/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2012,2013, by the GROMACS development team, led by
- * David van der Spoel, Berk Hess, Erik Lindahl, and including many
- * others, as listed in the AUTHORS file in the top-level source
- * directory and at http://www.gromacs.org.
+ * Copyright (c) 2010,2011,2012,2013,2014,2015, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
*
* GROMACS is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public License
*/
#include "distance.h"
+#include <string>
+
#include "gromacs/legacyheaders/pbc.h"
#include "gromacs/legacyheaders/vec.h"
#include "gromacs/analysisdata/analysisdata.h"
+#include "gromacs/analysisdata/modules/average.h"
+#include "gromacs/analysisdata/modules/histogram.h"
#include "gromacs/analysisdata/modules/plot.h"
#include "gromacs/options/basicoptions.h"
#include "gromacs/options/filenameoption.h"
#include "gromacs/selection/selection.h"
#include "gromacs/selection/selectionoption.h"
#include "gromacs/trajectoryanalysis/analysissettings.h"
+#include "gromacs/utility/arrayref.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/stringutil.h"
namespace analysismodules
{
-const char Distance::name[] = "distance";
-const char Distance::shortDescription[] =
- "Calculate distances";
+namespace
+{
-Distance::Distance()
- : TrajectoryAnalysisModule(name, shortDescription),
- avem_(new AnalysisDataAverageModule())
+class Distance : public TrajectoryAnalysisModule
{
- data_.setColumnCount(0, 4);
- registerAnalysisDataset(&data_, "distance");
-}
+ public:
+ Distance();
+
+ virtual void initOptions(Options *options,
+ TrajectoryAnalysisSettings *settings);
+ virtual void initAnalysis(const TrajectoryAnalysisSettings &settings,
+ const TopologyInformation &top);
+
+ virtual void analyzeFrame(int frnr, const t_trxframe &fr, t_pbc *pbc,
+ TrajectoryAnalysisModuleData *pdata);
+ virtual void finishAnalysis(int nframes);
+ virtual void writeOutput();
-Distance::~Distance()
+ private:
+ SelectionList sel_;
+ std::string fnAverage_;
+ std::string fnAll_;
+ std::string fnXYZ_;
+ std::string fnHistogram_;
+ std::string fnAllStats_;
+ double meanLength_;
+ double lengthDev_;
+ double binWidth_;
+
+ AnalysisData distances_;
+ AnalysisData xyz_;
+ AnalysisDataAverageModulePointer summaryStatsModule_;
+ AnalysisDataAverageModulePointer allStatsModule_;
+ AnalysisDataFrameAverageModulePointer averageModule_;
+ AnalysisDataSimpleHistogramModulePointer histogramModule_;
+
+ // Copy and assign disallowed by base.
+};
+
+Distance::Distance()
+ : TrajectoryAnalysisModule(DistanceInfo::name, DistanceInfo::shortDescription),
+ meanLength_(0.1), lengthDev_(1.0), binWidth_(0.001)
{
+ summaryStatsModule_.reset(new AnalysisDataAverageModule());
+ summaryStatsModule_->setAverageDataSets(true);
+ distances_.addModule(summaryStatsModule_);
+ allStatsModule_.reset(new AnalysisDataAverageModule());
+ distances_.addModule(allStatsModule_);
+ averageModule_.reset(new AnalysisDataFrameAverageModule());
+ distances_.addModule(averageModule_);
+ histogramModule_.reset(new AnalysisDataSimpleHistogramModule());
+ distances_.addModule(histogramModule_);
+
+ registerAnalysisDataset(&distances_, "dist");
+ registerAnalysisDataset(&xyz_, "xyz");
+ registerBasicDataset(summaryStatsModule_.get(), "stats");
+ registerBasicDataset(allStatsModule_.get(), "allstats");
+ registerBasicDataset(averageModule_.get(), "average");
+ registerBasicDataset(&histogramModule_->averager(), "histogram");
}
Distance::initOptions(Options *options, TrajectoryAnalysisSettings * /*settings*/)
{
static const char *const desc[] = {
- "g_dist can calculate the distance between two positions as",
- "a function of time. The total distance and its",
- "x, y and z components are plotted."
