Package chemaxon.checkers

Class PseudoAtomChecker

java.lang.Object

chemaxon.checkers.AbstractStructureChecker

chemaxon.checkers.ComponentChecker<MolAtom>

chemaxon.checkers.AtomChecker

chemaxon.checkers.PseudoAtomChecker

All Implemented Interfaces:

StructureChecker, chemaxon.license.Licensable, PropertyChangeListener, Cloneable, EventListener

@PublicApi
public class PseudoAtomChecker
extends AtomChecker

A descendant of AtomChecker detecting pseudo atoms.

Since:

Marvin 5.3

See Also:

• MolAtom.isPseudo()

Field Summary

Fields

Modifier and Type	Field	Description
static final String	PROPERTY_KEY_EXCLUDED	This public constant String represents the name of the property which is responsible for the list of excluded pseudo atom labels
static final String	PROPERTY_KEY_SEARCH_EXCLUDED

Fields inherited from class chemaxon.checkers.AbstractStructureChecker

errorType, propertyChangeSupport

Fields inherited from interface chemaxon.checkers.StructureChecker

PROPERTY_KEY_VALID

Constructor Summary

Constructors

Constructor	Description
PseudoAtomChecker()	Default constructor
PseudoAtomChecker(Map<String,String> params)

Method Summary

Modifier and Type	Method	Description
protected boolean	check(Molecule molecule, MolAtom atom)	Checks if the component with index i has problem
protected StructureCheckerResult	createResult(Molecule molecule, List<MolAtom> atoms)	Creates a StructureCheckerResult from a List containing the components.
AtomLabels	getExcluded()
boolean	isValid()	Returns true if the checker's configuration is valid, false otherwise
void	setExcluded(AtomLabels excluded)

Methods inherited from class chemaxon.checkers.AtomChecker

getComponent, getComponentCount

Methods inherited from class chemaxon.checkers.ComponentChecker

check1, initialize

Methods inherited from class chemaxon.checkers.AbstractStructureChecker

addPropertyChangeListener, addPropertyChangeListener, check, clone, cloneItem, convertResult, equals, expandMolecule, getDescription, getDescriptor, getEditorClassName, getErrorCode, getErrorDescription, getErrorType, getHelpText, getIcon, getLocalMenuName, getName, hashCode, isAvailable, isLicensed, propertyChange, removePropertyChangeListener, removePropertyChangeListener, setDescription, setHelpText, setIcon, setLicenseEnvironment, setLocalMenuName, setMoreErrorMessage, setName, setNoErrorMessage, setOneErrorMessage, toString

Methods inherited from class java.lang.Object

finalize, getClass, notify, notifyAll, wait, wait, wait

Field Details

PROPERTY_KEY_EXCLUDED

public static final String PROPERTY_KEY_EXCLUDED

This public constant String represents the name of the property which is responsible for the list of excluded pseudo atom labels

Since:

16.9.26

See Also:

• Constant Field Values

PROPERTY_KEY_SEARCH_EXCLUDED

public static final String PROPERTY_KEY_SEARCH_EXCLUDED

See Also:

• Constant Field Values

Constructor Details

PseudoAtomChecker

public PseudoAtomChecker()

Default constructor

PseudoAtomChecker

public PseudoAtomChecker(Map<String,String> params)

Method Details

getExcluded

public AtomLabels getExcluded()

setExcluded

public void setExcluded(AtomLabels excluded)

isValid

public boolean isValid()

Description copied from interface: StructureChecker

Returns true if the checker's configuration is valid, false otherwise

Specified by:

isValid in interface StructureChecker

Overrides:

isValid in class AbstractStructureChecker

Returns:

true if the checker's configuration is valid, false otherwise

check

protected boolean check(Molecule molecule,
 MolAtom atom)

Description copied from class: ComponentChecker

Checks if the component with index i has problem

Specified by:

check in class ComponentChecker<MolAtom>

Parameters:

molecule - is a Molecule instance

atom - the current component to check

Returns:

true if the component has problem, false otherwise

createResult

protected StructureCheckerResult createResult(Molecule molecule,
 List<MolAtom> atoms)

Description copied from class: ComponentChecker

Creates a StructureCheckerResult from a List containing the components.

Overrides:

createResult in class AtomChecker

Parameters:

molecule - is a Molecule instance

atoms - is an instance of List containing the problematic components

Returns:

a StructureCheckerResult containing all problematic component indices