysis
92 //! Tracks information on two nearest neighbors of a single surface dot.
95 //! Index of the second nearest neighbor dot.
97 //! Index of the nearest neighbor dot.
99 //! Squared distance to `aa`.
101 //! Squared distance to `ab`.
106 * Updates nearest neighbor information for a surface dot.
108 * \param[in,out] c Nearest neighbor information array to update.
109 * \param[in] i Index in `c` to update.
110 * \param[in] j Index of the other surface dot to add to the array.
111 * \param[in] d2 Squared distance between `i` and `j`.
113 void add_rec(t_conect c[], atom_id i, atom_id j, real d2)
115 if (c[i].aa == NO_ATID)
120 else if (c[i].ab == NO_ATID)
125 else if (d2 < c[i].d2a)
130 else if (d2 < c[i].d2b)
135 /* Swap them if necessary: a must be larger than b */
136 if (c[i].d2a < c[i].d2b)
148 * Adds CONECT records for surface dots.
150 * \param[in] fn PDB file to append the CONECT records to.
151 * \param[in] n Number of dots in `x`.
152 * \param[in] x Array of surface dot positions.
154 * Adds a CONECT record that connects each surface dot to its two nearest
155 * neighbors. The function is copied verbatim from the old gmx_sas.c
158 void do_conect(const char *fn, int n, rvec x[])
166 fprintf(stderr, "Building CONECT records\n");
168 for (i = 0; (i < n); i++)
170 c[i].aa = c[i].ab = NO_ATID;
173 for (i = 0; (i < n); i++)
175 for (j = i+1; (j < n); j++)
177 rvec_sub(x[i], x[j], dx);
179 add_rec(c, i, j, d2);
180 add_rec(c, j, i, d2);
183 fp = gmx_ffopen(fn, "a");
184 for (i = 0; (i < n); i++)
186 if ((c[i].aa == NO_ATID) || (c[i].ab == NO_ATID))
188 fprintf(stderr, "Warning dot %d has no conections\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, int ndots, real dots[], rvec x[], t_atoms *atoms,
200 t_symtab *symtab, int ePBC, const matrix box, gmx_bool bIncludeSolute)
202 const char *const atomnm = "DOT";
203 const char *const resnm = "DOT";
204 const char *const title = "Connolly Dot Surface Generated by gmx sasa";
206 int i, i0, r0, ii0, k;
214 srenew(atoms->atom, atoms->nr+ndots);
215 memset(&atoms->atom[i0], 0, sizeof(*atoms->atom)*ndots);
216 srenew(atoms->atomname, atoms->nr+ndots);
217 srenew(atoms->resinfo, r0+1);
218 atoms->atom[i0].resind = r0;
219 t_atoms_set_resinfo(atoms, i0, symtab, resnm, r0+1, ' ', 0, ' ');
220 if (atoms->pdbinfo != NULL)
222 srenew(atoms->pdbinfo, atoms->nr+ndots);
224 snew(xnew, atoms->nr+ndots);
225 for (i = 0; (i < atoms->nr); i++)
227 copy_rvec(x[i], xnew[i]);
229 for (i = k = 0; (i < ndots); i++)
232 atoms->atomname[ii0] = put_symtab(symtab, atomnm);
233 atoms->atom[ii0].resind = r0;
234 xnew[ii0][XX] = dots[k++];
235 xnew[ii0][YY] = dots[k++];
236 xnew[ii0][ZZ] = dots[k++];
237 if (atoms->pdbinfo != NULL)
239 atoms->pdbinfo[ii0].type = epdbATOM;
240 atoms->pdbinfo[ii0].atomnr = ii0;
241 atoms->pdbinfo[ii0].bfac = 0.0;
242 atoms->pdbinfo[ii0].occup = 0.0;
245 atoms->nr = i0+ndots;
247 write_sto_conf(fn, title, atoms, xnew, NULL, ePBC, const_cast<rvec *>(box));
253 init_t_atoms(&aaa, ndots, TRUE);
254 aaa.atom[0].resind = 0;
255 t_atoms_set_resinfo(&aaa, 0, symtab, resnm, 1, ' ', 0, ' ');
257 for (i = k = 0; (i < ndots); i++)
260 aaa.atomname[ii0] = put_symtab(symtab, atomnm);
261 aaa.pdbinfo[ii0].type = epdbATOM;
262 aaa.pdbinfo[ii0].atomnr = ii0;
263 aaa.atom[ii0].resind = 0;
264 xnew[ii0][XX] = dots[k++];
265 xnew[ii0][YY] = dots[k++];
266 xnew[ii0][ZZ] = dots[k++];
267 aaa.pdbinfo[ii0].bfac = 0.0;
268 aaa.pdbinfo[ii0].occup = 0.0;
271 write_sto_conf(fn, title, &aaa, xnew, NULL, ePBC, const_cast<rvec *>(box));
272 do_conect(fn, ndots, xnew);
273 free_t_atoms(&aaa, FALSE);
278 /********************************************************************
279 * Actual analysis module
283 * Implements `gmx sas` trajectory analysis module.
