GmxTopolApp Class Reference

Inheritance diagram for GmxTopolApp:

Collaboration diagram for GmxTopolApp:

Public Member Functions
string	ProgramName () override
	program name
void	HelpText (ostream &out) override
	help text of application without version information
bool	DoMapping (void) override
	overload and return true to enable mapping command line options
void	Initialize (void) override
	Initialize application data.
bool	EvaluateOptions (void) override
	Process command line options.
bool	EvaluateTopology (Topology *top, Topology *top_ref) override
	called after topology was loaded
Public Member Functions inherited from votca::csg::CsgApplication
	CsgApplication ()=default
	~CsgApplication () override=default
void	Run (void) override
	Main body of application.
void	ShowHelpText (std::ostream &out) override
virtual bool	DoMappingDefault (void)
	if DoMapping is true, will by default require mapping or not
virtual bool	DoTrajectory (void)
	overload and return true to enable trajectory command line options
virtual bool	DoThreaded (void)
virtual bool	SynchronizeThreads (void)
virtual bool	NeedsTopology (void)
	if topology is always needed
void	AddObserver (CGObserver *observer)
virtual void	BeginEvaluate (Topology *top, Topology *top_ref=nullptr)
	called before the first frame
virtual void	EndEvaluate ()
	called after the last frame
virtual void	EvalConfiguration (Topology *top, Topology *top_ref=nullptr)
bool	ProcessData (Worker *worker)
	Gets frames from TrajectoryReader in an ordered way and, if successful, calls Worker::EvalConfiguration for that frame.
virtual std::unique_ptr< Worker >	ForkWorker (void)
virtual void	MergeWorker (Worker *worker)
Public Member Functions inherited from votca::tools::Application
	Application ()
virtual	~Application ()
int	Exec (int argc, char **argv)
	executes the program
virtual std::string	VersionString ()
	version string of application
void	CheckRequired (const std::string &option_name, const std::string &error_msg="")
	Check weather required option is set.
boost::program_options::options_description_easy_init	AddProgramOptions (const std::string &group="")
	add option for command line
boost::program_options::variables_map &	OptionsMap ()
	get available program options & descriptions
boost::program_options::options_description &	OptionsDesc ()
boost::program_options::options_description &	VisibleOptions ()
	filters out the Hidden group from the options descriptions
void	StopExecution ()
	call StopExecution after EvaluateOptions

Protected Member Functions
void	WriteAtoms (ostream &out, Molecule &cg)
void	WriteInteractions (ostream &out, const Topology &top, Molecule &cg)
void	WriteMolecule (ostream &out, const Topology &top, Molecule &cg)
Protected Member Functions inherited from votca::tools::Application

Additional Inherited Members
Protected Attributes inherited from votca::csg::CsgApplication
std::list< CGObserver * >	observers_
bool	do_mapping_
std::vector< std::unique_ptr< Worker > >	myWorkers_
Index	nframes_
bool	is_first_frame_
Index	nthreads_
tools::Mutex	nframesMutex_
tools::Mutex	traj_readerMutex_
std::vector< std::unique_ptr< tools::Mutex > >	threadsMutexesIn_
	stores Mutexes used to impose order for input
std::vector< std::unique_ptr< tools::Mutex > >	threadsMutexesOut_
	stores Mutexes used to impose order for output
std::unique_ptr< TrajectoryReader >	traj_reader_
Protected Attributes inherited from votca::tools::Application
std::map< std::string, boost::program_options::options_description >	op_groups_
bool	continue_execution_ = true

Detailed Description

Definition at line 32 of file csg_gmxtopol.cc.

Member Function Documentation

DoMapping()

bool GmxTopolApp::DoMapping ( void )

inlineoverridevirtual

overload and return true to enable mapping command line options

Reimplemented from votca::csg::CsgApplication.

Definition at line 40 of file csg_gmxtopol.cc.

EvaluateOptions()

bool GmxTopolApp::EvaluateOptions ( void )

inlineoverridevirtual

Process command line options.

Returns

true to continue, false to stop

EvaluateOptions is called by Run after parsing the command line. return true if everything is ok, false to stop and show help text.

Reimplemented from votca::csg::CsgApplication.

Definition at line 43 of file csg_gmxtopol.cc.

EvaluateTopology()

bool GmxTopolApp::EvaluateTopology ( Topology * , Topology *  )

overridevirtual

called after topology was loaded

Reimplemented from votca::csg::CsgApplication.

Definition at line 63 of file csg_gmxtopol.cc.

HelpText()

void GmxTopolApp::HelpText ( ostream & out )

inlineoverridevirtual

help text of application without version information

Parameters

out	ostream for output

Implements votca::tools::Application.

Definition at line 35 of file csg_gmxtopol.cc.

Initialize()

void GmxTopolApp::Initialize ( void )

overridevirtual

Initialize application data.

Initialize is called by run before parsing the command line. All necessary command line arguments can be added here

Reimplemented from votca::csg::CsgApplication.

Definition at line 56 of file csg_gmxtopol.cc.

ProgramName()

string GmxTopolApp::ProgramName ( )

inlineoverridevirtual

program name

Returns

string with program name

overload this function to set the program name

Implements votca::tools::Application.

Definition at line 34 of file csg_gmxtopol.cc.

WriteAtoms()

void GmxTopolApp::WriteAtoms ( ostream & out, Molecule & cg )

protected

Definition at line 75 of file csg_gmxtopol.cc.

WriteInteractions()

void GmxTopolApp::WriteInteractions ( ostream & out, const Topology & top, Molecule & cg )

protected

Definition at line 86 of file csg_gmxtopol.cc.

WriteMolecule()

void GmxTopolApp::WriteMolecule ( ostream & out, const Topology & top, Molecule & cg )

protected

Definition at line 123 of file csg_gmxtopol.cc.

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The documentation for this class was generated from the following file:

• csg/src/tools/csg_gmxtopol.cc