Collaboration diagram for Framework for Trajectory Analysis (trajectoryanalysis):

Description

Provides functionality for implementing trajectory analysis modules.

This module implements a framework for implementing flexible trajectory analysis routines. It provides a base class for implementing analysis as reusable modules that can be used from different contexts and can also support per-frame parallelization. It integrally uses functionality from the following modules:

The main interface of this module is the gmx::TrajectoryAnalysisModule class. Analysis modules should derive from this class, and override the necessary virtual methods to provide the actual initialization and analysis routines. Classes gmx::TrajectoryAnalysisSettings and gmx::TopologyInformation (in addition to classes declared in the above-mentioned modules) are used to pass information to and from these methods. gmx::TrajectoryAnalysisModuleData can be used in advanced scenarios where the tool requires custom thread-local data for parallel analysis.

The sequence charts below provides an overview of how the trajectory analysis modules typically interact with other components. The first chart provides an overview of the call sequence of the most important methods in gmx::TrajectoryAnalysisModule. There is a runner, which is responsible for doing the work that is shared between all trajectory analysis (such as reading the trajectory and processing selections). The runner then calls different methods in the analysis module at appropriate points to perform the module-specific tasks. The analysis module is responsible for creating and managing gmx::AnalysisData objects, and the chart shows the most important interactions with this module as well. However, the runner takes responsibility of calling gmx::AnalysisData::finishFrameSerial(). Interactions with options (for command-line option processing) and selections is not shown for brevity: see Extensible Handling of Options (options) for an overview of how options work, and the second chart for a more detailed view of how selections are accessed from an analysis module.

The second chart below shows the interaction with selections and options with focus on selection options. The gmx::TrajectoryAnalysisModule object creates one or more gmx::Selection variables, and uses gmx::SelectionOption to indicate them as the destination for selections. This happens in gmx::TrajectoryAnalysisModule::initOptions(). After the options have been parsed (includes parsing any options present on the command-line or read from files, but not those provided interactively), gmx::TrajectoryAnalysisModule::optionsFinished() can adjust the selections using gmx::SelectionOptionInfo. This is done like this to allow the analysis module to influence the interactive prompt of selections based on what command-line options were given. After optionsFinished() returns, the interactive selection prompt is presented if necessary. After this point, all access to selections from the analysis module is through the gmx::Selection variables: the runner is responsible for calling methods in the selection library, and these methods update the content referenced by the gmx::Selection variables. See documentation of gmx::TrajectoryAnalysisModule for details of what the selections contain at each point.

The final chart shows the flow within the frame loop in the case of parallel (threaded) execution and the interaction with the Parallelizable Handling of Output Data (analysisdata) module in this case. Although parallelization has not yet been implemented, it has influenced the design and needs to be understood if one wants to write modules that can take advantage of the parallelization once it gets implemented. The parallelization takes part over frames: analyzing a single frame is one unit of work. When the frame loop is started, gmx::TrajectoryAnalysisModule::startFrames() is called for each thread, and initializes an object that contains thread-local data needed during the analysis. This includes selection information, gmx::AnalysisDataHandle objects, and possibly other module-specific variables. Then, the runner reads the frames in sequence and passes the work into the different threads, together with the appropriate thread-local data object. The gmx::TrajectoryAnalysisModule::analyzeFrame() calls are only allowed to modify the thread-local data object; everything else is read-only. For any output, they pass the information to gmx::AnalysisData, which together with the runner takes care of ordering the data from different frames such that it gets processed in the right order. When all frames are analyzed, gmx::TrajectoryAnalysisModule::finishFrames() is called for each thread-local data object to destroy them and to accumulate possible results from them into the main gmx::TrajectoryAnalysisModule object. Note that in the diagram, some part of the work attributed for the runner (e.g., evaluating selections) will actually be carried out in the analysis threads before gmx::TrajectoryAnalysisModule::analyzeFrame() gets called.

In addition to the framework for defining analysis modules, this module also provides gmx::TrajectoryAnalysisCommandLineRunner, which implements a command-line program that runs a certain analysis module.

Internally, the module also defines a set of trajectory analysis modules that can currently be accessed only through gmx::registerTrajectoryAnalysisModules.

For an example of how to implement an analysis tool using the framework, see template.cpp.

