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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_;
390 //! Calculation algorithm.
391 SurfaceAreaCalculator calculator_;
393 // Copy and assign disallowed by base.
397 : TrajectoryAnalysisModule(SasaInfo::name, SasaInfo::shortDescription),
398 solsize_(0.14), ndots_(24), dgsDefault_(0), bIncludeSolute_(true), top_(NULL)
401 registerAnalysisDataset(&area_, "area");
402 registerAnalysisDataset(&atomArea_, "atomarea");
403 registerAnalysisDataset(&residueArea_, "resarea");
404 registerAnalysisDataset(&dgSolv_, "dgsolv");
405 registerAnalysisDataset(&volume_, "volume");
409 Sasa::initOptions(Options *options, TrajectoryAnalysisSettings *settings)
411 static const char *const desc[] = {
412 "[THISMODULE] computes solvent accessible surface areas.",
413 "See Eisenhaber F, Lijnzaad P, Argos P, Sander C, & Scharf M",
414 "(1995) J. Comput. Chem. 16, 273-284 for the algorithm used.",
415 "With [TT]-q[tt], the Connolly surface can be generated as well",
416 "in a [REF].pdb[ref] file where the nodes are represented as atoms",
417 "and the edges connecting the nearest nodes as CONECT records.",
418 "[TT]-odg[tt] allows for estimation of solvation free energies",
419 "from per-atom solvation energies per exposed surface area.[PAR]",
421 "The program requires a selection for the surface calculation to be",
422 "specified with [TT]-surface[tt]. This should always consist of all",
423 "non-solvent atoms in the system. The area of this group is always",
424 "calculated. Optionally, [TT]-output[tt] can specify additional",
425 "selections, which should be subsets of the calculation group.",
426 "The solvent-accessible areas for these groups are also extracted",
427 "from the full surface.[PAR]",
429 "The average and standard deviation of the area over the trajectory",
430 "can be calculated per residue and atom (options [TT]-or[tt] and",
431 "[TT]-oa[tt]).[PAR]",
432 //"In combination with the latter option an [REF].itp[ref] file can be",
433 //"generated (option [TT]-i[tt])",
434 //"which can be used to restrain surface atoms.[PAR]",
436 "With the [TT]-tv[tt] option the total volume and density of the",
437 "molecule can be computed. With [TT]-pbc[tt] (the default), you",
438 "must ensure that your molecule/surface group is not split across PBC.",
439 "Otherwise, you will get non-sensical results.",
440 "Please also consider whether the normal probe radius is appropriate",
441 "in this case or whether you would rather use, e.g., 0. It is good",
442 "to keep in mind that the results for volume and density are very",
443 "approximate. For example, in ice Ih, one can easily fit water molecules in the",
444 "pores which would yield a volume that is too low, and surface area and density",
445 "that are both too high."