285 class Sasa : public TrajectoryAnalysisModule
290 virtual void initOptions(Options *options,
291 TrajectoryAnalysisSettings *settings);
292 virtual void initAnalysis(const TrajectoryAnalysisSettings &settings,
293 const TopologyInformation &top);
295 virtual TrajectoryAnalysisModuleDataPointer startFrames(
296 const AnalysisDataParallelOptions &opt,
297 const SelectionCollection &selections);
298 virtual void analyzeFrame(int frnr, const t_trxframe &fr, t_pbc *pbc,
299 TrajectoryAnalysisModuleData *pdata);
301 virtual void finishAnalysis(int nframes);
302 virtual void writeOutput();
306 * Surface areas as a function of time.
308 * First column is for the calculation group, and the rest for the
309 * output groups. This data is always produced.
313 * Per-atom surface areas as a function of time.
315 * Contains one data set for each column in `area_`.
316 * Each column corresponds to a selection position in `surfaceSel_`.
317 * This data is only produced if atom or residue areas have been
320 AnalysisData atomArea_;
322 * Per-residue surface areas as a function of time.
324 * Contains one data set for each column in `area_`.
325 * Each column corresponds to a distinct residue `surfaceSel_`.
326 * For example, if `surfaceSel_` selects residues 2, 5, and 7, there
327 * will be three columns here.
328 * This data is only produced if atom or residue areas have been
331 AnalysisData residueArea_;
333 * Free energy estimates as a function of time.
335 * Column layout is the same as for `area_`.
336 * This data is only produced if the output is requested.
338 AnalysisData dgSolv_;
340 * Total volume and density of the calculation group as a function of
343 * The first column is the volume and the second column is the density.
344 * This data is only produced if the output is requested.
346 AnalysisData volume_;
349 * The selection to calculate the surface for.
351 * Selection::originalId() and Selection::mappedId() store the mapping
352 * from the positions to the columns of `residueArea_`.
353 * The selection is computed with SelectionOption::dynamicMask(), i.e.,
354 * even in the presence of a dynamic selection, the number of returned
355 * positions is fixed, and SelectionPosition::selected() is used.
357 Selection surfaceSel_;
359 * List of optional additional output groups.
361 * Each of these must be a subset of the `surfaceSel_`.
362 * Selection::originalId() and Selection::mappedId() store the mapping
363 * from the positions to the corresponsing positions in `surfaceSel_`.
365 SelectionList outputSel_;
368 std::string fnAtomArea_;
369 std::string fnResidueArea_;
370 std::string fnDGSolv_;
371 std::string fnVolume_;
372 std::string fnConnolly_;
378 bool bIncludeSolute_;
381 //! Combined VdW and probe radii for each atom in the calculation group.