Author: Teemu Murtola teemu.nosp@m..mur.nosp@m.tola@.nosp@m.gmai.nosp@m.l.com

Classes
class	gmx::TrajectoryAnalysisModule::Impl
	Private implementation class for TrajectoryAnalysisModule. More...

class	gmx::anonymous_namespace{analysismodule.cpp}::TrajectoryAnalysisModuleDataBasic
	Basic thread-local trajectory analysis data storage class. More...

class	gmx::analysismodules::anonymous_namespace{angle.cpp}::AnglePositionIterator
	Helper to encapsulate logic for looping over input selections. More...

class	gmx::analysismodules::anonymous_namespace{freevolume.cpp}::FreeVolume
	Class used to compute free volume in a simulations box. More...

class	gmx::analysismodules::anonymous_namespace{pairdist.cpp}::PairDistance
	Implements `gmx pairdist` trajectory analysis module. More...

class	gmx::analysismodules::anonymous_namespace{pairdist.cpp}::PairDistanceModuleData
	Temporary memory for use within a single-frame calculation. More...

class	gmx::analysismodules::anonymous_namespace{rdf.cpp}::Rdf
	Implements `gmx rdf` trajectory analysis module. More...

class	gmx::analysismodules::anonymous_namespace{rdf.cpp}::RdfModuleData
	Temporary memory for use within a single-frame calculation. More...

struct	gmx::analysismodules::anonymous_namespace{sasa.cpp}::t_conect
	Tracks information on two nearest neighbors of a single surface dot. More...

class	gmx::analysismodules::anonymous_namespace{sasa.cpp}::Sasa
	Implements `gmx sas` trajectory analysis module. More...

class	gmx::analysismodules::anonymous_namespace{sasa.cpp}::SasaModuleData
	Temporary memory for use within a single-frame calculation. More...

class	gmx::SurfaceAreaCalculator
	Computes surface areas for a group of atoms/spheres. More...

class	gmx::UnionFinder
	Union-find data structure for keeping track of disjoint sets. More...

class	gmx::MappedUnionFinder
	Extension of UnionFind that supports non-consecutive integer indices as items. More...

class	gmx::TrajectoryAnalysisRunnerCommon
	Implements common trajectory analysis runner functionality. More...

class	gmx::test::AbstractTrajectoryAnalysisModuleTestFixture
	Test fixture for trajectory analysis modules. More...

class	gmx::test::TrajectoryAnalysisModuleTestFixture< ModuleInfo >
	Test fixture for a trajectory analysis module. More...

class	gmx::TrajectoryAnalysisModuleData
	Base class for thread-local data storage during trajectory analysis. More...

class	gmx::TrajectoryAnalysisModule
	Base class for trajectory analysis modules. More...

class	gmx::TrajectoryAnalysisSettings
	Trajectory analysis module configuration object. More...

class	gmx::TrajectoryAnalysisCommandLineRunner
	Runner for command-line trajectory analysis tools. More...

class	gmx::TopologyInformation
	Topology information available to a trajectory analysis module. More...

Enumerations
enum	gmx::analysismodules::anonymous_namespace{pairdist.cpp}::DistanceType : int { Min, Max, Count }
	Enum value to store the selected value for `-type`.

enum	gmx::analysismodules::anonymous_namespace{pairdist.cpp}::GroupType : int { All, Residue, Molecule, None, Count }
	Enum value to store the selected value for `-refgrouping`/`-selgrouping`.

enum	gmx::analysismodules::anonymous_namespace{rdf.cpp}::Normalization : int { Rdf, NumberDensity, None, Count }
	Normalization for the computed distribution.

enum	gmx::analysismodules::anonymous_namespace{rdf.cpp}::SurfaceType : int { None, Molecule, Residue, Count }
	Whether to compute RDF wrt. surface of the reference group.

Functions
int	gmx::analysismodules::anonymous_namespace{pairdist.cpp}::initSelectionGroups (Selection sel, const gmx_mtop_t top, GroupType type)
	Helper function to initialize the grouping for a selection.

void	gmx::analysismodules::anonymous_namespace{sasa.cpp}::add_rec (t_conect c[], int i, int j, real d2)
	Updates nearest neighbor information for a surface dot. More...

void	gmx::analysismodules::anonymous_namespace{sasa.cpp}::do_conect (const char *fn, int n, rvec x[])
	Adds CONECT records for surface dots. More...

void	gmx::analysismodules::anonymous_namespace{sasa.cpp}::connolly_plot (const char fn, int ndots, const real dots[], rvec x[], t_atoms atoms, t_symtab *symtab, PbcType pbcType, const matrix box, gmx_bool bIncludeSolute)
	Plots the surface into a PDB file, optionally including the original atoms.

void	gmx::analysismodules::anonymous_namespace{sasa.cpp}::computeAreas (const Selection &surfaceSel, const Selection &sel, const std::vector< real > &atomAreas, const std::vector< real > &dgsFactor, real totalAreaOut, real dgsolvOut, AnalysisDataHandle atomAreaHandle, AnalysisDataHandle resAreaHandle, std::vector< real > *resAreaWork)
	Helper method to compute the areas for a single selection. More...

template<class ModuleInfo >
void	gmx::anonymous_namespace{modules.cpp}::registerModule (CommandLineModuleManager *manager, CommandLineModuleGroup group)
	Convenience method for registering a command-line module for trajectory analysis. More...

void	gmx::registerTrajectoryAnalysisModules (CommandLineModuleManager *manager)
	Registers all trajectory analysis command-line modules. More...

void	gmx::analysismodules::anonymous_namespace{pairdist.cpp}::PairDistance::initOptions (IOptionsContainer options, TrajectoryAnalysisSettings settings) override
	Initializes options understood by the module. More...

void	gmx::analysismodules::anonymous_namespace{pairdist.cpp}::PairDistance::initAnalysis (const TrajectoryAnalysisSettings &settings, const TopologyInformation &top) override
	Initializes the analysis. More...

