chemaxon.checkers

Class AtomQueryPropertyChecker

java.lang.Object

chemaxon.checkers.AbstractStructureChecker

chemaxon.checkers.ComponentChecker<MolAtom>

chemaxon.checkers.AtomChecker

chemaxon.checkers.AtomQueryPropertyChecker

All Implemented Interfaces:

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

public class AtomQueryPropertyChecker
extends AtomChecker

A descendant of AtomChecker detecting atoms having an query property set.

Since:

Marvin 5.6

Version:

5.7

Author:

Gyorgy Pirok

Field Summary

Fields

Modifier and Type	Field and Description
static String	PROPERTY_KEY_AROMATCITY Aromaticity atom query property.
static String	PROPERTY_KEY_AROMATICITY_CHECKING Aromaticity checking property
static String	PROPERTY_KEY_CONNECTION_COUNT Connection count atom query property.
static String	PROPERTY_KEY_CONNECTION_COUNT_CHECKING Connection count checking property
static String	PROPERTY_KEY_EXPLICIT_CONNECTION_COUNT Explicit connection count atom query property.
static String	PROPERTY_KEY_EXPLICIT_CONNECTION_COUNT_CHECKING Explicit connection count checking property
static String	PROPERTY_KEY_HYDROGEN_COUNT Hydrogen count atom query property.
static String	PROPERTY_KEY_HYDROGEN_COUNT_CHECKING Hydrogen count checking property
static String	PROPERTY_KEY_IMPLICIT_HYDROGEN_COUNT Implicit hydrogen count atom query property.
static String	PROPERTY_KEY_IMPLICIT_HYDROGEN_COUNT_CHECKING Implicit hydrogen count checking property
static String	PROPERTY_KEY_RING_BOND_COUNT Ring bond count atom query property.
static String	PROPERTY_KEY_RING_BOND_COUNT_CHECKING Ring bond count checking property
static String	PROPERTY_KEY_RING_COUNT Ring count atom query property.
static String	PROPERTY_KEY_RING_COUNT_CHECKING Ring count checking property
static String	PROPERTY_KEY_SMALLEST_RING_SIZE Smallest ring size atom query property.
static String	PROPERTY_KEY_SMALLEST_RING_SIZE_CHECKING Smallest ring size checking property
static String	PROPERTY_KEY_SUBSTITUTION_COUNT Substitution count atom query property.
static String	PROPERTY_KEY_SUBSTITUTION_COUNT_CHECKING Substitution count checking property
static String	PROPERTY_KEY_UNSATURATION Unsaturation atom query property.
static String	PROPERTY_KEY_UNSATURATION_CHECKING Unsaturation checking property

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
AtomQueryPropertyChecker() Creates a new AtomQueryPropertyChecker instance, it detects all query properties by default.
AtomQueryPropertyChecker(Map<String,String> params) Creates a new AtomQueryPropertyChecker instance to detect the given query properties.