382 std::vector<real> radii_;
384 * Solvation free energy coefficients for each atom in the calculation
387 * Empty if the free energy output has not been requested.
389 std::vector<real> dgsFactor_;
391 // Copy and assign disallowed by base.
395 : TrajectoryAnalysisModule(SasaInfo::name, SasaInfo::shortDescription),
396 solsize_(0.14), ndots_(24), dgsDefault_(0), bIncludeSolute_(true), top_(NULL)
399 registerAnalysisDataset(&area_, "area");
400 registerAnalysisDataset(&atomArea_, "atomarea");
401 registerAnalysisDataset(&residueArea_, "resarea");
402 registerAnalysisDataset(&dgSolv_, "dgsolv");
403 registerAnalysisDataset(&volume_, "volume");
407 Sasa::initOptions(Options *options, TrajectoryAnalysisSettings *settings)
409 static const char *const desc[] = {
410 "[THISMODULE] computes solvent accessible surface areas.",
411 "See Eisenhaber F, Lijnzaad P, Argos P, Sander C, & Scharf M",
412 "(1995) J. Comput. Chem. 16, 273-284 for the algorithm used.",
413 "With [TT]-q[tt], the Connolly surface can be generated as well",
414 "in a [TT].pdb[tt] file where the nodes are represented as atoms",
415 "and the edges connecting the nearest nodes as CONECT records.",
416 "[TT]-odg[tt] allows for estimation of solvation free energies",
417 "from per-atom solvation energies per exposed surface area.[PAR]",
419 "The program requires a selection for the surface calculation to be",
420 "specified with [TT]-surface[tt]. This should always consist of all",
421 "non-solvent atoms in the system. The area of this group is always",
422 "calculated. Optionally, [TT]-output[tt] can specify additional",
423 "selections, which should be subsets of the calculation group.",
424 "The solvent-accessible areas for these groups are also extracted",
425 "from the full surface.[PAR]",
427 "The average and standard deviation of the area over the trajectory",
428 "can be calculated per residue and atom (options [TT]-or[tt] and",
429 "[TT]-oa[tt]).[PAR]",
430 //"In combination with the latter option an [TT].itp[tt] file can be",
431 //"generated (option [TT]-i[tt])",
432 //"which can be used to restrain surface atoms.[PAR]",
434 "With the [TT]-tv[tt] option the total volume and density of the",
435 "molecule can be computed.",
436 "Please consider whether the normal probe radius is appropriate",
437 "in this case or whether you would rather use, e.g., 0. It is good",
438 "to keep in mind that the results for volume and density are very",
439 "approximate. For example, in ice Ih, one can easily fit water molecules in the",
440 "pores which would yield a volume that is too low, and surface area and density",
441 "that are both too high."
444 options->setDescription(concatenateStrings(desc));
446 options->addOption(FileNameOption("o").filetype(eftPlot).outputFile().required()
447 .store(&fnArea_).defaultBasename("area")
448 .description("Total area as a function of time"));
449 options->addOption(FileNameOption("odg").filetype(eftPlot).outputFile()
450 .store(&fnDGSolv_).defaultBasename("dgsolv")
451 .description("Estimated solvation free energy as a function of time"));
452 options->addOption(FileNameOption("or").filetype(eftPlot).outputFile()
453 .store(&fnResidueArea_).defaultBasename("resarea")
454 .description("Average area per residue"));
455 options->addOption(FileNameOption("oa").filetype(eftPlot).outputFile()
456 .store(&fnAtomArea_).defaultBasename("atomarea")
457 .description("Average area per atom"));
458 options->addOption(FileNameOption("tv").filetype(eftPlot).outputFile()
459 .store(&fnVolume_).defaultBasename("volume")
460 .description("Total volume and density as a function of time"));
461 options->addOption(FileNameOption("q").filetype(eftPDB).outputFile()
462 .store(&fnConnolly_).defaultBasename("connolly")
463 .description("PDB file for Connolly surface"));
464 //options->addOption(FileNameOption("i").filetype(eftITP).outputFile()
465 // .store(&fnRestraints_).defaultBasename("surfat")
466 // .description("Topology file for position restraings on surface atoms"));
469 options->addOption(DoubleOption("probe").store(&solsize_)
470 .description("Radius of the solvent probe (nm)"));
471 options->addOption(IntegerOption("ndots").store(&ndots_)
472 .description("Number of dots per sphere, more dots means more accuracy"));
473 //options->addOption(DoubleOption("minarea").store(&minarea_)
474 // .description("The minimum area (nm^2) to count an atom as a surface atom when writing a position restraint file (see help)"));
475 options->addOption(BooleanOption("prot").store(&bIncludeSolute_)
476 .description("Output the protein to the Connolly [TT].pdb[tt] file too"));
477 options->addOption(DoubleOption("dgs").store(&dgsDefault_)
478 .description("Default value for solvation free energy per area (kJ/mol/nm^2)"));
480 // Selections must select atoms for the VdW radii lookup to work.
