chemaxon.checkers

Interface StructureChecker

All Known Implementing Classes:

AbbreviatedGroupChecker, AbsentChiralFlagChecker, AbsoluteStereoConfigurationChecker, AbstractStructureChecker, AliasChecker, AromaticityErrorChecker, AtomChecker, AtomMapChecker, AtomQueryPropertyChecker, AtomTypeChecker, AtomValueChecker, AtropisomerChecker, AttachedDataChecker, BondAngleChecker, BondChecker, BondLengthChecker, ChiralFlagChecker, ChiralFlagErrorChecker, CircularRGroupReferenceChecker, ComponentChecker, CoordinationSystemErrorChecker, CovalentCounterionChecker, CrossedDoubleBondChecker, EmptyStructureChecker, ExplicitHydrogenChecker, ExplicitLonePairChecker, ExternalStructureChecker, EZDoubleBondChecker, InvalidChecker, IsotopeChecker, MetalloceneErrorChecker, MissingAtomMapChecker, MissingRGroupChecker, MoleculeChargeChecker, MultiCenterChecker, MultiComponentChecker, MultipleStereocenterChecker, OCRErrorChecker, OverlappingAtomsChecker, OverlappingBondsChecker, PseudoAtomChecker, QueryAtomChecker, QueryBondChecker, RacemateChecker, RadicalChecker, RareElementChecker, RatomChecker, ReactingCenterBondMarkChecker, ReactionChecker, ReactionMapErrorChecker, RelativeStereoChecker, RgroupAttachmentCountErrorChecker, RgroupAttachmentErrorChecker, RgroupOrphanAttachmentErrorChecker, RgroupReferenceErrorChecker, RingStrainErrorChecker, SolventChecker, StarAtomChecker, StereoCareBoxChecker, StereoInversionRetentionMarkChecker, StraightDoubleBondChecker, SubstructureChecker, ThreeDimensionChecker, UnbalancedReactionChecker, UnusedRGroupChecker, ValenceErrorChecker, ValencePropertyChecker, WedgeErrorChecker, WigglyBondChecker, WigglyDoubleBondChecker

public interface StructureChecker

General interface describing functions that are available for a chemical structure checker. Structure checkers can detect various structural issues, but it is the responsibility of fixers to correct them. The result of checking contains information of the discovered issues.

Since:

Marvin 5.3

Version:

5.7

Author:

Attila Szabo, Istvan Rabel

Field Summary

Fields

Modifier and Type	Field and Description
static String	PROPERTY_KEY_VALID This property key used to be the key of the property change event of valid property

Method Summary

Methods

Modifier and Type	Method and Description
void	addPropertyChangeListener(PropertyChangeListener listener) Add a PropertyChangeListener to the listener list.
void	addPropertyChangeListener(String propertyName, PropertyChangeListener listener) Add a PropertyChangeListener for a specific property.
StructureCheckerResult	check(Molecule molecule) Detects a specific error in the molecule.
StructureChecker	cloneItem() Returns a clone of this StructureChecker instance
String	getDescription() Deprecated. This method isn't needed anymore and will be removed in 6.0
StructureCheckerDescriptor	getDescriptor() Returns a StructureCheckerDescriptor instance which represents the user interface related informations of the checker
String	getEditorClassName() Deprecated. This method isn't needed anymore and will be removed in 6.0
String	getErrorCode() Returns the String represented error code of the checker (this error code should be used for external implementation support instead of getErrorType())
StructureCheckerErrorType	getErrorType()
String	getHelpText() Deprecated. This method isn't needed anymore and will be removed in 6.0
Icon	getIcon() Deprecated. This method isn't needed anymore and will be removed in 6.0
String	getLocalMenuName() Deprecated. This method isn't needed anymore and will be removed in 6.0
String	getName() Deprecated. This method isn't needed anymore and will be removed in 6.0
boolean	isAvailable() Returns true if the checker is available, and can be used
boolean	isValid() Returns true if the checker's configuration is valid, false otherwise
void	removePropertyChangeListener(PropertyChangeListener listener) Remove a PropertyChangeListener from the listener list.
void	removePropertyChangeListener(String propertyName, PropertyChangeListener listener) Remove a PropertyChangeListener for a specific property.
void	setDescription(String description) Deprecated. This method isn't needed anymore and will be removed in 6.0
void	setHelpText(String helpText) Deprecated. This method isn't needed anymore and will be removed in 6.0
void	setIcon(Icon icon) Deprecated. This method isn't needed anymore and will be removed in 6.0
void	setLocalMenuName(String localMenuName) Deprecated. This method isn't needed anymore and will be removed in 6.0
void	setMoreErrorMessage(String moreError) Deprecated. This method isn't needed anymore and will be removed in 6.0
void	setName(String name) Deprecated. This method isn't needed anymore and will be removed in 6.0
void	setNoErrorMessage(String noError) Deprecated. This method isn't needed anymore and will be removed in 6.0
void	setOneErrorMessage(String oneError) Deprecated. This method isn't needed anymore and will be removed in 6.0