448 settings->setHelpText(desc);
450 options->addOption(FileNameOption("o").filetype(eftPlot).outputFile().required()
451 .store(&fnArea_).defaultBasename("area")
452 .description("Total area as a function of time"));
453 options->addOption(FileNameOption("odg").filetype(eftPlot).outputFile()
454 .store(&fnDGSolv_).defaultBasename("dgsolv")
455 .description("Estimated solvation free energy as a function of time"));
456 options->addOption(FileNameOption("or").filetype(eftPlot).outputFile()
457 .store(&fnResidueArea_).defaultBasename("resarea")
458 .description("Average area per residue"));
459 options->addOption(FileNameOption("oa").filetype(eftPlot).outputFile()
460 .store(&fnAtomArea_).defaultBasename("atomarea")
461 .description("Average area per atom"));
462 options->addOption(FileNameOption("tv").filetype(eftPlot).outputFile()
463 .store(&fnVolume_).defaultBasename("volume")
464 .description("Total volume and density as a function of time"));
465 options->addOption(FileNameOption("q").filetype(eftPDB).outputFile()
466 .store(&fnConnolly_).defaultBasename("connolly")
467 .description("PDB file for Connolly surface"));
468 //options->addOption(FileNameOption("i").filetype(eftITP).outputFile()
469 // .store(&fnRestraints_).defaultBasename("surfat")
470 // .description("Topology file for position restraings on surface atoms"));
473 options->addOption(DoubleOption("probe").store(&solsize_)
474 .description("Radius of the solvent probe (nm)"));
475 options->addOption(IntegerOption("ndots").store(&ndots_)
476 .description("Number of dots per sphere, more dots means more accuracy"));
477 //options->addOption(DoubleOption("minarea").store(&minarea_)
478 // .description("The minimum area (nm^2) to count an atom as a surface atom when writing a position restraint file (see help)"));
479 options->addOption(BooleanOption("prot").store(&bIncludeSolute_)
480 .description("Output the protein to the Connolly [REF].pdb[ref] file too"));
481 options->addOption(DoubleOption("dgs").store(&dgsDefault_)
482 .description("Default value for solvation free energy per area (kJ/mol/nm^2)"));
484 // Selections must select atoms for the VdW radii lookup to work.
485 // The calculation group uses dynamicMask() so that the coordinates
486 // match a static array of VdW radii.
487 options->addOption(SelectionOption("surface").store(&surfaceSel_)
488 .required().onlyAtoms().dynamicMask()
489 .description("Surface calculation selection"));
490 options->addOption(SelectionOption("output").storeVector(&outputSel_)
491 .onlyAtoms().multiValue()
492 .description("Output selection(s)"));
494 // Atom names etc. are required for the VdW radii lookup.
495 settings->setFlag(TrajectoryAnalysisSettings::efRequireTop);
499 Sasa::initAnalysis(const TrajectoryAnalysisSettings &settings,
500 const TopologyInformation &top)
502 const t_atoms &atoms = top.topology()->atoms;
503 top_ = top.topology();
505 //bITP = opt2bSet("-i", nfile, fnm);
507 !fnResidueArea_.empty() || !fnAtomArea_.empty(); // || bITP;
508 const bool bDGsol = !fnDGSolv_.empty();
513 fprintf(stderr, "Probe size too small, setting it to %g\n", solsize_);
518 fprintf(stderr, "Ndots too small, setting it to %d\n", ndots_);
521 please_cite(stderr, "Eisenhaber95");
522 //if ((top.ePBC() != epbcXYZ) || (TRICLINIC(fr.box)))
524 // fprintf(stderr, "\n\nWARNING: non-rectangular boxes may give erroneous results or crashes.\n"
525 // "Analysis based on vacuum simulations (with the possibility of evaporation)\n"
526 // "will certainly crash the analysis.\n\n");
531 if (!top.hasFullTopology())
533 GMX_THROW(InconsistentInputError("Cannot compute Delta G of solvation without a tpr file"));
537 if (strcmp(*(atoms.atomtype[0]), "?") == 0)
539 GMX_THROW(InconsistentInputError("Your input tpr file is too old (does not contain atom types). Cannot not compute Delta G of solvation"));
543 printf("Free energy of solvation predictions:\n");
544 please_cite(stdout, "Eisenberg86a");
549 // Now compute atomic radii including solvent probe size.
550 // Also, fetch solvation free energy coefficients and
551 // compute the residue indices that map the calculation atoms
552 // to the columns of residueArea_.
553 radii_.reserve(surfaceSel_.posCount());
556 dgsFactor_.reserve(surfaceSel_.posCount());
559 const int resCount = surfaceSel_.initOriginalIdsToGroup(top_, INDEX_RES);
561 // TODO: Not exception-safe, but nice solution would be to have a C++
562 // atom properties class...