481 // The calculation group uses dynamicMask() so that the coordinates
482 // match a static array of VdW radii.
483 options->addOption(SelectionOption("surface").store(&surfaceSel_)
484 .required().onlyAtoms().dynamicMask()
485 .description("Surface calculation selection"));
486 options->addOption(SelectionOption("output").storeVector(&outputSel_)
487 .onlyAtoms().multiValue()
488 .description("Output selection(s)"));
490 // Atom names etc. are required for the VdW radii lookup.
491 settings->setFlag(TrajectoryAnalysisSettings::efRequireTop);
495 Sasa::initAnalysis(const TrajectoryAnalysisSettings &settings,
496 const TopologyInformation &top)
498 const t_atoms &atoms = top.topology()->atoms;
499 top_ = top.topology();
501 //bITP = opt2bSet("-i", nfile, fnm);
503 !fnResidueArea_.empty() || !fnAtomArea_.empty(); // || bITP;
504 const bool bDGsol = !fnDGSolv_.empty();
509 fprintf(stderr, "Probe size too small, setting it to %g\n", solsize_);
514 fprintf(stderr, "Ndots too small, setting it to %d\n", ndots_);
517 please_cite(stderr, "Eisenhaber95");
518 //if ((top.ePBC() != epbcXYZ) || (TRICLINIC(fr.box)))
520 // fprintf(stderr, "\n\nWARNING: non-rectangular boxes may give erroneous results or crashes.\n"
521 // "Analysis based on vacuum simulations (with the possibility of evaporation)\n"
522 // "will certainly crash the analysis.\n\n");
527 if (!top.hasFullTopology())
529 GMX_THROW(InconsistentInputError("Cannot compute Delta G of solvation without a tpr file"));
533 if (strcmp(*(atoms.atomtype[0]), "?") == 0)
535 GMX_THROW(InconsistentInputError("Your input tpr file is too old (does not contain atom types). Cannot not compute Delta G of solvation"));
539 printf("Free energy of solvation predictions:\n");
540 please_cite(stdout, "Eisenberg86a");
545 // Now compute atomic radii including solvent probe size.
546 // Also, fetch solvation free energy coefficients and
547 // compute the residue indices that map the calculation atoms
548 // to the columns of residueArea_.
549 radii_.reserve(surfaceSel_.posCount());
552 dgsFactor_.reserve(surfaceSel_.posCount());
555 const int resCount = surfaceSel_.initOriginalIdsToGroup(top_, INDEX_RES);
557 // TODO: Not exception-safe, but nice solution would be to have a C++
558 // atom properties class...