+ "[THISMODULE] calculates distances between pairs of positions",
+ "as a function of time. Each selection specifies an independent set",
+ "of distances to calculate. Each selection should consist of pairs",
+ "of positions, and the distances are computed between positions 1-2,",
+ "3-4, etc.[PAR]",
+ "[TT]-oav[tt] writes the average distance as a function of time for",
+ "each selection.",
+ "[TT]-oall[tt] writes all the individual distances.",
+ "[TT]-oxyz[tt] does the same, but the x, y, and z components of the",
+ "distance are written instead of the norm.",
+ "[TT]-oh[tt] writes a histogram of the distances for each selection.",
+ "The location of the histogram is set with [TT]-len[tt] and",
+ "[TT]-tol[tt]. Bin width is set with [TT]-binw[tt].",
+ "[TT]-oallstat[tt] writes out the average and standard deviation for",
+ "each individual distance, calculated over the frames."
};
- options->setDescription(concatenateStrings(desc));
+ options->setDescription(desc);
- options->addOption(FileNameOption("o").filetype(eftPlot).outputFile()
- .store(&fnDist_).defaultBasename("dist")
- .description("Computed distances"));
- options->addOption(SelectionOption("select").required().valueCount(2)
- .store(sel_));
+ options->addOption(FileNameOption("oav").filetype(eftPlot).outputFile()
+ .store(&fnAverage_).defaultBasename("distave")
+ .description("Average distances as function of time"));
+ options->addOption(FileNameOption("oall").filetype(eftPlot).outputFile()
+ .store(&fnAll_).defaultBasename("dist")
+ .description("All distances as function of time"));
+ options->addOption(FileNameOption("oxyz").filetype(eftPlot).outputFile()
+ .store(&fnXYZ_).defaultBasename("distxyz")
+ .description("Distance components as function of time"));
+ options->addOption(FileNameOption("oh").filetype(eftPlot).outputFile()
+ .store(&fnHistogram_).defaultBasename("disthist")
+ .description("Histogram of the distances"));
+ options->addOption(FileNameOption("oallstat").filetype(eftPlot).outputFile()
+ .store(&fnAllStats_).defaultBasename("diststat")
+ .description("Statistics for individual distances"));
+ options->addOption(SelectionOption("select").storeVector(&sel_)
+ .required().dynamicMask().multiValue()
+ .description("Position pairs to calculate distances for"));
+ // TODO: Extend the histogramming implementation to allow automatic
+ // extension of the histograms to cover the data, removing the need for
+ // the first two options.
+ options->addOption(DoubleOption("len").store(&meanLength_)
+ .description("Mean distance for histogramming"));
+ options->addOption(DoubleOption("tol").store(&lengthDev_)
+ .description("Width of full distribution as fraction of [TT]-len[tt]"));
+ options->addOption(DoubleOption("binw").store(&binWidth_)
+ .description("Bin width for histogramming"));
+}
+
+
+/*! \brief
+ * Checks that selections conform to the expectations of the tool.
