Package chemaxon.checkers

Class AbbreviatedGroupChecker

java.lang.Object

chemaxon.checkers.AbstractStructureChecker

chemaxon.checkers.AbbreviatedGroupChecker

All Implemented Interfaces:

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

@PublicAPI
public class AbbreviatedGroupChecker
extends AbstractStructureChecker

A descendant of AbstractStructureChecker detecting abbreviations ("COOH", "Ala", "NO2", etc.) in a Molecule instance represented in abbreviated group form.

Since:

Marvin 5.3

Field Summary

Fields

Modifier and Type	Field	Description
static final String	PROPERTY_KEY_CONTRACTED	This public constant String represents the name of the configuration file property which is responsible for searching contracted abbreviated groups
static final String	PROPERTY_KEY_EXCLUDED	This public constant String represents the name of the property which is responsible for the list of excluded groups
static final String	PROPERTY_KEY_EXPANDED	This public constant String represents the name of the configuration file property which is responsible for searching expanded abbreviated groups
static final String	PROPERTY_KEY_SEARCH_CONTRACTED	This public constant String represents the name of the property which is responsible for searching contracted abbreviated groups
static final String	PROPERTY_KEY_SEARCH_EXCLUDED	This public constant String represents the name of the property which is responsible for the list of excluded groups
static final String	PROPERTY_KEY_SEARCH_EXPANDED	This public constant String represents the name of the property which is responsible for searching expanded abbreviated groups

Fields inherited from class chemaxon.checkers.AbstractStructureChecker

errorType, propertyChangeSupport

Fields inherited from interface chemaxon.checkers.StructureChecker

PROPERTY_KEY_VALID

Constructor Summary

Constructors

Constructor	Description
AbbreviatedGroupChecker()	Default constructor.
AbbreviatedGroupChecker(Map<String,String> params)	Parameterized constructor.

Method Summary

Modifier and Type	Method	Description
protected StructureCheckerResult	check1(Molecule molecule)	This method contains the current checking mechanism.
protected void	convertResult(Molecule originalMolecule, Molecule expandedMolecule, StructureCheckerResult result, Map<MolAtom,MolAtom> atomMap, Map<MolBond,MolBond> bondMap)	This implementation does nothing.
boolean	equals(Object obj)
protected Molecule	expandMolecule(Molecule molecule, Map<MolAtom,MolAtom> atomMap, Map<MolBond,MolBond> bondMap)	This implementation does nothing.
chemaxon.checkers.util.AtomLabels	getExcluded()	Gets the excluded abbreviations
int	hashCode()
boolean	isSearchContracted()	Returns if the checker is searching for contracted SGroups or not
boolean	isSearchExpanded()	Returns if the checker is searching for expanded SGroups or not
boolean	isValid()	Excluded object is initialized.
void	setExcluded(chemaxon.checkers.util.AtomLabels excluded)	Sets the abbreviations to be excluded
void	setSearchContracted(boolean searchContracted)	Sets the checker should search for contracted abbreviated groups or not
void	setSearchExpanded(boolean searchExpanded)	Sets the checker should search for expanded abbreviated groups or not

Methods inherited from class chemaxon.checkers.AbstractStructureChecker

addPropertyChangeListener, addPropertyChangeListener, check, clone, cloneItem, getDescription, getDescriptor, getEditorClassName, getErrorCode, getErrorDescription, getErrorType, getHelpText, getIcon, getLocalMenuName, getName, isAvailable, isLicensed, 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 Details

PROPERTY_KEY_EXPANDED

public static final String PROPERTY_KEY_EXPANDED

This public constant String represents the name of the configuration file property which is responsible for searching expanded abbreviated groups

Since:

5.4

See Also:

• Constant Field Values

PROPERTY_KEY_CONTRACTED

public static final String PROPERTY_KEY_CONTRACTED

This public constant String represents the name of the configuration file property which is responsible for searching contracted abbreviated groups

Since:

5.4

See Also:

• Constant Field Values

PROPERTY_KEY_SEARCH_CONTRACTED

public static final String PROPERTY_KEY_SEARCH_CONTRACTED

This public constant String represents the name of the property which is responsible for searching contracted abbreviated groups

Since:

5.7

See Also:

• Constant Field Values

PROPERTY_KEY_SEARCH_EXPANDED

public static final String PROPERTY_KEY_SEARCH_EXPANDED

This public constant String represents the name of the property which is responsible for searching expanded abbreviated groups

Since:

5.7

See Also:

• Constant Field Values

PROPERTY_KEY_EXCLUDED

public static final String PROPERTY_KEY_EXCLUDED

This public constant String represents the name of the property which is responsible for the list of excluded groups

Since:

5.12

See Also:

• Constant Field Values

PROPERTY_KEY_SEARCH_EXCLUDED

public static final String PROPERTY_KEY_SEARCH_EXCLUDED

This public constant String represents the name of the property which is responsible for the list of excluded groups

Since:

5.12

See Also:

• Constant Field Values

Constructor Details

AbbreviatedGroupChecker

public AbbreviatedGroupChecker()

Default constructor. Search for both expanded and contracted abbreviated groups.

AbbreviatedGroupChecker

public AbbreviatedGroupChecker(Map<String,String> params)

Parameterized constructor. If "expanded" parameter given, and its value is "true" expanded abbreviated groups will be detected during the checking mechanism. Otherwise no expanded group will be found. If "contracted" parameter given, and its value is "true" contracted abbreviated groups will be detected during the checking mechanism. Otherwise no contracted group will be found.

Parameters:

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

Method Details

isSearchContracted

public boolean isSearchContracted()

Returns if the checker is searching for contracted SGroups or not

Returns:

if the checker is searching for contracted SGroups or not

isSearchExpanded

public boolean isSearchExpanded()

Returns if the checker is searching for expanded SGroups or not

Returns:

if the checker is searching for expanded SGroups or not

expandMolecule

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

This implementation does nothing.

Overrides:

expandMolecule in class AbstractStructureChecker

Parameters:

molecule - the molecule to check

Returns:

the molecule

convertResult

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

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

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

equals

public boolean equals(Object obj)

Overrides:

equals in class AbstractStructureChecker

hashCode

public int hashCode()

Overrides:

hashCode in class AbstractStructureChecker

setSearchExpanded

public void setSearchExpanded(boolean searchExpanded)

Sets the checker should search for expanded abbreviated groups or not

Parameters:

searchExpanded - is a boolean property. If true expanded abbreviated groups will be checked during the checking mechanism.

Since:

5.4

setSearchContracted

public void setSearchContracted(boolean searchContracted)

Sets the checker should search for contracted abbreviated groups or not

Parameters:

searchContracted - is a boolean property. If true contracted abbreviated groups will be checked during the checking mechanism.

Since:

5.4

setExcluded

public void setExcluded(chemaxon.checkers.util.AtomLabels excluded)

Sets the abbreviations to be excluded

Parameters:

excluded - the abbreviations to be excluded

isValid

public boolean isValid()

Excluded object is initialized. If it is null, the parse was not successful.

Specified by:

isValid in interface StructureChecker

Overrides:

isValid in class AbstractStructureChecker

Returns:

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

getExcluded

public chemaxon.checkers.util.AtomLabels getExcluded()

Gets the excluded abbreviations

Returns:

the excluded abbreviations