Distill the results of file identification, producing clean lists of free topologies, free coordinate files, and linked topology / coordinate systems. Record output and trajectory files, if available. More...

#include <nml_files.h>

Public Member Functions
int	getStructureCount () const
	Get the structure count, based on the number of free coordinate files as well as the number of systems, with frame counts and replicas therein. If one of the systems does not have the requisite number of frames, this is an error and may be trapped. The structure count reported here is therefore a maximum that can be expected.

int	getFreeTopologyCount () const
	Get the free topology count.

int	getFreeCoordinatesCount () const
	Get the free coordinate file count.

int	getSystemDefinitionCount () const
	Get the number of system specifications made with the -sys keyword.

bool	readAllFreeFrames () const
	Get the indicator of whether to read all free coordinate files' frames.

CoordinateFileKind	getOutputCoordinateFormat () const
	Get the coordinate (trajectory) file output format.

CoordinateFileKind	getCheckpointFormat () const
	Get the coordinate (checkpoint) file output format.

TrajectoryFusion	getFileFusionProtocol () const
	Get the preferences for fusing output coordinate files.

MoleculeSystem	getSystem (int index) const
	Get a molecule system from this object's array.

std::string	getReportFile () const
	Get the name of the report file (equivalent to mdout in sander or pmemd)

std::string	getInputTranscriptFile () const
	Get the name of the input transcript file (there is no sander or pmemd equivalent other than the verbose reproduction of the input settings at the beginning of mdout)

std::string	getTrajectoryFileName () const
	Get the base name of trajectory files to write.

std::string	getCheckpointFileName () const
	Get the base name of (coordinate) checkpoint files to write.

std::string	getWarningFileName () const
	Get the name of the file containing warnings printed by the program.

ModificationPolicy	getSdfModificationPolicy () const
	Get the policy on modifying .sdf file outputs to conform to the Biovia standard.

ExceptionResponse	getSdfNotifications () const
	Get an indication of whether to alert the user when correcting minor mistakes in .sdf files.

const NamelistEmulator &	getTranscript () const
	Get the original namelist emulator object as a transcript of the user input.

void	setAllFreeFrameReading (const bool active)
	Set whether to read all frames from each free trajectory (true), or just the first (false).

void	addFreeTopologyName (const std::string &file_name)
	Add a free topology to the list, after checking for its prior existence in the list.

void	addFreeCoordinateName (const std::string &file_name)
	Add a free coordinate file to the list, after checking for its prior existence.

void	addSystem (const MoleculeSystem &new_mol)
	Add a system to the list.

void	removeSystem (int index, int stretch=1)
	Remove entries from the systems array.

void	setReportFileName (const std::string &file_name)
	Set the report file name.

void	setInputTranscriptFileName (const std::string &file_name)
	Set the input transcript file name.

void	setGeneralTrajectoryFileName (const std::string &proto_name)
	Set the general (fallback) coordinate output file name.

void	setGeneralCheckpointFileName (const std::string &proto_name)
	Set the general (fallback) checkpoint file name.

void	setWarningFileName (const std::string &file_name)
	Set the warning file name.

void	setSdfModficiationPolicy (ModificationPolicy policy_in)
	Set the .sdf output file modification policy.

void	setSdfNotifications (ExceptionResponse policy_in)
	Set whether to emit notifications about .sdf output file modifications.


	FilesControls (ExceptionResponse policy_in=ExceptionResponse::DIE, WrapTextSearch wrap=WrapTextSearch::NO)
	The constructor can prepare an object with default settings or read the corresponding namelist to accept user input.

	FilesControls (const TextFile &tf, int start_line, bool found_nml=nullptr, ExceptionResponse policy_in=ExceptionResponse::DIE, WrapTextSearch wrap=WrapTextSearch::NO, const std::vector< std::string > &alternatives={}, const std::vector< std::string > &sys_requirements={"-pe", "-ce"})


	FilesControls (const FilesControls &original)=default
	As with other control objects, copy and move constructors, plus copy and move assignment operators, can all take their default forms.