TrajectoryAnalysisModuleDataPointer	gmx::analysismodules::anonymous_namespace{pairdist.cpp}::PairDistance::startFrames (const AnalysisDataParallelOptions &opt, const SelectionCollection &selections) override
	Starts the analysis of frames. More...

void	gmx::analysismodules::anonymous_namespace{pairdist.cpp}::PairDistance::analyzeFrame (int frnr, const t_trxframe &fr, t_pbc pbc, TrajectoryAnalysisModuleData pdata) override
	Analyzes a single frame. More...

void	gmx::analysismodules::anonymous_namespace{pairdist.cpp}::PairDistance::finishAnalysis (int nframes) override
	Postprocesses data after frames have been read. More...

void	gmx::analysismodules::anonymous_namespace{pairdist.cpp}::PairDistance::writeOutput () override
	Writes output into files and/or standard output/error. More...

void	gmx::analysismodules::anonymous_namespace{rdf.cpp}::Rdf::initOptions (IOptionsContainer options, TrajectoryAnalysisSettings settings) override
	Initializes options understood by the module. More...

void	gmx::analysismodules::anonymous_namespace{rdf.cpp}::Rdf::optionsFinished (TrajectoryAnalysisSettings *settings) override
	Called after all option values have been set. More...

void	gmx::analysismodules::anonymous_namespace{rdf.cpp}::Rdf::initAnalysis (const TrajectoryAnalysisSettings &settings, const TopologyInformation &top) override
	Initializes the analysis. More...

void	gmx::analysismodules::anonymous_namespace{rdf.cpp}::Rdf::initAfterFirstFrame (const TrajectoryAnalysisSettings &settings, const t_trxframe &fr) override
	Performs additional initialization after reading the first frame. More...

TrajectoryAnalysisModuleDataPointer	gmx::analysismodules::anonymous_namespace{rdf.cpp}::Rdf::startFrames (const AnalysisDataParallelOptions &opt, const SelectionCollection &selections) override
	Starts the analysis of frames. More...

void	gmx::analysismodules::anonymous_namespace{rdf.cpp}::Rdf::analyzeFrame (int frnr, const t_trxframe &fr, t_pbc pbc, TrajectoryAnalysisModuleData pdata) override
	Analyzes a single frame. More...

void	gmx::analysismodules::anonymous_namespace{rdf.cpp}::Rdf::finishAnalysis (int nframes) override
	Postprocesses data after frames have been read. More...

void	gmx::analysismodules::anonymous_namespace{rdf.cpp}::Rdf::writeOutput () override
	Writes output into files and/or standard output/error. More...

void	gmx::analysismodules::anonymous_namespace{sasa.cpp}::Sasa::initOptions (IOptionsContainer options, TrajectoryAnalysisSettings settings) override
	Initializes options understood by the module. More...

void	gmx::analysismodules::anonymous_namespace{sasa.cpp}::Sasa::initAnalysis (const TrajectoryAnalysisSettings &settings, const TopologyInformation &top) override
	Initializes the analysis. More...

TrajectoryAnalysisModuleDataPointer	gmx::analysismodules::anonymous_namespace{sasa.cpp}::Sasa::startFrames (const AnalysisDataParallelOptions &opt, const SelectionCollection &selections) override
	Starts the analysis of frames. More...

void	gmx::analysismodules::anonymous_namespace{sasa.cpp}::Sasa::analyzeFrame (int frnr, const t_trxframe &fr, t_pbc pbc, TrajectoryAnalysisModuleData pdata) override
	Analyzes a single frame. More...

void	gmx::analysismodules::anonymous_namespace{sasa.cpp}::Sasa::finishAnalysis (int nframes) override
	Postprocesses data after frames have been read. More...

void	gmx::analysismodules::anonymous_namespace{sasa.cpp}::Sasa::writeOutput () override
	Writes output into files and/or standard output/error. More...

Variables
const EnumerationArray < DistanceType, const char * >	gmx::analysismodules::anonymous_namespace{pairdist.cpp}::c_distanceTypeNames = { { "min", "max" } }
	Strings corresponding to DistanceType.

const EnumerationArray < GroupType, const char * >	gmx::analysismodules::anonymous_namespace{pairdist.cpp}::c_groupTypeNames
	Strings corresponding to GroupType. More...

const EnumerationArray < Normalization, const char * >	gmx::analysismodules::anonymous_namespace{rdf.cpp}::c_normalizationNames
	String values corresponding to Normalization. More...

const EnumerationArray < SurfaceType, const char * >	gmx::analysismodules::anonymous_namespace{rdf.cpp}::c_surfaceTypeNames = { { "no", "mol", "res" } }
	String values corresponding to SurfaceType.

