Package ffx.potential.cli

Class AtomSelectionOptions

java.lang.Object

ffx.potential.cli.AtomSelectionOptions

public class AtomSelectionOptions
extends Object

Represents command line options for scripts that support atom selections.

Since:

1.0

Author:

Michael J. Schnieders

Constructor Summary

Constructors

Constructor	Description
AtomSelectionOptions()

Method Summary

Modifier and Type	Method	Description
static void	actOnAtoms(MolecularAssembly assembly, String selection, BiConsumer<Atom,Boolean> action, String description)
String	getActiveAtoms()	--aa or --activeAtoms Ranges of active atoms [NONE, ALL, Range(s): 1-3,6-N].
String	getInactiveAtoms()	--ia or --inactiveAtoms Ranges of inactive atoms [NONE, ALL, Range(s): 1-3,6-N].
boolean	isAtomSelectionSet()	Check if either the active or inactive atom selection is set.
void	setActiveAtoms(MolecularAssembly molecularAssembly)	Set active atoms for a MolecularAssembly.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details

AtomSelectionOptions

public AtomSelectionOptions()

Method Details

actOnAtoms

public static void actOnAtoms(@Nonnull
 MolecularAssembly assembly,
 @Nullable
 String selection,
 @Nonnull
 BiConsumer<Atom,Boolean> action,
 @Nonnull
 String description)

getActiveAtoms

public String getActiveAtoms()

--aa or --activeAtoms Ranges of active atoms [NONE, ALL, Range(s): 1-3,6-N].

Returns:

Returns active atoms.

setActiveAtoms

public void setActiveAtoms(MolecularAssembly molecularAssembly)

Set active atoms for a MolecularAssembly.

Parameters:

molecularAssembly - a MolecularAssembly object.

getInactiveAtoms

public String getInactiveAtoms()

--ia or --inactiveAtoms Ranges of inactive atoms [NONE, ALL, Range(s): 1-3,6-N].

Returns:

Returns inactive atoms.

isAtomSelectionSet

public boolean isAtomSelectionSet()

Check if either the active or inactive atom selection is set.

Returns:

True if one of the fields is not empty.