chemaxon.checkers

Class RgroupReferenceErrorChecker

java.lang.Object

chemaxon.checkers.AbstractStructureChecker

chemaxon.checkers.RgroupReferenceErrorChecker

All Implemented Interfaces:

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

Deprecated.

The following checkers are defined instead:

• MissingRGroupChecker
• UnusedRGroupChecker
• CircularRGroupReferenceChecker

@Deprecated
@SubjectToRemoval(date=OCT_01_2015)
public class RgroupReferenceErrorChecker
extends AbstractStructureChecker

A descendant of AbstractStructureChecker detecting R-group definition errors.

Since:

Marvin 5.7

Version:

5.10

Author:

Gyorgy Pirok, Attila Szabo

Field Summary

Fields

Modifier and Type	Field and Description
static String	PROPERTY_KEY_SEARCH_CIRCULAR_REFERENCE Deprecated. This private constant String represents the name of the property which is responsible for searching self references in the molecule
static String	PROPERTY_KEY_SEARCH_MISSING_RATOM Deprecated.
static String	PROPERTY_KEY_SEARCH_MISSING_RGROUP Deprecated. This private constant String represents the name of the property which is responsible for searching missing rgroups in the molecule
static String	PROPERTY_KEY_SEARCH_SELF_REFERENCE Deprecated.
static String	PROPERTY_KEY_SEARCH_UNUSED_RGROUP Deprecated. This private constant String represents the name of the property which is responsible for searching unused rgroups in the molecule

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
RgroupReferenceErrorChecker() Deprecated. Creates a new RgroupReferenceErrorChecker instance checking all R-group errors by default.
RgroupReferenceErrorChecker(Map<String,String> params) Deprecated. Creates a new RgroupRefereceErrorChecker instance reading checking options from the params argument.

Method Summary

Methods

Modifier and Type	Method and Description
protected StructureCheckerResult	check1(Molecule molecule) Deprecated. This method contains the current checking mechanism.
protected void	convertResult(Molecule originalMolecule, Molecule expandedMolecule, StructureCheckerResult result, Map<MolAtom,MolAtom> atomMap, Map<MolBond,MolBond> bondMap) Deprecated. This implementation does nothing.
protected Molecule	expandMolecule(Molecule molecule, Map<MolAtom,MolAtom> atomMap, Map<MolBond,MolBond> bondMap) Deprecated. This implementation does nothing.
boolean	isSearchCircularReference() Deprecated. Sets the option determining if the checker detects nested R-atoms referencing to their own R-groups directly or in circularly or not.
boolean	isSearchMissingRatom() Deprecated.
boolean	isSearchMissingRgroup() Deprecated. Gets the option determining if the checker detects missing R-groups or not.
boolean	isSearchSelfReference() Deprecated.
boolean	isSearchUnusedRgroup() Deprecated. Gets the option determining if the checker detects unused R-groups or not.
void	setSearchCircularReference(boolean value) Deprecated. 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) Deprecated.
void	setSearchMissingRgroup(boolean value) Deprecated. Sets the option determining if the checker detects missing R-groups or not.
void	setSearchSelfReference(boolean value) Deprecated.
void	setSearchUnusedRgroup(boolean value) Deprecated. Sets the option determining if the checker detects missing R-atoms or not.

Methods inherited from class chemaxon.checkers.AbstractStructureChecker

addPropertyChangeListener, addPropertyChangeListener, check, clone, cloneItem, 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

Methods inherited from class java.lang.Object

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

Field Detail

PROPERTY_KEY_SEARCH_MISSING_RATOM

@Deprecated
public static final String PROPERTY_KEY_SEARCH_MISSING_RATOM

Deprecated.

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

Since:

5.7

See Also:

Constant Field Values

PROPERTY_KEY_SEARCH_UNUSED_RGROUP

public static final String PROPERTY_KEY_SEARCH_UNUSED_RGROUP

Deprecated.

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

Since:

5.10

See Also:

Constant Field Values

PROPERTY_KEY_SEARCH_MISSING_RGROUP

public static final String PROPERTY_KEY_SEARCH_MISSING_RGROUP

Deprecated.

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

@Deprecated
public static final String PROPERTY_KEY_SEARCH_SELF_REFERENCE

Deprecated.

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

Since:

5.7

See Also:

Constant Field Values

PROPERTY_KEY_SEARCH_CIRCULAR_REFERENCE

public static final String PROPERTY_KEY_SEARCH_CIRCULAR_REFERENCE

Deprecated.

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

Since:

5.10

See Also:

Constant Field Values

Constructor Detail

RgroupReferenceErrorChecker

public RgroupReferenceErrorChecker()

Deprecated.

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

RgroupReferenceErrorChecker

public RgroupReferenceErrorChecker(Map<String,String> params)

Deprecated.

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)

Deprecated.

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

@Deprecated
public boolean isSearchMissingRatom()

Deprecated.

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

Returns:

true if the missing R-atoms are detected

isSearchUnusedRgroup

public boolean isSearchUnusedRgroup()

Deprecated.

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

Returns:

true if the missing R-atoms are detected

isSearchMissingRgroup

public boolean isSearchMissingRgroup()

Deprecated.

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

Returns:

true if the missing R-groups are detected

isSearchSelfReference

@Deprecated
public boolean isSearchSelfReference()

Deprecated.

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

Returns:

true if the self-referencing R-groups are detected

isSearchCircularReference

public boolean isSearchCircularReference()

Deprecated.

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

@Deprecated
public void setSearchMissingRatom(boolean value)

Deprecated.

Sets the option determining if the checker detects missing R-atoms or not. Use setSearchUnusedRgroup method instead.

Parameters:

value - if true, missing R-atoms are detected

setSearchUnusedRgroup

public void setSearchUnusedRgroup(boolean value)

Deprecated.

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)

Deprecated.

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

Parameters:

value - if true, missing R-groups are detected

setSearchSelfReference

@Deprecated
public void setSearchSelfReference(boolean value)

Deprecated.

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

Parameters:

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

setSearchCircularReference

public void setSearchCircularReference(boolean value)

Deprecated.

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

convertResult

protected void convertResult(Molecule originalMolecule,
                 Molecule expandedMolecule,
                 StructureCheckerResult result,
                 Map<MolAtom,MolAtom> atomMap,
                 Map<MolBond,MolBond> bondMap)

Deprecated.

This implementation does nothing.

Overrides:

convertResult in class AbstractStructureChecker

Parameters:

originalMolecule - the original molecule

expandedMolecule - the cloned then expanded molecule

result - the structure checker result on cloned molecule

atomMap - the mapping of cloned molecule and original molecule atoms

bondMap - the mapping of cloned molecule and original molecule bonds

expandMolecule

protected Molecule expandMolecule(Molecule molecule,
                      Map<MolAtom,MolAtom> atomMap,
                      Map<MolBond,MolBond> bondMap)

Deprecated.

This implementation does nothing.

Overrides:

expandMolecule in class AbstractStructureChecker

Parameters:

molecule - the molecule to check

Returns:

the molecule