Package 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
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 (
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
- See Also:
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Field Summary
Fields inherited from class chemaxon.checkers.AbstractStructureChecker
errorType, propertyChangeSupport
Fields inherited from interface chemaxon.checkers.StructureChecker
PROPERTY_KEY_VALID
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Constructor Summary
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Method Summary
Modifier and TypeMethodDescriptionprotected boolean
Checks if the component with index i has problemprotected StructureCheckerResult
Iterates through the components and checks every component.protected Molecule
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
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Constructor Details
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OverlappingAtomsChecker
public OverlappingAtomsChecker()
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Method Details
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check1
Description copied from class:ComponentChecker
Iterates through the components and checks every component. If a component has error it is added to aList
. After the iteration if no problem occurred the result is null otherwise the method creates aStructureCheckerResult
containing the atoms and bonds of the problematic components.- Overrides:
check1
in classComponentChecker<MolAtom>
- Parameters:
molecule
- theMolecule
instance to be checked for problems- Returns:
- a
StructureCheckerResult
which contains all the indices of the problematic components
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check
Description copied from class:ComponentChecker
Checks if the component with index i has problem- Specified by:
check
in classComponentChecker<MolAtom>
- Parameters:
molecule
- is aMolecule
instanceatom
- the current component to check- Returns:
- true if the component has problem, false otherwise
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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 classAbstractStructureChecker
- Parameters:
molecule
- the molecule to check- Returns:
- the original molecule, or a clone with expanded sgroups
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