563 gmx_atomprop_t aps = gmx_atomprop_init();
565 ConstArrayRef<int> atomIndices = surfaceSel_.atomIndices();
567 for (int i = 0; i < surfaceSel_.posCount(); i++)
569 const int ii = atomIndices[i];
570 const int resind = atoms.atom[ii].resind;
572 if (!gmx_atomprop_query(aps, epropVDW,
573 *(atoms.resinfo[resind].name),
574 *(atoms.atomname[ii]), &radius))
578 radii_.push_back(radius + solsize_);
582 if (!gmx_atomprop_query(aps, epropDGsol,
583 *(atoms.resinfo[resind].name),
584 *(atoms.atomtype[ii]), &dgsFactor))
586 dgsFactor = dgsDefault_;
588 dgsFactor_.push_back(dgsFactor);
593 fprintf(stderr, "WARNING: could not find a Van der Waals radius for %d atoms\n", ndefault);
595 gmx_atomprop_destroy(aps);
597 // Pre-compute mapping from the output groups to the calculation group,
598 // and store it in the selection ID map for easy lookup.
599 for (size_t g = 0; g < outputSel_.size(); ++g)
601 ConstArrayRef<int> outputIndices = outputSel_[g].atomIndices();
602 for (int i = 0, j = 0; i < outputSel_[g].posCount(); ++i)
604 while (j < surfaceSel_.posCount() && outputIndices[i] > atomIndices[j])
608 if (j == surfaceSel_.posCount() || outputIndices[i] != atomIndices[j])
610 GMX_THROW(InconsistentInputError("Output selection is not a subset of the input selection"));
612 outputSel_[g].setOriginalId(i, j);
616 calculator_.setDotCount(ndots_);
617 calculator_.setRadii(radii_);
619 // Initialize all the output data objects and initialize the output plotters.
621 area_.setColumnCount(0, 1 + outputSel_.size());
623 AnalysisDataPlotModulePointer plotm(
624 new AnalysisDataPlotModule(settings.plotSettings()));
625 plotm->setFileName(fnArea_);
626 plotm->setTitle("Solvent Accessible Surface");
627 plotm->setXAxisIsTime();
628 plotm->setYLabel("Area (nm\\S2\\N)");
629 plotm->appendLegend("Total");
630 for (size_t i = 0; i < outputSel_.size(); ++i)
632 plotm->appendLegend(outputSel_[i].name());
634 area_.addModule(plotm);
639 atomArea_.setDataSetCount(1 + outputSel_.size());
640 residueArea_.setDataSetCount(1 + outputSel_.size());
641 for (size_t i = 0; i <= outputSel_.size(); ++i)
643 atomArea_.setColumnCount(i, surfaceSel_.posCount());
644 residueArea_.setColumnCount(i, resCount);
647 AnalysisDataAverageModulePointer avem(new AnalysisDataAverageModule);
648 for (int i = 0; i < surfaceSel_.posCount(); ++i)
650 avem->setXAxisValue(i, surfaceSel_.position(i).atomIndices()[0] + 1);
652 atomArea_.addModule(avem);
653 if (!fnAtomArea_.empty())
655 AnalysisDataPlotModulePointer plotm(
656 new AnalysisDataPlotModule(settings.plotSettings()));
657 plotm->setFileName(fnAtomArea_);
658 plotm->setTitle("Area per atom over the trajectory");
659 plotm->setXLabel("Atom");
660 plotm->setXFormat(8, 0);
661 plotm->setYLabel("Area (nm\\S2\\N)");
662 plotm->setErrorsAsSeparateColumn(true);
663 plotm->appendLegend("Average (nm\\S2\\N)");
664 plotm->appendLegend("Standard deviation (nm\\S2\\N)");
665 avem->addModule(plotm);
669 AnalysisDataAverageModulePointer avem(new AnalysisDataAverageModule);
672 for (int i = 0; i < surfaceSel_.posCount(); ++i)
674 const int atomIndex = surfaceSel_.position(i).atomIndices()[0];
675 const int residueIndex = atoms.atom[atomIndex].resind;
676 if (residueIndex != prevResind)
678 avem->setXAxisValue(row, atoms.resinfo[residueIndex].nr);
679 prevResind = residueIndex;
683 residueArea_.addModule(avem);
684 if (!fnResidueArea_.empty())
