Package chemaxon.checkers

Class AtomChecker

java.lang.Object

chemaxon.checkers.AbstractStructureChecker

chemaxon.checkers.ComponentChecker<MolAtom>

chemaxon.checkers.AtomChecker

All Implemented Interfaces:

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

Direct Known Subclasses:

AliasChecker, AtomMapChecker, AtomQueryPropertyChecker, AtomTypeChecker, AtomValueChecker, ExplicitLonePairChecker, IsotopeChecker, MissingAtomMapChecker, MultiCenterChecker, OverlappingAtomsChecker, PseudoAtomChecker, QueryAtomChecker, RacemateChecker, RadicalChecker, StarAtomChecker, StereoInversionRetentionMarkChecker, ThreeDimensionChecker, ValencePropertyChecker

@PublicAPI
public abstract class AtomChecker
extends ComponentChecker<MolAtom>

Descendants of the abstract AtomChecker class check every atom for a specific error or property.

Since:

Marvin 5.3

Field Summary

Fields inherited from class chemaxon.checkers.AbstractStructureChecker

errorType, propertyChangeSupport

Fields inherited from interface chemaxon.checkers.StructureChecker

PROPERTY_KEY_VALID

Constructor Summary

Constructors

Constructor	Description
AtomChecker(StructureCheckerErrorType errorType)	Constructor to create a Structure checker instance with the given errorType.

Method Summary

Modifier and Type	Method	Description
protected StructureCheckerResult	createResult(Molecule molecule, List<MolAtom> atoms)	Creates a StructureCheckerResult from a List containing the components.
protected MolAtom	getComponent(Molecule molecule, int i)	Gets the component from the molecule with index i.
protected int	getComponentCount(Molecule molecule)	Gets the number of the components in the molecule

Methods inherited from class chemaxon.checkers.ComponentChecker

check, 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, isValid, 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

Constructor Detail

AtomChecker

public AtomChecker(StructureCheckerErrorType errorType)

Constructor to create a Structure checker instance with the given errorType.

Parameters:

errorType - element of StructureCheckerErrorType

Method Detail

getComponentCount

protected int getComponentCount(Molecule molecule)

Description copied from class: ComponentChecker

Gets the number of the components in the molecule

Specified by:

getComponentCount in class ComponentChecker<MolAtom>

Parameters:

molecule - the molecule to check

Returns:

the number of the components in the molecule

getComponent

protected MolAtom getComponent(Molecule molecule,
                               int i)

Description copied from class: ComponentChecker

Gets the component from the molecule with index i.

Specified by:

getComponent in class ComponentChecker<MolAtom>

Parameters:

molecule - the molecule to check

i - the index of the component

Returns:

the component

createResult

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

Description copied from class: ComponentChecker

Creates a StructureCheckerResult from a List containing the components.

Specified by:

createResult in class ComponentChecker<MolAtom>

Parameters:

molecule - is a Molecule instance

atoms - is an instance of List containing the problematic components

Returns:

a StructureCheckerResult containing all problematic component indices