Package chemaxon.checkers
Class 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
Descendants of the abstract AtomChecker class check every atom for a specific error or property.
- Since:
- Marvin 5.3
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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
ModifierConstructorDescriptionprotected
AtomChecker
(StructureCheckerErrorType errorType) Constructor to create a Structure checker instance with the given errorType. -
Method Summary
Modifier and TypeMethodDescriptionprotected StructureCheckerResult
createResult
(Molecule molecule, List<MolAtom> atoms) Creates aStructureCheckerResult
from aList
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 moleculeMethods 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
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Constructor Details
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AtomChecker
Constructor to create a Structure checker instance with the given errorType.- Parameters:
errorType
- element ofStructureCheckerErrorType
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Method Details
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getComponentCount
Description copied from class:ComponentChecker
Gets the number of the components in the molecule- Specified by:
getComponentCount
in classComponentChecker<MolAtom>
- Parameters:
molecule
- the molecule to check- Returns:
- the number of the components in the molecule
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getComponent
Description copied from class:ComponentChecker
Gets the component from the molecule with index i.- Specified by:
getComponent
in classComponentChecker<MolAtom>
- Parameters:
molecule
- the molecule to checki
- the index of the component- Returns:
- the component
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createResult
Description copied from class:ComponentChecker
Creates aStructureCheckerResult
from aList
containing the components.- Specified by:
createResult
in classComponentChecker<MolAtom>
- Parameters:
molecule
- is aMolecule
instanceatoms
- is an instance ofList
containing the problematic components- Returns:
- a
StructureCheckerResult
containing all problematic component indices
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