Package chemaxon.checkers

Class OverlappingBondsChecker

java.lang.Object

chemaxon.checkers.AbstractStructureChecker

chemaxon.checkers.ComponentChecker<MolBond>

chemaxon.checkers.BondChecker

chemaxon.checkers.OverlappingBondsChecker

All Implemented Interfaces:

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

@PublicAPI
public class OverlappingBondsChecker
extends BondChecker

OverlappingBondsChecker detects bonds that are too close to each other.

This checker checks two dimensional structures only.

Two bonds considered as overlapping when they crossing each other, or their distance is smaller then the 80% of the standard Chemaxon bond length ( MolBond.CCLENGTH ). Here distance means the distance of two line segments in euclidean space.

Since:

Marvin 5.3

See Also:

MolBond.CCLENGTH

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
OverlappingBondsChecker()	Default constructor

Method Summary

Modifier and Type	Method	Description
protected boolean	check(Molecule molecule, MolBond bond)	Detects bond of the molecule is crossing another bond or closer than the limit distance.
protected StructureCheckerResult	check1(Molecule molecule)	Iterates through the components and checks every component.
protected Molecule	expandMolecule(Molecule molecule, Map<MolAtom,MolAtom> atomMap, Map<MolBond,MolBond> bondMap)	Returns the original molecule if no groups to expand, or the clone of the original molecule with expanded groups.

Methods inherited from class chemaxon.checkers.BondChecker

createResult, getComponent, getComponentCount

Methods inherited from class chemaxon.checkers.ComponentChecker

initialize

Methods inherited from class chemaxon.checkers.AbstractStructureChecker

addPropertyChangeListener, addPropertyChangeListener, check, clone, cloneItem, convertResult, equals, 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

OverlappingBondsChecker

public OverlappingBondsChecker()

Default constructor

Method Detail

check1

protected StructureCheckerResult check1(Molecule molecule)

Description copied from class: ComponentChecker

Iterates through the components and checks every component. If a component has error it is added to a List. After the iteration if no problem occurred the result is null otherwise the method creates a StructureCheckerResult containing the atoms and bonds of the problematic components.

Overrides:

check1 in class ComponentChecker<MolBond>

Parameters:

molecule - the Molecule instance to be checked for problems

Returns:

a StructureCheckerResult which contains all the indices of the problematic components

check

protected boolean check(Molecule molecule,
                        MolBond bond)

Detects bond of the molecule is crossing another bond or closer than the limit distance.

Specified by:

check in class ComponentChecker<MolBond>

Parameters:

bond - the index of the bond (MolBond instance) in the molecule to check

molecule - is a Molecule instance

Returns:

true if the molecule contains crossing bonds, false otherwise

expandMolecule

protected Molecule expandMolecule(Molecule molecule,
                                  Map<MolAtom,MolAtom> atomMap,
                                  Map<MolBond,MolBond> bondMap)

Description copied from class: AbstractStructureChecker

Returns the original molecule if no groups to expand, or the clone of the original molecule with expanded groups.

Overrides:

expandMolecule in class AbstractStructureChecker

Parameters:

molecule - the molecule to check

Returns:

the original molecule, or a clone with expanded sgroups