	FilesControls (FilesControls &&original)=default

FilesControls &	operator= (const FilesControls &original)=default

FilesControls &	operator= (FilesControls &&original)=default


std::string	getFreeTopologyName (int index) const
	Get one or more free topology names.

std::vector< std::string >	getFreeTopologyNames () const


std::string	getFreeCoordinateName (int index) const
	Get one or more free coordinate file names.

std::vector< std::string >	getFreeCoordinateNames () const


void	setOutputCoordinateFormat (const std::string &traj_kind)
	Set the coordinate (trajectory) file output format.

void	setOutputCoordinateFormat (CoordinateFileKind traj_kind)


void	setCheckpointFormat (const std::string &chk_kind)
	Set the checkpoint (coordinate) file output format.

void	setCheckpointFormat (CoordinateFileKind chk_kind)


void	removeFreeTopologyName (int index, int stretch=1)
	Remove entries from the free topologies array.

void	removeFreeTopologyName (const std::string &fname)


void	removeFreeCoordinateName (int index, int stretch=1)
	Remove entries from the free coordinates array.

void	removeFreeCoordinateName (const std::string &fname)

Detailed Description

Distill the results of file identification, producing clean lists of free topologies, free coordinate files, and linked topology / coordinate systems. Record output and trajectory files, if available.

Constructor & Destructor Documentation

◆ FilesControls()

stormm::namelist::FilesControls::FilesControls	(	ExceptionResponse	policy_in = ExceptionResponse::DIE,
		WrapTextSearch	wrap = WrapTextSearch::NO )

The constructor can prepare an object with default settings or read the corresponding namelist to accept user input.

Parameters

policy_in	Requested error handling behavior
tf	Input file translated into RAM
start_line	Line of the input file to begin searching for the &solvent namelist
found_nml	Indication that the namelist was found
report_name_in	New default name of the report file (for application-specific naming conventions)
coord_base_in	New default base name of trajectory or other coordinate files (for application-specific naming conventions)
coord_ext_in	New default extension of trajectory or other coordinate files (for application-specific naming conventions)
sys_requirements	System requirements specifications. The -sys keyword will be critical under different circumstances and has no defaults. Some situations may not require the user to specify all four of the files associated with the -sys keyword, and some situations will require that certain files exist in addition to merely being specified. This array can hold four critical specifiers, -p, -c, -x, and -r, for "topology", "input coordinates", "trajectory", and "restart / checkpoint" files, respectively, and each can accept the extension "e" to indicate that the file must exist. Conversely, a "g" extension indicates that, in that particular context, the file subkey is bogus and should trigger an exception consistent with the stated policy (policy_in). Default requirements are a topology and input coordinates, both of which must exist.
wrap	Indicate that the search for a &files namelist should carry on from the beginning of an input file if no such namelist is found starting from the original starting point

Member Function Documentation

◆ addFreeCoordinateName()

void stormm::namelist::FilesControls::addFreeCoordinateName ( const std::string & file_name )

Add a free coordinate file to the list, after checking for its prior existence.

Parameters

file_name Name of the coordinate file to add

◆ addFreeTopologyName()

void stormm::namelist::FilesControls::addFreeTopologyName ( const std::string & file_name )

Add a free topology to the list, after checking for its prior existence in the list.

Parameters

file_name Name of the topology file to add

◆ addSystem()

void stormm::namelist::FilesControls::addSystem ( const MoleculeSystem & new_mol )

Add a system to the list.

Parameters

new_mol The new molecule system to push to the back of the list

◆ getFreeCoordinateName()

std::string stormm::namelist::FilesControls::getFreeCoordinateName ( int index ) const

Get one or more free coordinate file names.

Overloaded:

Get the free coordinate file named at one index of the array
Get all free coordinate file names in the array

Parameters

index The index to query

◆ getFreeTopologyName()

std::string stormm::namelist::FilesControls::getFreeTopologyName ( int index ) const

Get one or more free topology names.

Overloaded:

Get the free topology named at one index of the array
Get all free topology names in the array

Parameters

index The index to query

◆ getSystem()

MoleculeSystem stormm::namelist::FilesControls::getSystem ( int index ) const

Get a molecule system from this object's array.

Parameters

index The index to query

◆ removeFreeCoordinateName()

void stormm::namelist::FilesControls::removeFreeCoordinateName	(	int	index,
		int	stretch = 1 )

Remove entries from the free coordinates array.