Method Summary

Methods

Modifier and Type	Method and Description
protected boolean	check(Molecule molecule, MolAtom component) Checks if the component with index i has problem
protected StructureCheckerResult	createResult(Molecule molecule, List<MolAtom> atoms) Creates a StructureCheckerResult from a List containing the components.
boolean	equals(Object obj)
int	hashCode()
boolean	isAromaticityChecking() Gets the option determining if the checker detects aromaticity atom query properties or not.
boolean	isConnectionCountChecking() Gets the option determining if the checker detects connection count atom query properties or not.
boolean	isExplicitConnectionCountChecking() Gets the option determining if the checker detects explicit connection count atom query properties or not.
boolean	isHydrogenCountChecking() Gets the option determining if the checker detects hydrogen count atom query properties or not.
boolean	isImplicitHydrogenCountChecking() Gets the option determining if the checker detects implicit hydrogen count atom query properties or not.
boolean	isRingBondCountChecking() Gets the option determining if the checker detects ring bond count atom query properties or not.
boolean	isRingCountChecking() Gets the option determining if the checker detects ring count atom query properties or not.
boolean	isSmallestRingSizeChecking() Gets the option determining if the checker detects smallest ring size atom query properties or not.
boolean	isSubstitutionCountChecking() Gets the option determining if the checker detects substitution count atom query properties or not.
boolean	isUnsaturationChecking() Gets the option determining if the checker detects unsaturation atom query properties or not.
void	setAromaticityChecking(boolean value) Sets the option determining if the checker detects aromaticity atom query properties or not.
void	setConnectionCountChecking(boolean value) Sets the option determining if the checker detects connection count atom query properties or not.
void	setExplicitConnectionCountChecking(boolean value) Sets the option determining if the checker detects explicit connection count atom query properties or not.
void	setHydrogenCountChecking(boolean value) Sets the option determining if the checker detects hydrogen count atom query properties or not.
void	setImplicitHydrogenCountChecking(boolean value) Sets the option determining if the checker detects implicit hydrogen count atom query properties or not.
void	setRingBondCountChecking(boolean value) Sets the option determining if the checker detects ring bond count atom query properties or not.
void	setRingCountChecking(boolean value) Sets the option determining if the checker detects ring count atom query properties or not.
void	setSmallestRingSizeChecking(boolean value) Sets the option determining if the checker detects smallest ring size atom query properties or not.
void	setSubstitutionCountChecking(boolean value) Sets the option determining if the checker detects substitution count atom query properties or not.
void	setUnsaturationChecking(boolean value) Sets the option determining if the checker detects unsaturation atom query properties or not.
String	toString()

Methods inherited from class chemaxon.checkers.AtomChecker

getComponent, getComponentCount

Methods inherited from class chemaxon.checkers.ComponentChecker

check1, initialize

Methods inherited from class chemaxon.checkers.AbstractStructureChecker

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

Field Detail

PROPERTY_KEY_HYDROGEN_COUNT

public static final String PROPERTY_KEY_HYDROGEN_COUNT

Hydrogen count atom query property.

See Also:

Constant Field Values

PROPERTY_KEY_CONNECTION_COUNT

public static final String PROPERTY_KEY_CONNECTION_COUNT

Connection count atom query property.

See Also:

Constant Field Values

PROPERTY_KEY_EXPLICIT_CONNECTION_COUNT

public static final String PROPERTY_KEY_EXPLICIT_CONNECTION_COUNT

Explicit connection count atom query property.

See Also:

Constant Field Values

PROPERTY_KEY_RING_COUNT

public static final String PROPERTY_KEY_RING_COUNT

Ring count atom query property.

See Also:

Constant Field Values

PROPERTY_KEY_IMPLICIT_HYDROGEN_COUNT

public static final String PROPERTY_KEY_IMPLICIT_HYDROGEN_COUNT

Implicit hydrogen count atom query property.

See Also:

Constant Field Values

PROPERTY_KEY_SMALLEST_RING_SIZE

public static final String PROPERTY_KEY_SMALLEST_RING_SIZE

Smallest ring size atom query property.

See Also:

Constant Field Values

PROPERTY_KEY_AROMATCITY

public static final String PROPERTY_KEY_AROMATCITY

Aromaticity atom query property.

See Also:

Constant Field Values

PROPERTY_KEY_SUBSTITUTION_COUNT

public static final String PROPERTY_KEY_SUBSTITUTION_COUNT

Substitution count atom query property.

See Also:

Constant Field Values

PROPERTY_KEY_UNSATURATION

public static final String PROPERTY_KEY_UNSATURATION

Unsaturation atom query property.

See Also:

Constant Field Values

PROPERTY_KEY_RING_BOND_COUNT

public static final String PROPERTY_KEY_RING_BOND_COUNT

Ring bond count atom query property.

