chemaxon.checkers

Class OverlappingAtomsChecker

java.lang.Object

chemaxon.checkers.AbstractStructureChecker

chemaxon.checkers.ComponentChecker<MolAtom>

chemaxon.checkers.AtomChecker

chemaxon.checkers.OverlappingAtomsChecker

All Implemented Interfaces:

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

public class OverlappingAtomsChecker
extends AtomChecker

OverlappingAtomsChecker detects atoms that are too close to each other.

This checker checks 2D structures only.

Two atoms considered as overlapping when their euclidean distance is less than the half of the ChemAxon standard bond length ( MolBond.CCLENGTH ).

Since:

Marvin 5.3

Version:

5.7

Author:

Attila Szabo

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 and Description
OverlappingAtomsChecker() Default constructor

Method Summary

Methods

Modifier and Type	Method and Description
protected boolean	check(Molecule molecule, MolAtom atom) Examines if an atom is closer to another than the given distance limit.
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.AtomChecker

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

OverlappingAtomsChecker

public OverlappingAtomsChecker()

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<MolAtom>

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,
            MolAtom atom)

Examines if an atom is closer to another than the given distance limit.

Specified by:

check in class ComponentChecker<MolAtom>

Parameters:

atom - the index of atom in the molecule to check

molecule - is a Molecule instance

Returns:

true if the molecule contains overlapping atoms, otherwise false

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