Directories
directory	trajectoryanalysis
	Framework for Trajectory Analysis (trajectoryanalysis)

directory	tests
	Unit tests for Framework for Trajectory Analysis (trajectoryanalysis).

Files
file	analysismodule.cpp
	Implements classes in analysismodule.h.

file	analysissettings.cpp
	Implements classes in analysissettings.h.

file	analysissettings_impl.h
	Declares private implementation class for gmx::TrajectoryAnalysisSettings.

file	cmdlinerunner.cpp
	Implements gmx::TrajectoryAnalysisCommandLineRunner.

file	angle.cpp
	Implements gmx::analysismodules::Angle.

file	angle.h
	Declares trajectory analysis module for angle calculations.

file	convert_trj.cpp
	Implements gmx::analysismodules::ConvertTrj.

file	convert_trj.h
	Declares trajectory analysis module for trajectory conversion.

file	distance.cpp
	Implements gmx::analysismodules::Distance.

file	distance.h
	Declares trajectory analysis module for distance calculations.

file	dssp.cpp
	Implements gmx::analysismodules::Dssp.

file	dssp.h
	Declares trajectory analysis module for secondary structure asignment.

file	extract_cluster.cpp
	Implements gmx::analysismodules::ExtractCluster.

file	extract_cluster.h
	Declares trajectory analysis module for extracting frames corresponding to clusters.

file	freevolume.cpp
	Implements gmx::analysismodules::Freevolume.

file	freevolume.h
	Declares trajectory analysis module for free volume calculations.

file	gyrate.cpp
	Implements gmx::analysismodules::Gyrate.

file	gyrate.h
	Declares trajectory analysis module for distance calculations.

file	hbond.cpp
	Implements gmx::analysismodules::Hbond2.

file	hbond.h
	Declares trajectory analysis module for computation and analyzation of hydrogen bonds.

file	isotope.cpp
	Declares helper functions for assigning isotops from atom names.

file	isotope.h
	Declares helper functions for assigning isotops from atom names.

file	msd.cpp
	Defines the trajectory analysis module for mean squared displacement calculations.

file	msd.h
	Declares trajectory analysis module for Mean Squared Displacement calculations.

file	pairdist.cpp
	Implements gmx::analysismodules::PairDistance.

file	pairdist.h
	Declares trajectory analysis module for pairwise distance calculations.

file	rdf.cpp
	Implements gmx::analysismodules::Rdf.

file	rdf.h
	Declares trajectory analysis module for RDF calculations.

file	sasa.cpp
	Implements gmx::analysismodules::Sasa.

file	sasa.h
	Declares trajectory analysis module for surface area calculations.

file	scattering-debye-sans.cpp
	Implements class for SANS Debye Scattering.

file	scattering-debye-sans.h
	Declares class for SANS Debye Scattering.

file	scattering-debye-saxs.cpp
	Implements class for SAXS Debye Scattering.

file	scattering-debye-saxs.h
	Declares class for SAXS Debye Scattering.

file	scattering-debye.cpp
	Implementation of base class for Debye Scattering.

file	scattering-debye.h
	Declares base class for Debye Scattering.

file	scattering.cpp
	Implements gmx::analysismodules::scattering.

file	scattering.h
	Declares trajectory analysis module for small angle scattering calculations.

file	scatteringfactors.cpp
	Implements helper functions for reading structure factors from datafile.

file	scatteringfactors.h
	Declares helper functions for reading structure factors from datafile.

file	select.cpp
	Implements gmx::analysismodules::Select.

file	select.h
	Declares trajectory analysis module for basic selection information.

file	trajectory.cpp
	Implements gmx::analysismodules::Trajectory.

file	trajectory.h
	Declares trajectory analysis module for basic trajectory information.

file	unionfind.h
	Implements gmx::UnionFinder and gmx::MappedUnionFinder.

file	modules.cpp
	Implements registerTrajectoryAnalysisModules().

file	modules.h
	Generic interface for accessing trajectory analysis modules.

file	runnercommon.cpp
	Implements gmx::TrajectoryAnalysisRunnerCommon.

file	runnercommon.h
	Declares gmx::TrajectoryAnalysisRunnerCommon.

file	angle.cpp
	Tests for functionality of the "angle" trajectory analysis module.

file	clustsize.cpp
	Tests for gmx clustsize.

file	cmdlinerunner.cpp
	Tests for general functionality in gmx::TrajectoryAnalysisCommandLineRunner.