See Also:

Constant Field Values

PROPERTY_KEY_AROMATICITY_CHECKING

public static final String PROPERTY_KEY_AROMATICITY_CHECKING

Aromaticity checking property

See Also:

Constant Field Values

PROPERTY_KEY_CONNECTION_COUNT_CHECKING

public static final String PROPERTY_KEY_CONNECTION_COUNT_CHECKING

Connection count checking property

See Also:

Constant Field Values

PROPERTY_KEY_EXPLICIT_CONNECTION_COUNT_CHECKING

public static final String PROPERTY_KEY_EXPLICIT_CONNECTION_COUNT_CHECKING

Explicit connection count checking property

See Also:

Constant Field Values

PROPERTY_KEY_HYDROGEN_COUNT_CHECKING

public static final String PROPERTY_KEY_HYDROGEN_COUNT_CHECKING

Hydrogen count checking property

See Also:

Constant Field Values

PROPERTY_KEY_IMPLICIT_HYDROGEN_COUNT_CHECKING

public static final String PROPERTY_KEY_IMPLICIT_HYDROGEN_COUNT_CHECKING

Implicit hydrogen count checking property

See Also:

Constant Field Values

PROPERTY_KEY_RING_BOND_COUNT_CHECKING

public static final String PROPERTY_KEY_RING_BOND_COUNT_CHECKING

Ring bond count checking property

See Also:

Constant Field Values

PROPERTY_KEY_RING_COUNT_CHECKING

public static final String PROPERTY_KEY_RING_COUNT_CHECKING

Ring count checking property

See Also:

Constant Field Values

PROPERTY_KEY_SMALLEST_RING_SIZE_CHECKING

public static final String PROPERTY_KEY_SMALLEST_RING_SIZE_CHECKING

Smallest ring size checking property

See Also:

Constant Field Values

PROPERTY_KEY_SUBSTITUTION_COUNT_CHECKING

public static final String PROPERTY_KEY_SUBSTITUTION_COUNT_CHECKING

Substitution count checking property

See Also:

Constant Field Values

PROPERTY_KEY_UNSATURATION_CHECKING

public static final String PROPERTY_KEY_UNSATURATION_CHECKING

Unsaturation checking property

See Also:

Constant Field Values

Constructor Detail

AtomQueryPropertyChecker

public AtomQueryPropertyChecker()

Creates a new AtomQueryPropertyChecker instance, it detects all query properties by default.

AtomQueryPropertyChecker

public AtomQueryPropertyChecker(Map<String,String> params)

Creates a new AtomQueryPropertyChecker instance to detect the given query properties.

Parameters:

params - a Map instance which contains String pairs. Key is the name of the parameter, value is "true" or "false".

Method Detail

check

protected boolean check(Molecule molecule,
            MolAtom component)

Description copied from class: ComponentChecker

Checks if the component with index i has problem

Specified by:

check in class ComponentChecker<MolAtom>

Parameters:

molecule - is a Molecule instance

component - the current component to check

Returns:

true if the component has problem, false otherwise

createResult

protected StructureCheckerResult createResult(Molecule molecule,
                                  List<MolAtom> atoms)

Description copied from class: ComponentChecker

Creates a StructureCheckerResult from a List containing the components.

Overrides:

createResult in class AtomChecker

Parameters:

molecule - is a Molecule instance

atoms - is an instance of List containing the problematic components

Returns:

a StructureCheckerResult containing all problematic component indices

equals

public boolean equals(Object obj)

Overrides:

equals in class AbstractStructureChecker

hashCode

public int hashCode()

Overrides:

hashCode in class AbstractStructureChecker

isAromaticityChecking

public boolean isAromaticityChecking()

Gets the option determining if the checker detects aromaticity atom query properties or not.

Returns:

true if the aromaticity atom query properties are detected

isConnectionCountChecking

public boolean isConnectionCountChecking()

Gets the option determining if the checker detects connection count atom query properties or not.