+ */
+void checkSelections(const SelectionList &sel)
+{
+ for (size_t g = 0; g < sel.size(); ++g)
+ {
+ if (sel[g].posCount() % 2 != 0)
+ {
+ std::string message = formatString(
+ "Selection '%s' does not evaluate into an even number of positions "
+ "(there are %d positions)",
+ sel[g].name(), sel[g].posCount());
+ GMX_THROW(InconsistentInputError(message));
+ }
+ if (sel[g].isDynamic())
+ {
+ for (int i = 0; i < sel[g].posCount(); i += 2)
+ {
+ if (sel[g].position(i).selected() != sel[g].position(i+1).selected())
+ {
+ std::string message =
+ formatString("Dynamic selection %d does not select "
+ "a consistent set of pairs over the frames",
+ static_cast<int>(g + 1));
+ GMX_THROW(InconsistentInputError(message));
+ }
+ }
+ }
+ }
}
Distance::initAnalysis(const TrajectoryAnalysisSettings &settings,
const TopologyInformation & /*top*/)
{
- if (sel_[0].posCount() != 1)
+ checkSelections(sel_);
+
+ distances_.setDataSetCount(sel_.size());
+ xyz_.setDataSetCount(sel_.size());
+ for (size_t i = 0; i < sel_.size(); ++i)
+ {
+ const int distCount = sel_[i].posCount() / 2;
+ distances_.setColumnCount(i, distCount);
+ xyz_.setColumnCount(i, distCount * 3);
+ }
+ const double histogramMin = (1.0 - lengthDev_) * meanLength_;
+ const double histogramMax = (1.0 + lengthDev_) * meanLength_;
+ histogramModule_->init(histogramFromRange(histogramMin, histogramMax)
+ .binWidth(binWidth_).includeAll());
+
+ if (!fnAverage_.empty())
+ {
+ AnalysisDataPlotModulePointer plotm(
+ new AnalysisDataPlotModule(settings.plotSettings()));
+ plotm->setFileName(fnAverage_);
+ plotm->setTitle("Average distance");
+ plotm->setXAxisIsTime();
+ plotm->setYLabel("Distance (nm)");
+ for (size_t g = 0; g < sel_.size(); ++g)
+ {
+ plotm->appendLegend(sel_[g].name());
+ }
+ averageModule_->addModule(plotm);
+ }
+
+ if (!fnAll_.empty())
{
- GMX_THROW(InvalidInputError("The first selection does not define a single position"));
+ AnalysisDataPlotModulePointer plotm(
+ new AnalysisDataPlotModule(settings.plotSettings()));
+ plotm->setFileName(fnAll_);
+ plotm->setTitle("Distance");
+ plotm->setXAxisIsTime();
+ plotm->setYLabel("Distance (nm)");
+ // TODO: Add legends? (there can be a massive amount of columns)
+ distances_.addModule(plotm);
}
- if (sel_[1].posCount() != 1)
+
+ if (!fnXYZ_.empty())
{
- GMX_THROW(InvalidInputError("The second selection does not define a single position"));
+ AnalysisDataPlotModulePointer plotm(
+ new AnalysisDataPlotModule(settings.plotSettings()));
+ plotm->setFileName(fnXYZ_);
+ plotm->setTitle("Distance");
+ plotm->setXAxisIsTime();
+ plotm->setYLabel("Distance (nm)");
+ // TODO: Add legends? (there can be a massive amount of columns)
+ xyz_.addModule(plotm);
}
- data_.addModule(avem_);
- AnalysisDataPlotModulePointer plotm_(new AnalysisDataPlotModule());
- plotm_->setSettings(settings.plotSettings());
- plotm_->setFileName(fnDist_);
- plotm_->setTitle("Distance");
- plotm_->setXAxisIsTime();
- plotm_->setYLabel("Distance (nm)");
- data_.addModule(plotm_);
+ if (!fnHistogram_.empty())
+ {
+ AnalysisDataPlotModulePointer plotm(
+ new AnalysisDataPlotModule(settings.plotSettings()));
+ plotm->setFileName(fnHistogram_);
+ plotm->setTitle("Distance histogram");
+ plotm->setXLabel("Distance (nm)");
+ plotm->setYLabel("Probability");
+ for (size_t g = 0; g < sel_.size(); ++g)
+ {
+ plotm->appendLegend(sel_[g].name());
+ }
+ histogramModule_->averager().addModule(plotm);
+ }
+
+ if (!fnAllStats_.empty())
+ {
+ AnalysisDataPlotModulePointer plotm(
+ new AnalysisDataPlotModule(settings.plotSettings()));
+ plotm->setFileName(fnAllStats_);
+ plotm->setErrorsAsSeparateColumn(true);
+ plotm->setTitle("Statistics for individual distances");
+ plotm->setXLabel("Distance index");
+ plotm->setYLabel("Average/standard deviation (nm)");
+ for (size_t g = 0; g < sel_.size(); ++g)
+ {
+ plotm->appendLegend(std::string(sel_[g].name()) + " avg");
+ plotm->appendLegend(std::string(sel_[g].name()) + " std.dev.");
+ }
+ // TODO: Consider whether this output format is the best possible.
