chemaxon.checkers

Class RatomChecker

java.lang.Object

chemaxon.checkers.AbstractStructureChecker

chemaxon.checkers.RatomChecker

All Implemented Interfaces:

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

public class RatomChecker
extends AbstractStructureChecker

A descendant of AbstractStructureChecker detecting R-atoms.

Since:

Marvin 5.7

Version:

5.7

Author:

Gyorgy Pirok, Attila Szabo

Field Summary

Fields

Modifier and Type	Field and Description
static String	PROPERTY_KEY_SEARCH_ALL This constant String represents the name of the property which is responsible for searching all ratoms in the molecule
static String	PROPERTY_KEY_SEARCH_DISCONNECTED This constant String represents the name of the property which is responsible for searching disconnected ratoms in the molecule
static String	PROPERTY_KEY_SEARCH_GENERIC This constant String represents the name of the property which is responsible for searching generic ratoms in the molecule
static String	PROPERTY_KEY_SEARCH_LINKER This private constant String represents the name of the property which is responsible for searching linker ratoms in the molecule
static String	PROPERTY_KEY_SEARCH_NESTED This private constant String represents the name of the property which is responsible for searching nested ratoms 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
RatomChecker() Creates a new anyChecker instance detecting all R-atoms.
RatomChecker(Map<String,String> params) Creates a new anyChecker instance reading checking options from the params argument.

Method Summary

Methods

Modifier and Type	Method and Description
protected StructureCheckerResult	check1(Molecule molecule) This method contains the current checking mechanism.
boolean	isSearchAll() Gets the option determining if the checker detects all R-atoms or not.
boolean	isSearchDisconnected() Gets the option determining if the checker detects R-atoms not connected to any other atoms or not.
boolean	isSearchGeneric() Gets the option determining if the checker detects R-atoms without identifier numbers or not.
boolean	isSearchLinker() Gets the option determining if the checker detects R-atoms with more than one connection or not.
boolean	isSearchNested() Gets the option determining if the checker detects R-atoms within R-groups or not.
void	setSearchAll(boolean value) Sets the option determining if the checker detects all R-atoms or not.
void	setSearchDisconnected(boolean value) Sets the option determining if the checker detects R-atoms not connected to any other atoms or not.
void	setSearchGeneric(boolean value) Sets the option determining if the checker detects R-atoms without identifier numbers or not.
void	setSearchLinker(boolean value) Sets the option determining if the checker detects R-atoms with more than one connection or not.
void	setSearchNested(boolean value) Sets the option determining if the checker detects R-atoms within R-groups 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_ALL

public static final String PROPERTY_KEY_SEARCH_ALL

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

Since:

5.7

See Also:

Constant Field Values

PROPERTY_KEY_SEARCH_DISCONNECTED

public static final String PROPERTY_KEY_SEARCH_DISCONNECTED

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

Since:

5.7

See Also:

Constant Field Values

PROPERTY_KEY_SEARCH_GENERIC

public static final String PROPERTY_KEY_SEARCH_GENERIC

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

Since:

5.7

See Also:

Constant Field Values

PROPERTY_KEY_SEARCH_LINKER

public static final String PROPERTY_KEY_SEARCH_LINKER

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

Since:

5.7

See Also:

Constant Field Values

PROPERTY_KEY_SEARCH_NESTED

public static final String PROPERTY_KEY_SEARCH_NESTED

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

Since:

5.7

See Also:

Constant Field Values

Constructor Detail

RatomChecker

public RatomChecker()

Creates a new anyChecker instance detecting all R-atoms.

RatomChecker

public RatomChecker(Map<String,String> params)

Creates a new anyChecker 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

isSearchAll

public boolean isSearchAll()

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

Returns:

true if all R-atoms are detected

isSearchDisconnected

public boolean isSearchDisconnected()

Gets the option determining if the checker detects R-atoms not connected to any other atoms or not.

Returns:

true if the nested R-atoms are detected

isSearchGeneric

public boolean isSearchGeneric()

Gets the option determining if the checker detects R-atoms without identifier numbers or not.

Returns:

true if the generic R-atoms are detected

isSearchLinker

public boolean isSearchLinker()

Gets the option determining if the checker detects R-atoms with more than one connection or not.

Returns:

true if the linker R-atoms are detected

isSearchNested

public boolean isSearchNested()

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

Returns:

true if the nested R-atoms are detected

setSearchAll

public void setSearchAll(boolean value)

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

Parameters:

value - if true, all R-atoms are detected

setSearchDisconnected

public void setSearchDisconnected(boolean value)

Sets the option determining if the checker detects R-atoms not connected to any other atoms or not.

Parameters:

value - if true, disconnected R-atoms are detected

setSearchGeneric

public void setSearchGeneric(boolean value)

Sets the option determining if the checker detects R-atoms without identifier numbers or not.

Parameters:

value - if true, generic R-atoms are detected

setSearchLinker

public void setSearchLinker(boolean value)

Sets the option determining if the checker detects R-atoms with more than one connection or not.

Parameters:

value - if true, linker R-atoms are detected

setSearchNested

public void setSearchNested(boolean value)

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

Parameters:

value - if true, nested R-atoms are detected