686 AnalysisDataPlotModulePointer plotm(
687 new AnalysisDataPlotModule(settings.plotSettings()));
688 plotm->setFileName(fnResidueArea_);
689 plotm->setTitle("Area per residue over the trajectory");
690 plotm->setXLabel("Residue");
691 plotm->setXFormat(8, 0);
692 plotm->setYLabel("Area (nm\\S2\\N)");
693 plotm->setErrorsAsSeparateColumn(true);
694 plotm->appendLegend("Average (nm\\S2\\N)");
695 plotm->appendLegend("Standard deviation (nm\\S2\\N)");
696 avem->addModule(plotm);
701 if (!fnDGSolv_.empty())
703 dgSolv_.setColumnCount(0, 1 + outputSel_.size());
704 AnalysisDataPlotModulePointer plotm(
705 new AnalysisDataPlotModule(settings.plotSettings()));
706 plotm->setFileName(fnDGSolv_);
707 plotm->setTitle("Free Energy of Solvation");
708 plotm->setXAxisIsTime();
709 plotm->setYLabel("D Gsolv");
710 plotm->appendLegend("Total");
711 for (size_t i = 0; i < outputSel_.size(); ++i)
713 plotm->appendLegend(outputSel_[i].name());
715 dgSolv_.addModule(plotm);
718 if (!fnVolume_.empty())
720 volume_.setColumnCount(0, 2);
721 AnalysisDataPlotModulePointer plotm(
722 new AnalysisDataPlotModule(settings.plotSettings()));
723 plotm->setFileName(fnVolume_);
724 plotm->setTitle("Volume and Density");
725 plotm->setXAxisIsTime();
726 plotm->appendLegend("Volume (nm\\S3\\N)");
727 plotm->appendLegend("Density (g/l)");
728 volume_.addModule(plotm);
733 * Temporary memory for use within a single-frame calculation.
735 class SasaModuleData : public TrajectoryAnalysisModuleData
739 * Reserves memory for the frame-local data.
741 * `residueCount` will be zero if per-residue data is not being
744 SasaModuleData(TrajectoryAnalysisModule *module,
745 const AnalysisDataParallelOptions &opt,
746 const SelectionCollection &selections,
747 int atomCount, int residueCount)
748 : TrajectoryAnalysisModuleData(module, opt, selections)
750 index_.reserve(atomCount);
751 // If the calculation group is not dynamic, pre-calculate
752 // the index, since it is not going to change.
753 for (int i = 0; i < atomCount; ++i)
757 atomAreas_.resize(atomCount);
758 res_a_.resize(residueCount);
761 virtual void finish() { finishDataHandles(); }
763 //! Indices of the calculation selection positions selected for the frame.
764 std::vector<int> index_;
766 * Atom areas for each calculation selection position for the frame.
768 * One entry for each position in the calculation group.
769 * Values for atoms not selected are set to zero.
771 std::vector<real> atomAreas_;
773 * Working array to accumulate areas for each residue.
775 * One entry for each distinct residue in the calculation group;
776 * indices are not directly residue numbers or residue indices.
778 * This vector is empty if residue area calculations are not being
781 std::vector<real> res_a_;
784 TrajectoryAnalysisModuleDataPointer Sasa::startFrames(
785 const AnalysisDataParallelOptions &opt,
786 const SelectionCollection &selections)
788 return TrajectoryAnalysisModuleDataPointer(
789 new SasaModuleData(this, opt, selections, surfaceSel_.posCount(),
790 residueArea_.columnCount(0)));
794 * Helper method to compute the areas for a single selection.
796 * \param[in] surfaceSel The calculation selection.
797 * \param[in] sel The selection to compute the areas for (can be
798 * `surfaceSel` or one of the output selections).
799 * \param[in] atomAreas Atom areas for each position in `surfaceSel`.