+ allStatsModule_->addModule(plotm);
+ }
}
Distance::analyzeFrame(int frnr, const t_trxframe &fr, t_pbc *pbc,
TrajectoryAnalysisModuleData *pdata)
{
- AnalysisDataHandle dh = pdata->dataHandle(data_);
- const Selection &sel1 = pdata->parallelSelection(sel_[0]);
- const Selection &sel2 = pdata->parallelSelection(sel_[1]);
- rvec dx;
- real r;
- const SelectionPosition &p1 = sel1.position(0);
- const SelectionPosition &p2 = sel2.position(0);
-
- if (pbc != NULL)
- {
- pbc_dx(pbc, p1.x(), p2.x(), dx);
- }
- else
+ AnalysisDataHandle distHandle = pdata->dataHandle(distances_);
+ AnalysisDataHandle xyzHandle = pdata->dataHandle(xyz_);
+ const SelectionList &sel = pdata->parallelSelections(sel_);
+
+ checkSelections(sel);
+
+ distHandle.startFrame(frnr, fr.time);
+ xyzHandle.startFrame(frnr, fr.time);
+ for (size_t g = 0; g < sel.size(); ++g)
{
- rvec_sub(p1.x(), p2.x(), dx);
+ distHandle.selectDataSet(g);
+ xyzHandle.selectDataSet(g);
+ for (int i = 0, n = 0; i < sel[g].posCount(); i += 2, ++n)
+ {
+ const SelectionPosition &p1 = sel[g].position(i);
+ const SelectionPosition &p2 = sel[g].position(i+1);
+ rvec dx;
+ if (pbc != NULL)
+ {
+ pbc_dx(pbc, p2.x(), p1.x(), dx);
+ }
+ else
+ {
+ rvec_sub(p2.x(), p1.x(), dx);
+ }
+ real dist = norm(dx);
+ bool bPresent = p1.selected() && p2.selected();
+ distHandle.setPoint(n, dist, bPresent);
+ xyzHandle.setPoints(n*3, 3, dx);
+ }
}
- r = norm(dx);
- dh.startFrame(frnr, fr.time);
- dh.setPoint(0, r);
- dh.setPoints(1, 3, dx);
- dh.finishFrame();
+ distHandle.finishFrame();
+ xyzHandle.finishFrame();
}
void
Distance::finishAnalysis(int /*nframes*/)
{
+ AbstractAverageHistogram &averageHistogram = histogramModule_->averager();
+ averageHistogram.normalizeProbability();
+ averageHistogram.done();
}
void
Distance::writeOutput()
{
- fprintf(stderr, "Average distance: %f\n", avem_->average(0));
- fprintf(stderr, "Std. deviation: %f\n", avem_->stddev(0));
+ SelectionList::const_iterator sel;
+ int index;
+ for (sel = sel_.begin(), index = 0; sel != sel_.end(); ++sel, ++index)
+ {
+ printf("%s:\n", sel->name());
+ printf(" Number of samples: %d\n",
+ summaryStatsModule_->sampleCount(index, 0));
+ printf(" Average distance: %-6.3f nm\n",
+ summaryStatsModule_->average(index, 0));
+ printf(" Standard deviation: %-6.3f nm\n",
+ summaryStatsModule_->standardDeviation(index, 0));
+ }
+}
+
+} // namespace
+
+const char DistanceInfo::name[] = "distance";
+const char DistanceInfo::shortDescription[] =
+ "Calculate distances between pairs of positions";
+
+TrajectoryAnalysisModulePointer DistanceInfo::create()
+{
+ return TrajectoryAnalysisModulePointer(new Distance);
}
} // namespace analysismodules
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff