chemaxon.checkers
Class RgroupReferenceErrorChecker

java.lang.Object
  chemaxon.checkers.AbstractStructureChecker
      chemaxon.checkers.RgroupReferenceErrorChecker

All Implemented Interfaces:

StructureChecker, chemaxon.license.Licensable, java.beans.PropertyChangeListener, java.lang.Cloneable, java.util.EventListener

public class RgroupReferenceErrorChecker
extends AbstractStructureChecker

A descendant of AbstractStructureChecker detecting R-group definition errors.

Since:

Marvin 5.7

Version:

5.7

Author:

Gyorgy Pirok, Attila Szabo

Field Summary

static java.lang.String	PROPERTY_KEY_SEARCH_MISSING_RATOM This private constant String represents the name of the property which is responsible for searching missing ratoms in the molecule
static java.lang.String	PROPERTY_KEY_SEARCH_MISSING_RGROUP This private constant String represents the name of the property which is responsible for searching missing rgroups in the molecule
static java.lang.String	PROPERTY_KEY_SEARCH_SELF_REFERENCE This private constant String represents the name of the property which is responsible for searching self references in the molecule

Fields inherited from class chemaxon.checkers.AbstractStructureChecker

errorType, propertyChangeSupport

Fields inherited from interface chemaxon.checkers.StructureChecker

PROPERTY_KEY_VALID

Constructor Summary

RgroupReferenceErrorChecker()
Creates a new RgroupReferenceErrorChecker instance checking all R-group errors by default.

RgroupReferenceErrorChecker(java.util.Map<java.lang.String,java.lang.String> params)
Creates a new RgroupRefereceErrorChecker instance reading checking options from the params argument.

Method Summary

protected StructureCheckerResult	check1(Molecule molecule) This method contains the current checking mechanism.
boolean	isSearchMissingRatom() Gets the option determining if the checker detects missing R-atoms or not.
boolean	isSearchMissingRgroup() Gets the option determining if the checker detects missing R-groups or not.
boolean	isSearchSelfReference() Sets the option determining if the checker detects nested R-atoms referencing to their own R-groups directly or in circularly or not.
void	setSearchMissingRatom(boolean value) Sets the option determining if the checker detects missing R-atoms or not.
void	setSearchMissingRgroup(boolean value) Sets the option determining if the checker detects missing R-groups or not.
void	setSearchSelfReference(boolean value) Sets the option determining if the checker detects nested R-atoms referencing to their own R-groups directly or in circularly or not.

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

Methods inherited from class java.lang.Object

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

Field Detail

PROPERTY_KEY_SEARCH_MISSING_RATOM

public static final java.lang.String PROPERTY_KEY_SEARCH_MISSING_RATOM

This private constant String represents the name of the property which is responsible for searching missing ratoms in the molecule

Since:

5.7

See Also:

Constant Field Values

PROPERTY_KEY_SEARCH_MISSING_RGROUP

public static final java.lang.String PROPERTY_KEY_SEARCH_MISSING_RGROUP

This private constant String represents the name of the property which is responsible for searching missing rgroups in the molecule

Since:

5.7

See Also:

Constant Field Values

PROPERTY_KEY_SEARCH_SELF_REFERENCE

public static final java.lang.String PROPERTY_KEY_SEARCH_SELF_REFERENCE

This private constant String represents the name of the property which is responsible for searching self references in the molecule

Since:

5.7

See Also:

Constant Field Values

Constructor Detail

RgroupReferenceErrorChecker

public RgroupReferenceErrorChecker()

Creates a new RgroupReferenceErrorChecker instance checking all R-group errors by default.

RgroupReferenceErrorChecker

public RgroupReferenceErrorChecker(java.util.Map<java.lang.String,java.lang.String> params)

Creates a new RgroupRefereceErrorChecker instance reading checking options from the params argument.

Parameters:

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

Method Detail

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

isSearchMissingRatom

public boolean isSearchMissingRatom()

Gets the option determining if the checker detects missing R-atoms or not.

Returns:

true if the missing R-atoms are detected

isSearchMissingRgroup

public boolean isSearchMissingRgroup()

Gets the option determining if the checker detects missing R-groups or not.

Returns:

true if the missing R-groups are detected

isSearchSelfReference

public boolean isSearchSelfReference()

Sets the option determining if the checker detects nested R-atoms referencing to their own R-groups directly or in circularly or not.

Returns:

true if the self-referencing R-groups are detected

setSearchMissingRatom

public void setSearchMissingRatom(boolean value)

Sets the option determining if the checker detects missing R-atoms or not.

Parameters:

value - if true, missing R-atoms are detected

setSearchMissingRgroup

public void setSearchMissingRgroup(boolean value)

Sets the option determining if the checker detects missing R-groups or not.

Parameters:

value - if true, missing R-groups are detected

setSearchSelfReference

public void setSearchSelfReference(boolean value)

Sets the option determining if the checker detects nested R-atoms referencing to their own R-groups directly or in circularly or not.

Parameters:

value - if true, self-referencing R-atoms are detected