800 * \param[in] dgsFactor Free energy coefficients for each position in
801 * `surfaceSel`. If empty, free energies are not calculated.
802 * \param[out] totalAreaOut Total area of `sel` (sum of atom areas it selects).
803 * \param[out] dgsolvOut Solvation free energy.
804 * Will be zero of `dgsFactor` is empty.
805 * \param atomAreaHandle Data handle to use for storing atom areas for `sel`.
806 * \param resAreaHandle Data handle to use for storing residue areas for `sel`.
807 * \param resAreaWork Work array for accumulating the residue areas.
808 * If empty, atom and residue areas are not calculated.
810 * `atomAreaHandle` and `resAreaHandle` are not used if `resAreaWork` is empty.
812 void computeAreas(const Selection &surfaceSel, const Selection &sel,
813 const std::vector<real> &atomAreas,
814 const std::vector<real> &dgsFactor,
815 real *totalAreaOut, real *dgsolvOut,
816 AnalysisDataHandle atomAreaHandle,
817 AnalysisDataHandle resAreaHandle,
818 std::vector<real> *resAreaWork)
820 const bool bResAt = !resAreaWork->empty();
821 const bool bDGsolv = !dgsFactor.empty();
827 std::fill(resAreaWork->begin(), resAreaWork->end(),
828 static_cast<real>(0.0));
830 for (int i = 0; i < sel.posCount(); ++i)
832 // Get the index of the atom in the calculation group.
833 // For the output groups, the mapping has been precalculated in
835 const int ii = (sel != surfaceSel ? sel.position(i).mappedId() : i);
836 if (!surfaceSel.position(ii).selected())
838 // For the calculation group, skip unselected atoms.
839 if (sel == surfaceSel)
843 GMX_THROW(InconsistentInputError("Output selection is not a subset of the surface selection"));
845 // Get the internal index of the matching residue.
846 // These have been precalculated in initAnalysis().
847 const int ri = surfaceSel.position(ii).mappedId();
848 const real atomArea = atomAreas[ii];
849 totalArea += atomArea;
852 atomAreaHandle.setPoint(ii, atomArea);
853 (*resAreaWork)[ri] += atomArea;
857 dgsolv += atomArea * dgsFactor[ii];
862 for (size_t i = 0; i < (*resAreaWork).size(); ++i)
864 resAreaHandle.setPoint(i, (*resAreaWork)[i]);
867 *totalAreaOut = totalArea;
872 Sasa::analyzeFrame(int frnr, const t_trxframe &fr, t_pbc *pbc,
873 TrajectoryAnalysisModuleData *pdata)
875 AnalysisDataHandle ah = pdata->dataHandle(area_);
876 AnalysisDataHandle dgh = pdata->dataHandle(dgSolv_);
877 AnalysisDataHandle aah = pdata->dataHandle(atomArea_);
878 AnalysisDataHandle rah = pdata->dataHandle(residueArea_);
879 AnalysisDataHandle vh = pdata->dataHandle(volume_);
880 const Selection &surfaceSel = pdata->parallelSelection(surfaceSel_);
881 const SelectionList &outputSel = pdata->parallelSelections(outputSel_);
882 SasaModuleData &frameData = *static_cast<SasaModuleData *>(pdata);
884 const bool bResAt = !frameData.res_a_.empty();
885 const bool bDGsol = !dgsFactor_.empty();
886 const bool bConnolly = (frnr == 0 && !fnConnolly_.empty());
888 // Update indices of selected atoms in the work array.
889 if (surfaceSel.isDynamic())
891 frameData.index_.clear();
892 for (int i = 0; i < surfaceSel.posCount(); ++i)
894 if (surfaceSel.position(i).selected())
896 frameData.index_.push_back(i);
901 // Determine what needs to be calculated.
903 if (bResAt || bDGsol || !outputSel.empty())
905 flag |= FLAG_ATOM_AREA;
911 if (volume_.columnCount() > 0)
916 // Do the low-level calculation.
