chemaxon.checkers

Class SubstructureChecker

java.lang.Object

chemaxon.checkers.AbstractStructureChecker

chemaxon.checkers.SubstructureChecker

All Implemented Interfaces:

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

public class SubstructureChecker
extends AbstractStructureChecker

This descendant of AbstractStructureChecker is responsible for detecting substructures in a Molecule instance. Query has to be given as a reaction smarts (reactant->product type)

Since:

JChem 5.5, Marvin 5.6

Version:

6.1

Author:

Attila Szabo, Zsolt Mohacsi

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
SubstructureChecker() Default constructor.
SubstructureChecker(Map<String,String> params) Parameterized constructor.
SubstructureChecker(String areactionSmarts) Parameterized constructor.

Method Summary

Methods

Modifier and Type	Method and Description
protected StructureCheckerResult	check1(Molecule molecule) This method contains the current checking mechanism.
SubstructureChecker	clone()
StructureCheckerErrorType	getErrorType()
String	getReactionSmarts() Returns the reactionSmarts
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	setReactionSmarts(String reactionSmarts) Sets the reactionSmarts
String	toString()

Methods inherited from class chemaxon.checkers.AbstractStructureChecker

addPropertyChangeListener, addPropertyChangeListener, check, cloneItem, convertResult, equals, expandMolecule, getDescription, getDescriptor, getEditorClassName, getErrorCode, getErrorDescription, getHelpText, getIcon, getLocalMenuName, getName, hashCode, isLicensed, propertyChange, removePropertyChangeListener, removePropertyChangeListener, setDescription, setHelpText, setIcon, setLicenseEnvironment, setLocalMenuName, setMoreErrorMessage, setName, setNoErrorMessage, setOneErrorMessage

Methods inherited from class java.lang.Object

finalize, getClass, notify, notifyAll, wait, wait, wait

Constructor Detail

SubstructureChecker

public SubstructureChecker()

Default constructor. Calling this constructor developer has to set explicitly the needed smarts reaction directly.

SubstructureChecker

public SubstructureChecker(Map<String,String> params)

Parameterized constructor. If the reactionsmarts parameter given it sets the reaction smarts property.

Parameters:

params - a Map instance which contains String pairs. Key is the name of the parameter.

SubstructureChecker

public SubstructureChecker(String areactionSmarts)
                    throws MolFormatException

Parameterized constructor.

Parameters:

areactionSmarts - is the s

Throws:

MolFormatException - when the given smarts string could not be recognized

Method Detail

getReactionSmarts

public String getReactionSmarts()

Returns the reactionSmarts

Returns:

the reactionSmarts

setReactionSmarts

public void setReactionSmarts(String reactionSmarts)
                       throws MolFormatException

Sets the reactionSmarts

Parameters:

reactionSmarts - the reactionSmarts to set. If reaction smarts is an empty string the change is ignored.

Throws:

MolFormatException - when the given smarts string could not be recognized

getErrorType

public StructureCheckerErrorType getErrorType()

Specified by:

getErrorType in interface StructureChecker

Overrides:

getErrorType in class AbstractStructureChecker

Returns:

the error type of this checker

check1

protected StructureCheckerResult check1(Molecule molecule)

Description copied from class: AbstractStructureChecker

This method contains the current checking mechanism.

Specified by:

check1 in class AbstractStructureChecker

Parameters:

molecule - the Molecule instance to be checked for problems

Returns:

a StructureCheckerResult which represents the problem or null if no problem found

isValid

public boolean isValid()

Description copied from interface: StructureChecker

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

Specified by:

isValid in interface StructureChecker

Overrides:

isValid in class AbstractStructureChecker

Returns:

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

isAvailable

public boolean isAvailable()

Description copied from interface: StructureChecker

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

Specified by:

isAvailable in interface StructureChecker

Overrides:

isAvailable in class AbstractStructureChecker

Returns:

true if the checker is available, and can be used

clone

public SubstructureChecker clone()
                          throws CloneNotSupportedException

Overrides:

clone in class AbstractStructureChecker

Throws:

CloneNotSupportedException

toString

public String toString()

Overrides:

toString in class AbstractStructureChecker