559 gmx_atomprop_t aps = gmx_atomprop_init();
561 ConstArrayRef<int> atomIndices = surfaceSel_.atomIndices();
563 for (int i = 0; i < surfaceSel_.posCount(); i++)
565 const int ii = atomIndices[i];
566 const int resind = atoms.atom[ii].resind;
568 if (!gmx_atomprop_query(aps, epropVDW,
569 *(atoms.resinfo[resind].name),
570 *(atoms.atomname[ii]), &radius))
574 radii_.push_back(radius + solsize_);
578 if (!gmx_atomprop_query(aps, epropDGsol,
579 *(atoms.resinfo[resind].name),
580 *(atoms.atomtype[ii]), &dgsFactor))
582 dgsFactor = dgsDefault_;
584 dgsFactor_.push_back(dgsFactor);
589 fprintf(stderr, "WARNING: could not find a Van der Waals radius for %d atoms\n", ndefault);
591 gmx_atomprop_destroy(aps);
593 // Pre-compute mapping from the output groups to the calculation group,
594 // and store it in the selection ID map for easy lookup.
595 for (size_t g = 0; g < outputSel_.size(); ++g)
597 ConstArrayRef<int> outputIndices = outputSel_[g].atomIndices();
598 for (int i = 0, j = 0; i < outputSel_[g].posCount(); ++i)
600 while (j < surfaceSel_.posCount() && outputIndices[i] > atomIndices[j])
604 if (j == surfaceSel_.posCount() || outputIndices[i] != atomIndices[j])
606 GMX_THROW(InconsistentInputError("Output selection is not a subset of the input selection"));
608 outputSel_[g].setOriginalId(i, j);
612 // Initialize all the output data objects and initialize the output plotters.
614 area_.setColumnCount(0, 1 + outputSel_.size());
616 AnalysisDataPlotModulePointer plotm(
617 new AnalysisDataPlotModule(settings.plotSettings()));
618 plotm->setFileName(fnArea_);
619 plotm->setTitle("Solvent Accessible Surface");
620 plotm->setXAxisIsTime();
621 plotm->setYLabel("Area (nm\\S2\\N)");
622 plotm->appendLegend("Total");
623 for (size_t i = 0; i < outputSel_.size(); ++i)
625 plotm->appendLegend(outputSel_[i].name());
627 area_.addModule(plotm);
632 atomArea_.setDataSetCount(1 + outputSel_.size());
633 residueArea_.setDataSetCount(1 + outputSel_.size());
634 for (size_t i = 0; i <= outputSel_.size(); ++i)
636 atomArea_.setColumnCount(i, surfaceSel_.posCount());
637 residueArea_.setColumnCount(i, resCount);
640 AnalysisDataAverageModulePointer avem(new AnalysisDataAverageModule);
641 for (int i = 0; i < surfaceSel_.posCount(); ++i)
643 avem->setXAxisValue(i, surfaceSel_.position(i).atomIndices()[0] + 1);
645 atomArea_.addModule(avem);
646 if (!fnAtomArea_.empty())
648 AnalysisDataPlotModulePointer plotm(
649 new AnalysisDataPlotModule(settings.plotSettings()));
650 plotm->setFileName(fnAtomArea_);
651 plotm->setTitle("Area per residue over the trajectory");
652 plotm->setXLabel("Atom");
653 plotm->setXFormat(8, 0);
654 plotm->setYLabel("Area (nm\\S2\\N)");
655 plotm->setErrorsAsSeparateColumn(true);
656 plotm->appendLegend("Average (nm\\S2\\N)");
657 plotm->appendLegend("Standard deviation (nm\\S2\\N)");
658 avem->addModule(plotm);
662 AnalysisDataAverageModulePointer avem(new AnalysisDataAverageModule);
663 for (int i = 0; i < surfaceSel_.posCount(); ++i)
665 const int atomIndex = surfaceSel_.position(i).atomIndices()[0];
666 const int residueIndex = atoms.atom[atomIndex].resind;
667 avem->setXAxisValue(i, atoms.resinfo[residueIndex].nr);
669 residueArea_.addModule(avem);
670 if (!fnResidueArea_.empty())
672 AnalysisDataPlotModulePointer plotm(
673 new AnalysisDataPlotModule(settings.plotSettings()));
674 plotm->setFileName(fnResidueArea_);
675 plotm->setTitle("Area per atom over the trajectory");
