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Framework for Trajectory Analysis (trajectoryanalysis)
+ 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.

msc_inline_mscgraph_9

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.

msc_inline_mscgraph_10

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.

msc_inline_mscgraph_11

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

Enumerations

enum  gmx::analysismodules::anonymous_namespace{pairdist.cpp}::DistanceType { eDistanceType_Min, eDistanceType_Max }
 Enum value to store the selected value for -type.
 
enum  gmx::analysismodules::anonymous_namespace{pairdist.cpp}::GroupType { eGroupType_All, eGroupType_Residue, eGroupType_Molecule, eGroupType_None }
 Enum value to store the selected value for -refgrouping/-selgrouping.
 
enum  gmx::analysismodules::anonymous_namespace{rdf.cpp}::Normalization { Normalization_Rdf, Normalization_NumberDensity, Normalization_None }
 Normalization for the computed distribution.
 
enum  gmx::analysismodules::anonymous_namespace{rdf.cpp}::SurfaceType { SurfaceType_None, SurfaceType_Molecule, SurfaceType_Residue }
 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, int 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, int ePBC, 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 char *const gmx::analysismodules::anonymous_namespace{pairdist.cpp}::c_distanceTypes [] = { "min", "max" }
 Strings corresponding to DistanceType.
 
const char *const gmx::analysismodules::anonymous_namespace{pairdist.cpp}::c_groupTypes [] = { "all", "res", "mol", "none" }
 Strings corresponding to GroupType.
 
const char *const gmx::analysismodules::anonymous_namespace{rdf.cpp}::c_NormalizationEnum [] = { "rdf", "number_density", "none" }
 String values corresponding to Normalization.
 
const char *const gmx::analysismodules::anonymous_namespace{rdf.cpp}::c_SurfaceEnum [] = { "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  analysismodule.h
 Declares gmx::TrajectoryAnalysisModule and gmx::TrajectoryAnalysisModuleData.
 
file  analysissettings.cpp
 Implements classes in analysissettings.h.
 
file  analysissettings.h
 Declares gmx::TrajectoryAnalysisSettings.
 
file  analysissettings_impl.h
 Declares private implementation class for gmx::TrajectoryAnalysisSettings.
 
file  cmdlinerunner.cpp
 Implements gmx::TrajectoryAnalysisCommandLineRunner.
 
file  cmdlinerunner.h
 Declares 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  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  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  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  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  moduletest.cpp
 Implements classes in moduletest.h.
 
file  moduletest.h
 Declares test fixture for TrajectoryAnalysisModule subclasses.
 
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  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  topologyinformation.h
 Declares gmx::TopologyInformation.
 
file  trajectoryanalysis.h
 Public API convenience header for trajectory analysis framework.
 

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]cNearest neighbor information array to update.
[in]iIndex in c to update.
[in]jIndex of the other surface dot to add to the array.
[in]d2Squared 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]frnrFrame number, a zero-based index that uniquely identifies the frame.
[in]frCurrent frame.
[in]pbcPeriodic boundary conditions for fr.
[in,out]pdataData 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]frnrFrame number, a zero-based index that uniquely identifies the frame.
[in]frCurrent frame.
[in]pbcPeriodic boundary conditions for fr.
[in,out]pdataData 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]frnrFrame number, a zero-based index that uniquely identifies the frame.
[in]frCurrent frame.
[in]pbcPeriodic boundary conditions for fr.
[in,out]pdataData 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]surfaceSelThe calculation selection.
[in]selThe selection to compute the areas for (can be surfaceSel or one of the output selections).
[in]atomAreasAtom areas for each position in surfaceSel.
[in]dgsFactorFree energy coefficients for each position in surfaceSel. If empty, free energies are not calculated.
[out]totalAreaOutTotal area of sel (sum of atom areas it selects).
[out]dgsolvOutSolvation free energy. Will be zero of dgsFactor is empty.
atomAreaHandleData handle to use for storing atom areas for sel.
resAreaHandleData handle to use for storing residue areas for sel.
resAreaWorkWork 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]fnPDB file to append the CONECT records to.
[in]nNumber of dots in x.
[in]xArray 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]nframesTotal 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]nframesTotal 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]nframesTotal 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]settingsSettings to pass to and from the module.
[in]topTopology 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]settingsSettings to pass to and from the module.
[in]topTopology 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]settingsSettings to pass to and from the module.
[in]topTopology 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]optionsOptions object to add the options to.
[in,out]settingsSettings 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]optionsOptions object to add the options to.
[in,out]settingsSettings 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]optionsOptions object to add the options to.
[in,out]settingsSettings 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]settingsSettings 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
ModuleInfoInfo 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]managerCommand-line module manager to receive the modules.
Exceptions
std::bad_allocif 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]optParallel options
[in]selectionsFrame-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]optParallel options
[in]selectionsFrame-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]optParallel options
[in]selectionsFrame-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.