file	convert_trj.cpp
	Tests for functionality of the "convert-trj" trajectory analysis module.

file	distance.cpp
	Tests for functionality of the "distance" trajectory analysis module.

file	dssp.cpp
	Tests for functionality of the "dssp" trajectory analysis module.

file	extract_cluster.cpp
	Tests for functionality of the "extract-cluster" trajectory analysis module.

file	freevolume.cpp
	Tests for functionality of the "angle" trajectory analysis module.

file	gyrate.cpp
	Tests for functionality of the "gyrate" trajectory analysis module.

file	hbond.cpp
	Tests for functionality of the "hbond" trajectory analysis module.

file	moduletest.cpp
	Implements classes in moduletest.h.

file	moduletest.h
	Declares test fixture for TrajectoryAnalysisModule subclasses.

file	msd.cpp
	Tests for functionality of the "msd" trajectory analysis module.

file	pairdist.cpp
	Tests for functionality of the "pairdist" trajectory analysis module.

file	rdf.cpp
	Tests for functionality of the "rdf" trajectory analysis module.

file	sasa.cpp
	Tests for functionality of the "sasa" trajectory analysis module.

file	scattering.cpp
	Tests for scattering trajectory analysis module.

file	select.cpp
	Tests for functionality of the "select" trajectory analysis module.

file	surfacearea.cpp
	Tests for the surface area calculation used by the `sasa` analysis module.

file	test_selection.cpp
	Testing/debugging tool for the selection engine.

file	topologyinformation.cpp
	Tests for TopologyInformation.

file	trajectory.cpp
	Tests for functionality of the "trajectory" trajectory analysis module.

file	unionfind.cpp
	Tests for the union-find implementation in unionfind.h.

file	topologyinformation.cpp
	Implements classes in topologyinformation.h.

file	analysismodule.h
	Declares gmx::TrajectoryAnalysisModule and gmx::TrajectoryAnalysisModuleData.

file	analysissettings.h
	Declares gmx::TrajectoryAnalysisSettings.

file	cmdlinerunner.h
	Declares gmx::TrajectoryAnalysisCommandLineRunner.

file	topologyinformation.h
	Declares gmx::TopologyInformation.

Function Documentation

void gmx::analysismodules::anonymous_namespace{sasa.cpp}::add_rec	(	t_conect	c[],
		int	i,
		int	j,
		real	d2
	)

Updates nearest neighbor information for a surface dot.

Parameters

[in,out]	c	Nearest neighbor information array to update.
[in]	i	Index in `c` to update.
[in]	j	Index of the other surface dot to add to the array.
[in]	d2	Squared distance between `i` and `j`.

void gmx::analysismodules::anonymous_namespace{pairdist.cpp}::PairDistance::analyzeFrame	(	int	frnr,
		const t_trxframe &	fr,
		t_pbc *	pbc,
		TrajectoryAnalysisModuleData *	pdata
	)

overridevirtual

Analyzes a single frame.

Parameters

[in]	frnr	Frame number, a zero-based index that uniquely identifies the frame.
[in]	fr	Current frame.
[in]	pbc	Periodic boundary conditions for `fr`.
[in,out]	pdata	Data structure for frame-local data.

This method is called once for each frame to be analyzed, and should analyze the positions provided in the selections. Data handles and selections should be obtained from the pdata structure.

For threaded analysis, this method is called asynchronously in different threads to analyze different frames. The pdata structure is one of the structures created with startFrames(), but no assumptions should be made about which of these data structures is used. It is guaranteed that two instances of analyzeFrame() are not running concurrently with the same pdata data structure. Any access to data structures not stored in pdata should be designed to be thread-safe.

Implements gmx::TrajectoryAnalysisModule.

void gmx::analysismodules::anonymous_namespace{rdf.cpp}::Rdf::analyzeFrame	(	int	frnr,
		const t_trxframe &	fr,
		t_pbc *	pbc,
		TrajectoryAnalysisModuleData *	pdata
	)

overridevirtual

Analyzes a single frame.

Parameters

[in]	frnr	Frame number, a zero-based index that uniquely identifies the frame.
[in]	fr	Current frame.
[in]	pbc	Periodic boundary conditions for `fr`.
[in,out]	pdata	Data structure for frame-local data.

This method is called once for each frame to be analyzed, and should analyze the positions provided in the selections. Data handles and selections should be obtained from the pdata structure.

For threaded analysis, this method is called asynchronously in different threads to analyze different frames. The pdata structure is one of the structures created with startFrames(), but no assumptions should be made about which of these data structures is used. It is guaranteed that two instances of analyzeFrame() are not running concurrently with the same pdata data structure. Any access to data structures not stored in pdata should be designed to be thread-safe.