676 plotm->setXLabel("Residue");
677 plotm->setXFormat(8, 0);
678 plotm->setYLabel("Area (nm\\S2\\N)");
679 plotm->setErrorsAsSeparateColumn(true);
680 plotm->appendLegend("Average (nm\\S2\\N)");
681 plotm->appendLegend("Standard deviation (nm\\S2\\N)");
682 avem->addModule(plotm);
687 if (!fnDGSolv_.empty())
689 dgSolv_.setColumnCount(0, 1 + outputSel_.size());
690 AnalysisDataPlotModulePointer plotm(
691 new AnalysisDataPlotModule(settings.plotSettings()));
692 plotm->setFileName(fnDGSolv_);
693 plotm->setTitle("Free Energy of Solvation");
694 plotm->setXAxisIsTime();
695 plotm->setYLabel("D Gsolv");
696 plotm->appendLegend("Total");
697 for (size_t i = 0; i < outputSel_.size(); ++i)
699 plotm->appendLegend(outputSel_[i].name());
701 dgSolv_.addModule(plotm);
704 if (!fnVolume_.empty())
706 volume_.setColumnCount(0, 2);
707 AnalysisDataPlotModulePointer plotm(
708 new AnalysisDataPlotModule(settings.plotSettings()));
709 plotm->setFileName(fnVolume_);
710 plotm->setTitle("Volume and Density");
711 plotm->setXAxisIsTime();
712 plotm->appendLegend("Volume (nm\\S3\\N)");
713 plotm->appendLegend("Density (g/l)");
714 volume_.addModule(plotm);
719 * Temporary memory for use within a single-frame calculation.
721 class SasaModuleData : public TrajectoryAnalysisModuleData
725 * Reserves memory for the frame-local data.
727 * `residueCount` will be zero if per-residue data is not being
730 SasaModuleData(TrajectoryAnalysisModule *module,
731 const AnalysisDataParallelOptions &opt,
732 const SelectionCollection &selections,
733 int atomCount, int residueCount)
734 : TrajectoryAnalysisModuleData(module, opt, selections)
736 index_.reserve(atomCount);
737 // If the calculation group is not dynamic, pre-calculate
738 // the index, since it is not going to change.
739 for (int i = 0; i < atomCount; ++i)
743 atomAreas_.resize(atomCount);
744 res_a_.resize(residueCount);
747 virtual void finish() { finishDataHandles(); }
749 //! Indices of the calculation selection positions selected for the frame.
750 std::vector<int> index_;
752 * Atom areas for each calculation selection position for the frame.
754 * One entry for each position in the calculation group.
755 * Values for atoms not selected are set to zero.
757 std::vector<real> atomAreas_;
759 * Working array to accumulate areas for each residue.
761 * One entry for each distinct residue in the calculation group;
762 * indices are not directly residue numbers or residue indices.
764 * This vector is empty if residue area calculations are not being
767 std::vector<real> res_a_;
770 TrajectoryAnalysisModuleDataPointer Sasa::startFrames(
771 const AnalysisDataParallelOptions &opt,
772 const SelectionCollection &selections)
774 return TrajectoryAnalysisModuleDataPointer(
775 new SasaModuleData(this, opt, selections, surfaceSel_.posCount(),
776 residueArea_.columnCount(0)));
780 * Helper method to compute the areas for a single selection.
782 * \param[in] surfaceSel The calculation selection.
783 * \param[in] sel The selection to compute the areas for (can be
784 * `surfaceSel` or one of the output selections).
785 * \param[in] atomAreas Atom areas for each position in `surfaceSel`.
786 * \param[in] dgsFactor Free energy coefficients for each position in
787 * `surfaceSel`. If empty, free energies are not calculated.
788 * \param[out] totalAreaOut Total area of `sel` (sum of atom areas it selects).