Field Detail

PROPERTY_KEY_VALID

static final String PROPERTY_KEY_VALID

This property key used to be the key of the property change event of valid property

See Also:

Constant Field Values

Method Detail

check

StructureCheckerResult check(Molecule molecule)
                             throws NullPointerException

Detects a specific error in the molecule.

Parameters:

molecule - a Molecule instance have to be checked

Returns:

an instance of StructureCheckerResult (which contains all data needed to fix the problem) if the molecule contains the examined error, null otherwise

Throws:

NullPointerException - if molecule is null

getName

@Deprecated
String getName()

Deprecated. This method isn't needed anymore and will be removed in 6.0

Gets the name of the checker

Returns:

a human readable name

setName

@Deprecated
void setName(String name)

Deprecated. This method isn't needed anymore and will be removed in 6.0

Sets the name of the checker

Parameters:

name - the human readable name of the checker

getLocalMenuName

@Deprecated
String getLocalMenuName()

Deprecated. This method isn't needed anymore and will be removed in 6.0

Gets the local menu name of the checker

Returns:

the name for the local menu

setLocalMenuName

@Deprecated
void setLocalMenuName(String localMenuName)

Deprecated. This method isn't needed anymore and will be removed in 6.0

Set the local menu name of the checker

Parameters:

localMenuName - a String to be shown in the local menu

getHelpText

@Deprecated
String getHelpText()

Deprecated. This method isn't needed anymore and will be removed in 6.0

Gets the help text of the checker

Returns:

the help text of the checker

setHelpText

@Deprecated
void setHelpText(String helpText)

Deprecated. This method isn't needed anymore and will be removed in 6.0

Sets the detailed help of the checker which will shown in the tooltip on the GUI

Parameters:

helpText - a String to be shown in the tooltip

setNoErrorMessage

@Deprecated
void setNoErrorMessage(String noError)

Deprecated. This method isn't needed anymore and will be removed in 6.0

Sets the message which will given in the result if no error found

Parameters:

noError - the error message if no error found

setOneErrorMessage

@Deprecated
void setOneErrorMessage(String oneError)

Deprecated. This method isn't needed anymore and will be removed in 6.0

Sets the message which will given in the result if one error found

Parameters:

oneError - the error message if one error found

setMoreErrorMessage

@Deprecated
void setMoreErrorMessage(String moreError)

Deprecated. This method isn't needed anymore and will be removed in 6.0

Sets the message which will given in the result if two or more error found

Parameters:

moreError - the error message if two or more error found

getIcon

@Deprecated
Icon getIcon()

Deprecated. This method isn't needed anymore and will be removed in 6.0

Gets the Icon of the current checker

Returns:

the Icon of the current checker

setIcon

@Deprecated
void setIcon(Icon icon)