Implements gmx::TrajectoryAnalysisModule.

void gmx::analysismodules::anonymous_namespace{sasa.cpp}::Sasa::analyzeFrame	(	int	frnr,
		const t_trxframe &	fr,
		t_pbc *	pbc,
		TrajectoryAnalysisModuleData *	pdata
	)

overridevirtual

Analyzes a single frame.

Parameters

[in]	frnr	Frame number, a zero-based index that uniquely identifies the frame.
[in]	fr	Current frame.
[in]	pbc	Periodic boundary conditions for `fr`.
[in,out]	pdata	Data structure for frame-local data.

This method is called once for each frame to be analyzed, and should analyze the positions provided in the selections. Data handles and selections should be obtained from the pdata structure.

For threaded analysis, this method is called asynchronously in different threads to analyze different frames. The pdata structure is one of the structures created with startFrames(), but no assumptions should be made about which of these data structures is used. It is guaranteed that two instances of analyzeFrame() are not running concurrently with the same pdata data structure. Any access to data structures not stored in pdata should be designed to be thread-safe.

Implements gmx::TrajectoryAnalysisModule.

void gmx::analysismodules::anonymous_namespace{sasa.cpp}::computeAreas	(	const Selection &	surfaceSel,
		const Selection &	sel,
		const std::vector< real > &	atomAreas,
		const std::vector< real > &	dgsFactor,
		real *	totalAreaOut,
		real *	dgsolvOut,
		AnalysisDataHandle	atomAreaHandle,
		AnalysisDataHandle	resAreaHandle,
		std::vector< real > *	resAreaWork
	)

Helper method to compute the areas for a single selection.

Parameters

[in]	surfaceSel	The calculation selection.
[in]	sel	The selection to compute the areas for (can be `surfaceSel` or one of the output selections).
[in]	atomAreas	Atom areas for each position in `surfaceSel`.
[in]	dgsFactor	Free energy coefficients for each position in `surfaceSel`. If empty, free energies are not calculated.
[out]	totalAreaOut	Total area of `sel` (sum of atom areas it selects).
[out]	dgsolvOut	Solvation free energy. Will be zero of `dgsFactor` is empty.
	atomAreaHandle	Data handle to use for storing atom areas for `sel`.
	resAreaHandle	Data handle to use for storing residue areas for `sel`.
	resAreaWork	Work array for accumulating the residue areas. If empty, atom and residue areas are not calculated.

atomAreaHandle and resAreaHandle are not used if resAreaWork is empty.

void gmx::analysismodules::anonymous_namespace{sasa.cpp}::do_conect	(	const char *	fn,
		int	n,
		rvec	x[]
	)

Adds CONECT records for surface dots.

Parameters

[in]	fn	PDB file to append the CONECT records to.
[in]	n	Number of dots in `x`.
[in]	x	Array of surface dot positions.

Adds a CONECT record that connects each surface dot to its two nearest neighbors. The function is copied verbatim from the old gmx_sas.c implementation.

void gmx::analysismodules::anonymous_namespace{pairdist.cpp}::PairDistance::finishAnalysis ( int nframes )

overridevirtual

Postprocesses data after frames have been read.

Parameters

[in] nframes Total number of frames processed.

This function is called after all finishFrames() calls have been called. nframes will equal the number of calls to analyzeFrame() that have occurred.

Implements gmx::TrajectoryAnalysisModule.

void gmx::analysismodules::anonymous_namespace{rdf.cpp}::Rdf::finishAnalysis ( int nframes )

overridevirtual

Postprocesses data after frames have been read.

Parameters

[in] nframes Total number of frames processed.

This function is called after all finishFrames() calls have been called. nframes will equal the number of calls to analyzeFrame() that have occurred.

Implements gmx::TrajectoryAnalysisModule.

void gmx::analysismodules::anonymous_namespace{sasa.cpp}::Sasa::finishAnalysis ( int nframes )

overridevirtual

Postprocesses data after frames have been read.

Parameters

[in] nframes Total number of frames processed.

This function is called after all finishFrames() calls have been called. nframes will equal the number of calls to analyzeFrame() that have occurred.

Implements gmx::TrajectoryAnalysisModule.

void gmx::analysismodules::anonymous_namespace{rdf.cpp}::Rdf::initAfterFirstFrame	(	const TrajectoryAnalysisSettings &	settings,
		const t_trxframe &	fr
	)

overridevirtual

Performs additional initialization after reading the first frame.

When this function is called, selections are the same as in initAnalysis(), i.e., they have not been evaluated for the first frame.

It is necessary to override this method only if the module needs to do initialization for which it requires data from the first frame.

The default implementation does nothing.

Reimplemented from gmx::TrajectoryAnalysisModule.

void gmx::analysismodules::anonymous_namespace{pairdist.cpp}::PairDistance::initAnalysis	(	const TrajectoryAnalysisSettings &	settings,
		const TopologyInformation &	top
	)

overridevirtual

Initializes the analysis.

Parameters

[in]	settings	Settings to pass to and from the module.
[in]	top	Topology information.