Returns:

true if the connection count atom query properties are detected

isExplicitConnectionCountChecking

public boolean isExplicitConnectionCountChecking()

Gets the option determining if the checker detects explicit connection count atom query properties or not.

Returns:

true if the explicit connection count atom query properties are detected

isHydrogenCountChecking

public boolean isHydrogenCountChecking()

Gets the option determining if the checker detects hydrogen count atom query properties or not.

Returns:

true if the hydrogen count atom query properties are detected

isImplicitHydrogenCountChecking

public boolean isImplicitHydrogenCountChecking()

Gets the option determining if the checker detects implicit hydrogen count atom query properties or not.

Returns:

true if the implicit hydrogen count atom query properties are detected

isRingBondCountChecking

public boolean isRingBondCountChecking()

Gets the option determining if the checker detects ring bond count atom query properties or not.

Returns:

true if the ring bond count atom query properties are detected

isRingCountChecking

public boolean isRingCountChecking()

Gets the option determining if the checker detects ring count atom query properties or not.

Returns:

true if the ring count atom query properties are detected

isSmallestRingSizeChecking

public boolean isSmallestRingSizeChecking()

Gets the option determining if the checker detects smallest ring size atom query properties or not.

Returns:

true if the smallest ring size atom query properties are detected

isSubstitutionCountChecking

public boolean isSubstitutionCountChecking()

Gets the option determining if the checker detects substitution count atom query properties or not.

Returns:

true if the substitution count atom query properties are detected

isUnsaturationChecking

public boolean isUnsaturationChecking()

Gets the option determining if the checker detects unsaturation atom query properties or not.

Returns:

true if the unsaturation atom query properties are detected

setAromaticityChecking

public void setAromaticityChecking(boolean value)

Sets the option determining if the checker detects aromaticity atom query properties or not.

Parameters:

value - if true, aromaticity atom query properties are detected

setConnectionCountChecking

public void setConnectionCountChecking(boolean value)

Sets the option determining if the checker detects connection count atom query properties or not.

Parameters:

value - if true, connection count atom query properties are detected

setExplicitConnectionCountChecking

public void setExplicitConnectionCountChecking(boolean value)

Sets the option determining if the checker detects explicit connection count atom query properties or not.

Parameters:

value - if true, explicit connection count atom query properties are detected

setHydrogenCountChecking

public void setHydrogenCountChecking(boolean value)

Sets the option determining if the checker detects hydrogen count atom query properties or not.

Parameters:

value - if true, hydrogen count atom query properties are detected

setImplicitHydrogenCountChecking

public void setImplicitHydrogenCountChecking(boolean value)

Sets the option determining if the checker detects implicit hydrogen count atom query properties or not.

Parameters:

value - if true, implicit hydrogen count atom query properties are detected

setRingBondCountChecking

public void setRingBondCountChecking(boolean value)

Sets the option determining if the checker detects ring bond count atom query properties or not.

Parameters:

value - if true, ring bond count atom query properties are detected

setRingCountChecking

public void setRingCountChecking(boolean value)

Sets the option determining if the checker detects ring count atom query properties or not.

Parameters:

value - if true, ring count atom query properties are detected

setSmallestRingSizeChecking

public void setSmallestRingSizeChecking(boolean value)

Sets the option determining if the checker detects smallest ring size atom query properties or not.

Parameters:

value - if true, smallest ring size atom query properties are detected

setSubstitutionCountChecking

public void setSubstitutionCountChecking(boolean value)

Sets the option determining if the checker detects substitution count atom query properties or not.

Parameters:

value - if true, substitution count atom query properties are detected

setUnsaturationChecking

public void setUnsaturationChecking(boolean value)

Sets the option determining if the checker detects unsaturation atom query properties or not.

Parameters:

value - if true, unsaturation query properties are detected

toString

public String toString()

Overrides:

toString in class AbstractStructureChecker