789 * \param[out] dgsolvOut Solvation free energy.
790 * Will be zero of `dgsFactor` is empty.
791 * \param atomAreaHandle Data handle to use for storing atom areas for `sel`.
792 * \param resAreaHandle Data handle to use for storing residue areas for `sel`.
793 * \param resAreaWork Work array for accumulating the residue areas.
794 * If empty, atom and residue areas are not calculated.
796 * `atomAreaHandle` and `resAreaHandle` are not used if `resAreaWork` is empty.
798 void computeAreas(const Selection &surfaceSel, const Selection &sel,
799 const std::vector<real> &atomAreas,
800 const std::vector<real> &dgsFactor,
801 real *totalAreaOut, real *dgsolvOut,
802 AnalysisDataHandle atomAreaHandle,
803 AnalysisDataHandle resAreaHandle,
804 std::vector<real> *resAreaWork)
806 const bool bResAt = !resAreaWork->empty();
807 const bool bDGsolv = !dgsFactor.empty();
813 std::fill(resAreaWork->begin(), resAreaWork->end(),
814 static_cast<real>(0.0));
816 for (int i = 0; i < sel.posCount(); ++i)
818 // Get the index of the atom in the calculation group.
819 // For the output groups, the mapping has been precalculated in
821 const int ii = (sel != surfaceSel ? sel.position(i).mappedId() : i);
822 if (!surfaceSel.position(ii).selected())
824 // For the calculation group, skip unselected atoms.
825 if (sel == surfaceSel)
829 GMX_THROW(InconsistentInputError("Output selection is not a subset of the surface selection"));
831 // Get the internal index of the matching residue.
832 // These have been precalculated in initAnalysis().
833 const int ri = surfaceSel.position(ii).mappedId();
834 const real atomArea = atomAreas[ii];
835 totalArea += atomArea;
838 atomAreaHandle.setPoint(ii, atomArea);
839 (*resAreaWork)[ri] += atomArea;
843 dgsolv += atomArea * dgsFactor[ii];
848 for (size_t i = 0; i < (*resAreaWork).size(); ++i)
850 resAreaHandle.setPoint(i, (*resAreaWork)[i]);
853 *totalAreaOut = totalArea;
858 Sasa::analyzeFrame(int frnr, const t_trxframe &fr, t_pbc *pbc,
859 TrajectoryAnalysisModuleData *pdata)
861 AnalysisDataHandle ah = pdata->dataHandle(area_);
862 AnalysisDataHandle dgh = pdata->dataHandle(dgSolv_);
863 AnalysisDataHandle aah = pdata->dataHandle(atomArea_);
864 AnalysisDataHandle rah = pdata->dataHandle(residueArea_);
865 AnalysisDataHandle vh = pdata->dataHandle(volume_);
866 const Selection &surfaceSel = pdata->parallelSelection(surfaceSel_);
867 const SelectionList &outputSel = pdata->parallelSelections(outputSel_);
868 SasaModuleData &frameData = *static_cast<SasaModuleData *>(pdata);
870 const bool bResAt = !frameData.res_a_.empty();
871 const bool bDGsol = !dgsFactor_.empty();
872 const bool bConnolly = (frnr == 0 && !fnConnolly_.empty());
874 // Update indices of selected atoms in the work array.
875 if (surfaceSel.isDynamic())
877 frameData.index_.clear();
878 for (int i = 0; i < surfaceSel.posCount(); ++i)
880 if (surfaceSel.position(i).selected())
882 frameData.index_.push_back(i);
887 // Determine what needs to be calculated.
889 if (bResAt || bDGsol || !outputSel.empty())
891 flag |= FLAG_ATOM_AREA;
897 if (volume_.columnCount() > 0)
902 // Do the low-level calculation.
903 // totarea and totvolume receive the values for the calculation group.
904 // area array contains the per-atom areas for the selected positions.