Deprecated. This method isn't needed anymore and will be removed in 6.0

Sets the icon of the checker

Parameters:

icon - is an instance of Icon

getErrorType

StructureCheckerErrorType getErrorType()

Returns:

the error type of this checker

Since:

5.4

getErrorCode

String getErrorCode()

Returns the String represented error code of the checker (this error code should be used for external implementation support instead of getErrorType())

Returns:

the String represented error code of the checker (this error code should be used for external implementation support instead of getErrorType())

Since:

5.6

getEditorClassName

@Deprecated
String getEditorClassName()

Deprecated. This method isn't needed anymore and will be removed in 6.0

Returns:

the name of the editor class of the checker

Since:

5.4

setDescription

@Deprecated
void setDescription(String description)

Deprecated. This method isn't needed anymore and will be removed in 6.0

Sets the description of the checker

Parameters:

description - the description of the checker

Since:

5.4

getDescription

@Deprecated
String getDescription()

Deprecated. This method isn't needed anymore and will be removed in 6.0

Returns:

the description of the checker

Since:

5.4

cloneItem

StructureChecker cloneItem()

Returns a clone of this StructureChecker instance

Returns:

a clone of this StructureChecker instance

Since:

5.4

isValid

boolean isValid()

Returns true if the checker's configuration is valid, false otherwise

Returns:

true if the checker's configuration is valid, false otherwise

Since:

5.7

isAvailable

boolean isAvailable()

Returns true if the checker is available, and can be used

Returns:

true if the checker is available, and can be used

Since:

5.7

getDescriptor

StructureCheckerDescriptor getDescriptor()

Returns a StructureCheckerDescriptor instance which represents the user interface related informations of the checker

Returns:

a StructureCheckerDescriptor instance which represents the user interface related informations of the checker

Since:

5.7

removePropertyChangeListener

void removePropertyChangeListener(String propertyName,
                                PropertyChangeListener listener)

Remove a PropertyChangeListener for a specific property. If listener was added more than once to the same event source for the specified property, it will be notified one less time after being removed. If propertyName is null, no exception is thrown and no action is taken. If listener is null, or was never added for the specified property, no exception is thrown and no action is taken.

Parameters:

propertyName - The name of the property that was listened on.

listener - The PropertyChangeListener to be removed

Since:

5.7

See Also:

PropertyChangeSupport.removePropertyChangeListener(String, PropertyChangeListener)

addPropertyChangeListener

void addPropertyChangeListener(String propertyName,
                             PropertyChangeListener listener)

Add a PropertyChangeListener for a specific property. The listener will be invoked only when a call on firePropertyChange names that specific property. The same listener object may be added more than once. For each property, the listener will be invoked the number of times it was added for that property. If propertyName or listener is null, no exception is thrown and no action is taken.

Parameters:

propertyName - The name of the property to listen on.

listener - The PropertyChangeListener to be added

Since:

5.7

See Also:

PropertyChangeSupport.addPropertyChangeListener(String, PropertyChangeListener)

removePropertyChangeListener

void removePropertyChangeListener(PropertyChangeListener listener)

Remove a PropertyChangeListener from the listener list. This removes a PropertyChangeListener that was registered for all properties. If listener was added more than once to the same event source, it will be notified one less time after being removed. If listener is null, or was never added, no exception is thrown and no action is taken.

Parameters:

listener - The PropertyChangeListener to be removed

Since:

5.7

See Also:

PropertyChangeSupport.removePropertyChangeListener(PropertyChangeListener)

addPropertyChangeListener

void addPropertyChangeListener(PropertyChangeListener listener)

Add a PropertyChangeListener to the listener list. The listener is registered for all properties. The same listener object may be added more than once, and will be called as many times as it is added. If listener is null, no exception is thrown and no action is taken.

Parameters:

listener - The PropertyChangeListener to be added

Since:

5.7

See Also:

PropertyChangeSupport.addPropertyChangeListener(PropertyChangeListener)