When this function is called, selections have been initialized based on user input, and a topology has been loaded if provided by the user. For dynamic selections, the selections have been evaluated to the largest possible selection, i.e., the selections passed to analyzeFrame() are always a subset of the selections provided here.

Implements gmx::TrajectoryAnalysisModule.

void gmx::analysismodules::anonymous_namespace{rdf.cpp}::Rdf::initAnalysis	(	const TrajectoryAnalysisSettings &	settings,
		const TopologyInformation &	top
	)

overridevirtual

Initializes the analysis.

Parameters

[in]	settings	Settings to pass to and from the module.
[in]	top	Topology information.

When this function is called, selections have been initialized based on user input, and a topology has been loaded if provided by the user. For dynamic selections, the selections have been evaluated to the largest possible selection, i.e., the selections passed to analyzeFrame() are always a subset of the selections provided here.

Implements gmx::TrajectoryAnalysisModule.

void gmx::analysismodules::anonymous_namespace{sasa.cpp}::Sasa::initAnalysis	(	const TrajectoryAnalysisSettings &	settings,
		const TopologyInformation &	top
	)

overridevirtual

Initializes the analysis.

Parameters

[in]	settings	Settings to pass to and from the module.
[in]	top	Topology information.

When this function is called, selections have been initialized based on user input, and a topology has been loaded if provided by the user. For dynamic selections, the selections have been evaluated to the largest possible selection, i.e., the selections passed to analyzeFrame() are always a subset of the selections provided here.

Implements gmx::TrajectoryAnalysisModule.

void gmx::analysismodules::anonymous_namespace{pairdist.cpp}::PairDistance::initOptions	(	IOptionsContainer *	options,
		TrajectoryAnalysisSettings *	settings
	)

overridevirtual

Initializes options understood by the module.

Parameters

[in,out]	options	Options object to add the options to.
[in,out]	settings	Settings to pass to and from the module.

This method is called first after the constructor, and it should add options understood by the module to options. Output values from options (including selections) should be stored in member variables.

In addition to initializing the options, this method can also provide information about the module's requirements using the settings object; see TrajectoryAnalysisSettings for more details.

If settings depend on the option values provided by the user, see optionsFinished().

Implements gmx::TrajectoryAnalysisModule.

void gmx::analysismodules::anonymous_namespace{rdf.cpp}::Rdf::initOptions	(	IOptionsContainer *	options,
		TrajectoryAnalysisSettings *	settings
	)

overridevirtual

Initializes options understood by the module.

Parameters

[in,out]	options	Options object to add the options to.
[in,out]	settings	Settings to pass to and from the module.

This method is called first after the constructor, and it should add options understood by the module to options. Output values from options (including selections) should be stored in member variables.

In addition to initializing the options, this method can also provide information about the module's requirements using the settings object; see TrajectoryAnalysisSettings for more details.

If settings depend on the option values provided by the user, see optionsFinished().

Implements gmx::TrajectoryAnalysisModule.

void gmx::analysismodules::anonymous_namespace{sasa.cpp}::Sasa::initOptions	(	IOptionsContainer *	options,
		TrajectoryAnalysisSettings *	settings
	)

overridevirtual

Initializes options understood by the module.

Parameters

[in,out]	options	Options object to add the options to.
[in,out]	settings	Settings to pass to and from the module.

This method is called first after the constructor, and it should add options understood by the module to options. Output values from options (including selections) should be stored in member variables.

In addition to initializing the options, this method can also provide information about the module's requirements using the settings object; see TrajectoryAnalysisSettings for more details.

If settings depend on the option values provided by the user, see optionsFinished().

Implements gmx::TrajectoryAnalysisModule.

void gmx::analysismodules::anonymous_namespace{rdf.cpp}::Rdf::optionsFinished ( TrajectoryAnalysisSettings * settings )

overridevirtual

Called after all option values have been set.

Parameters

[in,out] settings Settings to pass to and from the module.

This method is called after option values have been assigned (but interactive selection input has not yet been performed).

If the module needs to change settings that affect topology loading (can be done using the settings object) or selection initialization (can be done using SelectionOptionInfo) based on option values, this method has to be overridden.

The default implementation does nothing.

Reimplemented from gmx::TrajectoryAnalysisModule.

template<class ModuleInfo >

void gmx::anonymous_namespace{modules.cpp}::registerModule	(	CommandLineModuleManager *	manager,
		CommandLineModuleGroup	group
	)

Convenience method for registering a command-line module for trajectory analysis.

Template Parameters

ModuleInfo Info about trajectory analysis module to wrap.

ModuleInfo should have static public members const char name[], const char shortDescription[], and gmx::TrajectoryAnalysisModulePointer create().

void gmx::registerTrajectoryAnalysisModules ( CommandLineModuleManager * manager )

Registers all trajectory analysis command-line modules.