905 // surfacedots contains nsurfacedots entries, and contains the actual
907 real totarea, totvolume;
908 real *area = NULL, *surfacedots = NULL;
910 int retval = nsc_dclm_pbc(surfaceSel.coordinates().data(), &radii_[0],
911 frameData.index_.size(), ndots_, flag, &totarea,
912 &area, &totvolume, &surfacedots, &nsurfacedots,
913 &frameData.index_[0],
914 pbc != NULL ? pbc->ePBC : epbcNONE,
915 pbc != NULL ? pbc->box : NULL);
916 // Unpack the atomwise areas into the frameData.atomAreas_ array for easier
917 // indexing in the case of dynamic surfaceSel.
920 if (surfaceSel.isDynamic())
922 std::fill(frameData.atomAreas_.begin(), frameData.atomAreas_.end(),
923 static_cast<real>(0.0));
924 for (size_t i = 0; i < frameData.index_.size(); ++i)
926 frameData.atomAreas_[frameData.index_[i]] = area[i];
931 std::copy(area, area + surfaceSel.posCount(),
932 frameData.atomAreas_.begin());
936 scoped_guard_sfree dotsGuard(surfacedots);
939 GMX_THROW(InternalError("nsc_dclm_pbc failed"));
944 // This is somewhat nasty, as it modifies the atoms and symtab
945 // structures. But since it is only used in the first frame, and no
946 // one else uses the topology after initialization, it may just work
947 // even with future parallelization.
948 connolly_plot(fnConnolly_.c_str(),
949 nsurfacedots, surfacedots, fr.x, &top_->atoms,
950 &top_->symtab, fr.ePBC, fr.box, bIncludeSolute_);
953 ah.startFrame(frnr, fr.time);
956 aah.startFrame(frnr, fr.time);
957 rah.startFrame(frnr, fr.time);
961 dgh.startFrame(frnr, fr.time);
964 ah.setPoint(0, totarea);
966 real totalArea, dgsolv;
967 if (bResAt || bDGsol)
969 computeAreas(surfaceSel, surfaceSel, frameData.atomAreas_, dgsFactor_,
970 &totalArea, &dgsolv, aah, rah, &frameData.res_a_);
973 dgh.setPoint(0, dgsolv);
976 for (size_t g = 0; g < outputSel.size(); ++g)
980 aah.selectDataSet(g + 1);
981 rah.selectDataSet(g + 1);
983 computeAreas(surfaceSel, outputSel[g], frameData.atomAreas_, dgsFactor_,
984 &totalArea, &dgsolv, aah, rah, &frameData.res_a_);
985 ah.setPoint(g + 1, totalArea);
988 dgh.setPoint(g + 1, dgsolv);
1006 for (int i = 0; i < surfaceSel.posCount(); ++i)
1008 totmass += surfaceSel.position(i).mass();
1010 const real density = totmass*AMU/(totvolume*NANO*NANO*NANO);
1011 vh.startFrame(frnr, fr.time);
1012 vh.setPoint(0, totvolume);
1013 vh.setPoint(1, density);
1019 Sasa::finishAnalysis(int /*nframes*/)
1023 // fp3 = ftp2FILE(efITP, nfile, fnm, "w");
1024 // fprintf(fp3, "[ position_restraints ]\n"
1025 // "#define FCX 1000\n"
1026 // "#define FCY 1000\n"
1027 // "#define FCZ 1000\n"
1028 // "; Atom Type fx fy fz\n");
1029 // for (i = 0; i < nx[0]; i++)
1031 // if (atom_area[i] > minarea)
1033 // fprintf(fp3, "%5d 1 FCX FCX FCZ\n", ii+1);
1049 const char SasaInfo::name[] = "sasa";
1050 const char SasaInfo::shortDescription[] =
1051 "Compute solvent accessible surface area";
1053 TrajectoryAnalysisModulePointer SasaInfo::create()
1055 return TrajectoryAnalysisModulePointer(new Sasa);
1058 } // namespace analysismodules