class for writing dlpoly topology files More...

Inheritance diagram for DLPTopolApp:

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Collaboration diagram for DLPTopolApp:

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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	Initialize () override
	Initialize application data.

bool	EvaluateOptions () override
	Process command line options.

void	Run (void) override
	Main body of application.

void	ShowHelpText (std::ostream &out) override

virtual bool	DoMapping (void)
	overload and return true to enable mapping command line options

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

virtual bool	EvaluateTopology (Topology , Topology =nullptr)
	called after topology was loaded

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	ProgramName ()=0
	program name

virtual std::string	VersionString ()
	version string of application

virtual void	HelpText (std::ostream &out)=0
	help text of application without version information

virtual void	Initialize ()=0
	Initialize application data.

virtual bool	EvaluateOptions ()=0
	Process command line options.

void	CheckRequired (const std::string &option_name, const std::string &error_msg="")
	Check weather required option is set.

virtual void	Run ()=0
	Main body of application.

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	WriteMoleculeAtoms (ostream &out, const Molecule &cg)

void	WriteMoleculeInteractions (ostream &out, const Molecule &cg)

void	WriteVDWInteractions (ostream &out, const Molecule &cg)

void	WriteMolecularType (ostream &out, const Molecule &cg, votca::Index nummol)

virtual void	ShowHelpText (std::ostream &out)

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

class for writing dlpoly topology files

This class encapsulates the dlpoly topology writing functions

Definition at line 39 of file csg_dlptopol.cc.

Member Function Documentation

◆ DoMapping()

bool DLPTopolApp::DoMapping ( void )

inlineoverridevirtual

overload and return true to enable mapping command line options

Reimplemented from votca::csg::CsgApplication.

Definition at line 56 of file csg_dlptopol.cc.

◆ EvaluateOptions()

bool DLPTopolApp::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 59 of file csg_dlptopol.cc.

◆ EvaluateTopology()

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

overridevirtual

called after topology was loaded

Reimplemented from votca::csg::CsgApplication.

Definition at line 84 of file csg_dlptopol.cc.

◆ HelpText()

void DLPTopolApp::HelpText ( ostream & out )

inlineoverridevirtual

help text of application without version information

Parameters

out	ostream for output

Implements votca::tools::Application.

Definition at line 42 of file csg_dlptopol.cc.

◆ Initialize()

void DLPTopolApp::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 74 of file csg_dlptopol.cc.

◆ ProgramName()

string DLPTopolApp::ProgramName ( )

inlineoverridevirtual

program name

Returns: string with program name

overload this function to set the program name

Implements votca::tools::Application.

Definition at line 41 of file csg_dlptopol.cc.

◆ WriteMolecularType()

void DLPTopolApp::WriteMolecularType	(	ostream &	out,
		const Molecule &	cg,
		votca::Index	nummol
	)

protected

Definition at line 300 of file csg_dlptopol.cc.

◆ WriteMoleculeAtoms()

void DLPTopolApp::WriteMoleculeAtoms	(	ostream &	out,
		const Molecule &	cg
	)

protected

Definition at line 222 of file csg_dlptopol.cc.

◆ WriteMoleculeInteractions()

void DLPTopolApp::WriteMoleculeInteractions	(	ostream &	out,
		const Molecule &	cg
	)

protected

Definition at line 245 of file csg_dlptopol.cc.

◆ WriteVDWInteractions()

void DLPTopolApp::WriteVDWInteractions	(	ostream &	out,
		const Molecule &	cg
	)

protected

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

csg/src/tools/csg_dlptopol.cc

Public Member Functions

Protected Member Functions

Additional Inherited Members

Detailed Description

Member Function Documentation

◆ DoMapping()

◆ EvaluateOptions()

◆ EvaluateTopology()

◆ HelpText()

◆ Initialize()

◆ ProgramName()

◆ WriteMolecularType()

◆ WriteMoleculeAtoms()

◆ WriteMoleculeInteractions()

◆ WriteVDWInteractions()