Overloaded:

Remove coordinate files in a numbered range
Remove a coordinate file by name

Parameters

index	Starting index for system removal, or the one system to remove
stretch	Number of systems, including the starting index, to remove from the list

◆ removeFreeTopologyName()

void stormm::namelist::FilesControls::removeFreeTopologyName	(	int	index,
		int	stretch = 1 )

Remove entries from the free topologies array.

Overloaded:

Remove topologies in a numbered range
Remove a topology by name

Parameters

index	Starting index for system removal, or the one system to remove
stretch	Number of systems, including the starting index, to remove from the list

◆ removeSystem()

void stormm::namelist::FilesControls::removeSystem	(	int	index,
		int	stretch = 1 )

Remove entries from the systems array.

Parameters

index	Starting index for system removal, or the one system to remove
stretch	Number of systems, including the starting index, to remove from the list

◆ setAllFreeFrameReading()

void stormm::namelist::FilesControls::setAllFreeFrameReading ( const bool active )

Set whether to read all frames from each free trajectory (true), or just the first (false).

Parameters

active Indicator of whether to have all free frames read (true), or not (false)

◆ setCheckpointFormat()

void stormm::namelist::FilesControls::setCheckpointFormat ( const std::string & chk_kind )

Set the checkpoint (coordinate) file output format.

Overloaded:

Take a string value specifying the coordinate file kind
Take the literal, enumerated type

Parameters

chk_kind The selected checkpoint format

◆ setGeneralCheckpointFileName()

void stormm::namelist::FilesControls::setGeneralCheckpointFileName ( const std::string & proto_name )

Set the general (fallback) checkpoint file name.

Parameters

proto_name New generic name for unspecified checkpoint files

◆ setGeneralTrajectoryFileName()

void stormm::namelist::FilesControls::setGeneralTrajectoryFileName ( const std::string & proto_name )

Set the general (fallback) coordinate output file name.

Parameters

proto_name New generic name for unspecified trajectory files

◆ setInputTranscriptFileName()

void stormm::namelist::FilesControls::setInputTranscriptFileName ( const std::string & file_name )

Set the input transcript file name.

Parameters

file_name New name for the input transcript file

◆ setOutputCoordinateFormat()

void stormm::namelist::FilesControls::setOutputCoordinateFormat ( const std::string & traj_kind )

Set the coordinate (trajectory) file output format.

Overloaded:

Take a string value specifying the coordinate file kind
Take the literal, enumerated type

Parameters

traj_kind The selected trajectory format

◆ setReportFileName()

void stormm::namelist::FilesControls::setReportFileName ( const std::string & file_name )

Set the report file name.

Parameters

file_name New name for the calculation report file

◆ setSdfModficiationPolicy()

void stormm::namelist::FilesControls::setSdfModficiationPolicy ( ModificationPolicy policy_in )

Set the .sdf output file modification policy.

Parameters

policy_in The new policy to follow when encountering minor issues in .sdf file data

◆ setSdfNotifications()

void stormm::namelist::FilesControls::setSdfNotifications ( ExceptionResponse policy_in )

Set whether to emit notifications about .sdf output file modifications.

Parameters

policy_in The policy to follow on making alerts

◆ setWarningFileName()

void stormm::namelist::FilesControls::setWarningFileName ( const std::string & file_name )

Set the warning file name.

Parameters

file_name New name for the warnings file

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

src/Namelists/nml_files.h
src/Namelists/nml_files.cpp

Public Member Functions

Detailed Description

Constructor & Destructor Documentation

◆ FilesControls()

Member Function Documentation

◆ addFreeCoordinateName()

◆ addFreeTopologyName()

◆ addSystem()

◆ getFreeCoordinateName()

◆ getFreeTopologyName()

◆ getSystem()

◆ removeFreeCoordinateName()

◆ removeFreeTopologyName()

◆ removeSystem()

◆ setAllFreeFrameReading()

◆ setCheckpointFormat()

◆ setGeneralCheckpointFileName()

◆ setGeneralTrajectoryFileName()

◆ setInputTranscriptFileName()

◆ setOutputCoordinateFormat()

◆ setReportFileName()

◆ setSdfModficiationPolicy()

◆ setSdfNotifications()

◆ setWarningFileName()