stormm::synthesis::MoleculeSystem Class Reference

Object to encapsulate a system, a coupled set of coordinates and a single topology. This can be used to enforce conf.stormm to read certain coordinates in the context of a particular topology, even when other viable topologies might be available. More...

#include <nml_files.h>

Public Member Functions
const std::string &	getTopologyFileName () const
	Get the name of the topology file in this system.
const std::string &	getInputCoordinateFileName () const
	Get the name of the input coordinates file.
const std::string &	getTrajectoryFileName () const
	Get the name of the trajectory file.
const std::string &	getCheckpointFileName () const
	Get the name of the checkpoint file to write for this system.
const std::string &	getLabel () const
	Get the assigned label for this system.
int	getStartingFrame () const
	Get the starting frame that this system will read for initial coordinate states.
int	getFinalFrame () const
	Get the last frame that this system will read for initial coordinate states.
int	getTotalFrames () const
	Get the total number of frames, thus initial states, that this system expects.
int	getReplicaCount () const
	Get the replica count for this system, the number of copies of each initial coordinate frame that it will spawn.
CoordinateFileKind	getInputCoordinateFileKind () const
	Get the type of input coordinate file.
CoordinateFileKind	getTrajectoryFileKind () const
	Get the type of trajectory file.
CoordinateFileKind	getCheckpointFileKind () const
	Get the type of checkpoint file.
void	setTopologyFileName (const std::string &file_name)
	Set the topology file name. This is useful if pre-allocating an array of MoleculeSystems and then filling it up later.
void	setInputCoordinateFileName (const std::string &file_name)
	Set the input coordinates file name.
void	setTrajectoryFileName (const std::string &file_name)
	Set the trajectory file name.
void	setCheckpointFileName (const std::string &file_name)
	Set the checkpoint file name.
void	setStartingFrame (int frame_number)
	Set the starting frame. This can be necessary if the input coordinates file does not contain the requested numbers of frames.
void	setFinalFrame (int frame_number)
	Set the final frame. This can be necessary if the input coordinates file does not contain the requested numbers of frames.
void	setReplicaCount (int count)
	Set the number of replicas.
bool	validateTopologyFile () const
	Report whether the topology file named in this system is a valid file. This validator is public so that it can be called by a wholistic validation strategy employed in the containing FilesControls object.
bool	validateInputCoordinateFile () const
	Report whether the input coordinate file named in this system is a valid file.
	MoleculeSystem ()
	The constructor can make a blank system or automatically fill values.
	MoleculeSystem (const std::string &topology_file_in, const std::string &coordinate_file_in, const std::string &trajectory_file_in, const std::string &checkpoint_file_in, const std::string &label_in, int frame_start_in, int frame_end_in, int replica_count_in, CoordinateFileKind coordinate_kind_in, CoordinateFileKind trajectory_kind_in, CoordinateFileKind checkpoint_kind_in)
	MoleculeSystem (const MoleculeSystem &original)=default
	This object, containing no const members or pointers to repair, can take the default copy and move constructors, plus copy and move assignment operators.
	MoleculeSystem (MoleculeSystem &&original)=default
MoleculeSystem &	operator= (const MoleculeSystem &original)=default
MoleculeSystem &	operator= (MoleculeSystem &&original)=default
void	setInputCoordinateFileKind (const std::string &kind)
	Set the input coordinates file type.
void	setInputCoordinateFileKind (CoordinateFileKind kind)
void	setTrajectoryFileKind (const std::string &kind)
	Set the trajectory file type.
void	setTrajectoryFileKind (CoordinateFileKind kind)
void	setCheckpointFileKind (const std::string &kind)
	Set the checkpoint file type.
void	setCheckpointFileKind (CoordinateFileKind kind)

Detailed Description

Object to encapsulate a system, a coupled set of coordinates and a single topology. This can be used to enforce conf.stormm to read certain coordinates in the context of a particular topology, even when other viable topologies might be available.

Constructor & Destructor Documentation

MoleculeSystem()

stormm::namelist::MoleculeSystem::MoleculeSystem

(

)

The constructor can make a blank system or automatically fill values.

Overloaded:

• Create a blank object
• Create an object with a complete list of files and read settings

Parameters

topology_file_in	Topology file for the system (its type will be detected later)
coordinate_file_in	Coordinate file for the system (input)
trajectory_file_in	Trajectory file for the system (output)
checkpoint_file_in	Restart file to write for the system (output)
label_in	System label, i.e. "MyBigProtein"
frame_start_in	Starting frame to begin reading input coordinates, if the input coordinate file is a trajectory
frame_end_in	Frame at which to stop reading coordinates, if the input coordinate file is a trajectory
replica_count_in	Number of replicas of this system to produce in the resulting SystemCache object
coordinate_kind_in	File type of the input coordinates file
trajectory_kind_in	File type of the resulting trajectory file
checkpoint_kind_in	File type of the checkpoint file

Member Function Documentation

setCheckpointFileKind()

void stormm::namelist::MoleculeSystem::setCheckpointFileKind

(

const std::string &

kind

)

Set the checkpoint file type.

Overloaded:

• Get the file type from a string (will be validated)
• Get the file type from a direct enumeration

Parameters

kind	The type of checkpoint file to write

setCheckpointFileName()

void stormm::namelist::MoleculeSystem::setCheckpointFileName

(

const std::string &

file_name

)

Set the checkpoint file name.

Parameters

file_name

The chosen file name

setFinalFrame()

void stormm::namelist::MoleculeSystem::setFinalFrame

(

int

frame_number

)

Set the final frame. This can be necessary if the input coordinates file does not contain the requested numbers of frames.

Parameters

frame_number

The selected frame number

setInputCoordinateFileKind()

void stormm::namelist::MoleculeSystem::setInputCoordinateFileKind

(

const std::string &

kind

)

Set the input coordinates file type.

Overloaded:

• Get the file type from a string (will be validated)
• Get the file type from a direct enumeration

Parameters

kind	The type of input coordinates file to expect (or that was detected)

setInputCoordinateFileName()

void stormm::namelist::MoleculeSystem::setInputCoordinateFileName

(

const std::string &

file_name

)

Set the input coordinates file name.

Parameters

file_name

The chosen file name

setReplicaCount()

void stormm::namelist::MoleculeSystem::setReplicaCount

(

int

count

)

Set the number of replicas.

Parameters

count

The number of system replicas to spawn

setStartingFrame()

void stormm::namelist::MoleculeSystem::setStartingFrame

(

int

frame_number

)

Set the starting frame. This can be necessary if the input coordinates file does not contain the requested numbers of frames.

Parameters

frame_number

The selected frame number

setTrajectoryFileKind()

void stormm::namelist::MoleculeSystem::setTrajectoryFileKind

(

const std::string &

kind

)

Set the trajectory file type.

Overloaded:

• Get the file type from a string (will be validated)
• Get the file type from a direct enumeration

Parameters

kind	The type of trajectory file to write

setTrajectoryFileName()

void stormm::namelist::MoleculeSystem::setTrajectoryFileName

(

const std::string &

file_name

)

Set the trajectory file name.

Parameters

file_name

The chosen file name

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

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