Parameters

[in] manager Command-line module manager to receive the modules.

Exceptions

std::bad_alloc if out of memory.

Registers all trajectory analysis modules declared in the library such that they can be run through manager.

TrajectoryAnalysisModuleDataPointer gmx::analysismodules::anonymous_namespace{pairdist.cpp}::PairDistance::startFrames	(	const AnalysisDataParallelOptions &	opt,
		const SelectionCollection &	selections
	)

overridevirtual

Starts the analysis of frames.

Parameters

[in]	opt	Parallel options
[in]	selections	Frame-local selection collection object.

Returns: Data structure for thread-local data.

This function is necessary only for threaded parallelization. It is called once for each thread and should initialize a class that contains any required frame-local data in the returned value. The default implementation creates a basic data structure that holds thread-local data handles for all data objects registered with registerAnalysisDataset(), as well as the thread-local selection collection. These can be accessed in analyzeFrame() using the methods in TrajectoryAnalysisModuleData. If other thread-local data is needed, this function should be overridden and it should create an instance of a class derived from TrajectoryAnalysisModuleData.

See Also: TrajectoryAnalysisModuleData

Reimplemented from gmx::TrajectoryAnalysisModule.

TrajectoryAnalysisModuleDataPointer gmx::analysismodules::anonymous_namespace{rdf.cpp}::Rdf::startFrames	(	const AnalysisDataParallelOptions &	opt,
		const SelectionCollection &	selections
	)

overridevirtual

Starts the analysis of frames.

Parameters

[in]	opt	Parallel options
[in]	selections	Frame-local selection collection object.

Returns: Data structure for thread-local data.

This function is necessary only for threaded parallelization. It is called once for each thread and should initialize a class that contains any required frame-local data in the returned value. The default implementation creates a basic data structure that holds thread-local data handles for all data objects registered with registerAnalysisDataset(), as well as the thread-local selection collection. These can be accessed in analyzeFrame() using the methods in TrajectoryAnalysisModuleData. If other thread-local data is needed, this function should be overridden and it should create an instance of a class derived from TrajectoryAnalysisModuleData.

See Also: TrajectoryAnalysisModuleData

Reimplemented from gmx::TrajectoryAnalysisModule.

TrajectoryAnalysisModuleDataPointer gmx::analysismodules::anonymous_namespace{sasa.cpp}::Sasa::startFrames	(	const AnalysisDataParallelOptions &	opt,
		const SelectionCollection &	selections
	)

overridevirtual

Starts the analysis of frames.

Parameters

[in]	opt	Parallel options
[in]	selections	Frame-local selection collection object.

Returns: Data structure for thread-local data.

This function is necessary only for threaded parallelization. It is called once for each thread and should initialize a class that contains any required frame-local data in the returned value. The default implementation creates a basic data structure that holds thread-local data handles for all data objects registered with registerAnalysisDataset(), as well as the thread-local selection collection. These can be accessed in analyzeFrame() using the methods in TrajectoryAnalysisModuleData. If other thread-local data is needed, this function should be overridden and it should create an instance of a class derived from TrajectoryAnalysisModuleData.

See Also: TrajectoryAnalysisModuleData

Reimplemented from gmx::TrajectoryAnalysisModule.

void gmx::analysismodules::anonymous_namespace{pairdist.cpp}::PairDistance::writeOutput ( )

overridevirtual

Writes output into files and/or standard output/error.

All output from the module, excluding data written out for each frame during analyzeFrame(), should be confined into this function. This function is guaranteed to be called only after finishAnalysis().

Implements gmx::TrajectoryAnalysisModule.

void gmx::analysismodules::anonymous_namespace{rdf.cpp}::Rdf::writeOutput ( )

overridevirtual

Writes output into files and/or standard output/error.

All output from the module, excluding data written out for each frame during analyzeFrame(), should be confined into this function. This function is guaranteed to be called only after finishAnalysis().

Implements gmx::TrajectoryAnalysisModule.

void gmx::analysismodules::anonymous_namespace{sasa.cpp}::Sasa::writeOutput ( )

overridevirtual

Writes output into files and/or standard output/error.

All output from the module, excluding data written out for each frame during analyzeFrame(), should be confined into this function. This function is guaranteed to be called only after finishAnalysis().

Implements gmx::TrajectoryAnalysisModule.

Variable Documentation

const EnumerationArray<GroupType, const char*> gmx::analysismodules::anonymous_namespace{pairdist.cpp}::c_groupTypeNames

Initial value:

= {
    { "all", "res", "mol", "none" }
}

Strings corresponding to GroupType.

const EnumerationArray<Normalization, const char*> gmx::analysismodules::anonymous_namespace{rdf.cpp}::c_normalizationNames

Initial value:

= {
    { "rdf", "number_density", "none" }
}

String values corresponding to Normalization.

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Variable Documentation