gmx::SelectionOptionBehavior Class Reference

#include <gromacs/selection/selectionoptionbehavior.h>

Inheritance diagram for gmx::SelectionOptionBehavior:

Collaboration diagram for gmx::SelectionOptionBehavior:

Description

Options behavior to allow using SelectionOptions.

This behavior wraps SelectionOptionManager, as well as all calls to SelectionCollection up to and including selection compilation.

To use selections through SelectionOption options in a ICommandLineOptionsModule, you need to

• create a SelectionCollection object,
• implement ITopologyProvider to return the topology or number of atoms to be used with the selections,
• create and add a SelectionOptionBehavior, and call initOptions() to add common options for selection control,
• use SelectionOption options to specify the selections used, and
• evaluate the selections when running the module for the desired sets of coordinates (see SelectionCollection::evaluate()).

The SelectionOptionBehavior provides the following functionalities to the module:

• Creates SelectionOptionManager and manages all calls to it.
• Creates an option to provide an ndx file, and loads it when necessary.
• Creates options to control general aspects of selections (see SelectionCollection::initOptions()), as well as a generic option to provide selections from a file.
• After all options have been processed, provides an interactive command-line prompt for any missing selections.
• Compiles the selections.

The behavior needs to be added before any options are created.

Public Member Functions
	SelectionOptionBehavior (SelectionCollection *selections, ITopologyProvider *topologyProvider)
	Creates a behavior to use selections. More...
void	initOptions (IOptionsContainer *options)
	Add common options for controlling selections. More...
void	initBehavior (Options *options) override
	Called when the behavior is associated with an options object. More...
void	optionsFinishing (Options *) override
	Called when all option values have been assigned. More...
void	optionsFinished () override
	Called when all option values have been processed. More...

Constructor & Destructor Documentation

gmx::SelectionOptionBehavior::SelectionOptionBehavior	(	SelectionCollection *	selections,
		ITopologyProvider *	topologyProvider
	)

Creates a behavior to use selections.

Parameters

[in,out]	selections	Selection collection to use.
[in]	topologyProvider	Callback to load/provide topology information to selections when required.

The methods in topologyProvider are called after all options have been parsed and finished, so the caller can, e.g., load the topology from a file specified by a file option.

Member Function Documentation

void gmx::SelectionOptionBehavior::initBehavior ( Options *  options )

overridevirtual

Called when the behavior is associated with an options object.

This method can, e.g., use Options::addManager() to associate managers with the options object.

Implements gmx::IOptionsBehavior.

void gmx::SelectionOptionBehavior::initOptions

(

IOptionsContainer *

options

)

Add common options for controlling selections.

This method is separate from the constructor so that the caller can control the order of options better.

void gmx::SelectionOptionBehavior::optionsFinished ( )

overridevirtual

Called when all option values have been processed.

This is called after Options::finish() (and typically after higher-level optionsFinished() methods, such as that in ICommandLineOptionsModule). This can add behavior that performs tasks based on the option values provided.

Implements gmx::IOptionsBehavior.

void gmx::SelectionOptionBehavior::optionsFinishing ( Options *  options )

inlineoverridevirtual

Called when all option values have been assigned.

This is called just before Options::finish(), and can, e.g., do operations that still influence the option values.

Implements gmx::IOptionsBehavior.

---

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

• api/legacy/include/gromacs/selection/selectionoptionbehavior.h
• src/gromacs/selection/selectionoptionbehavior.cpp