917 // totarea and totvolume receive the values for the calculation group.
918 // area array contains the per-atom areas for the selected positions.
919 // surfacedots contains nsurfacedots entries, and contains the actual
921 real totarea, totvolume;
922 real *area = NULL, *surfacedots = NULL;
924 calculator_.calculate(surfaceSel.coordinates().data(), pbc,
925 frameData.index_.size(), &frameData.index_[0], flag,
926 &totarea, &totvolume, &area,
927 &surfacedots, &nsurfacedots);
928 // Unpack the atomwise areas into the frameData.atomAreas_ array for easier
929 // indexing in the case of dynamic surfaceSel.
932 if (surfaceSel.isDynamic())
934 std::fill(frameData.atomAreas_.begin(), frameData.atomAreas_.end(),
935 static_cast<real>(0.0));
936 for (size_t i = 0; i < frameData.index_.size(); ++i)
938 frameData.atomAreas_[frameData.index_[i]] = area[i];
943 std::copy(area, area + surfaceSel.posCount(),
944 frameData.atomAreas_.begin());
948 scoped_guard_sfree dotsGuard(surfacedots);
952 // This is somewhat nasty, as it modifies the atoms and symtab
953 // structures. But since it is only used in the first frame, and no
954 // one else uses the topology after initialization, it may just work
955 // even with future parallelization.
956 connolly_plot(fnConnolly_.c_str(),
957 nsurfacedots, surfacedots, fr.x, &top_->atoms,
958 &top_->symtab, fr.ePBC, fr.box, bIncludeSolute_);
961 ah.startFrame(frnr, fr.time);
964 aah.startFrame(frnr, fr.time);
965 rah.startFrame(frnr, fr.time);
969 dgh.startFrame(frnr, fr.time);
972 ah.setPoint(0, totarea);
974 real totalArea, dgsolv;
975 if (bResAt || bDGsol)
977 computeAreas(surfaceSel, surfaceSel, frameData.atomAreas_, dgsFactor_,
978 &totalArea, &dgsolv, aah, rah, &frameData.res_a_);
981 dgh.setPoint(0, dgsolv);
984 for (size_t g = 0; g < outputSel.size(); ++g)
988 aah.selectDataSet(g + 1);
989 rah.selectDataSet(g + 1);
991 computeAreas(surfaceSel, outputSel[g], frameData.atomAreas_, dgsFactor_,
992 &totalArea, &dgsolv, aah, rah, &frameData.res_a_);
993 ah.setPoint(g + 1, totalArea);
996 dgh.setPoint(g + 1, dgsolv);
1014 for (int i = 0; i < surfaceSel.posCount(); ++i)
1016 totmass += surfaceSel.position(i).mass();
1018 const real density = totmass*AMU/(totvolume*NANO*NANO*NANO);
1019 vh.startFrame(frnr, fr.time);
1020 vh.setPoint(0, totvolume);
1021 vh.setPoint(1, density);
1027 Sasa::finishAnalysis(int /*nframes*/)
1031 // fp3 = ftp2FILE(efITP, nfile, fnm, "w");
1032 // fprintf(fp3, "[ position_restraints ]\n"
1033 // "#define FCX 1000\n"
1034 // "#define FCY 1000\n"
1035 // "#define FCZ 1000\n"
1036 // "; Atom Type fx fy fz\n");
1037 // for (i = 0; i < nx[0]; i++)
1039 // if (atom_area[i] > minarea)
1041 // fprintf(fp3, "%5d 1 FCX FCX FCZ\n", ii+1);
1057 const char SasaInfo::name[] = "sasa";
1058 const char SasaInfo::shortDescription[] =
1059 "Compute solvent accessible surface area";
1061 TrajectoryAnalysisModulePointer SasaInfo::create()
1063 return TrajectoryAnalysisModulePointer(new Sasa);
1066 } // namespace analysismodules