chemaxon.standardizer.actions

Class ReplaceAtomsAction

java.lang.Object

chemaxon.standardizer.AbstractStandardizerAction

chemaxon.standardizer.actions.ReplaceAtomsAction

All Implemented Interfaces:

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

@PublicAPI
public class ReplaceAtomsAction
extends AbstractStandardizerAction

Replace atoms standardizer action

Since:

6.0

Author:

Imre Barna

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	PROPERTY_KEY_ALLOW_VALENCE_ERROR Property key for serialization/deserialization an event changes for valence check (boolean value type)
static java.lang.String	PROPERTY_KEY_QUERY_ATOM Property key for serialization/deserialization an event changes for query atom (MolAtom value type)
static java.lang.String	PROPERTY_KEY_REPLACE_ATOM Property key for serialization/deserialization an event changes for replace atom (MolAtom value type)

Fields inherited from class chemaxon.standardizer.AbstractStandardizerAction

CONFIG_PATH_KEY, FORMAT_KEY, ID_KEY, support

Constructor Summary

Constructors

Constructor and Description
ReplaceAtomsAction(java.util.Map<java.lang.String,java.lang.String> params) Initializes a replace atom standardizer action

Method Summary

Modifier and Type	Method and Description
ReplaceAtomsAction	clone()
MolAtom	getQueryAtom() Gets the atom to be searched for by the action (the query atom)
MolAtom	getReplaceAtom() Gets the atom to replaced with by the action
boolean	isAllowValenceError() Gets whether replace should be applied even in case of invalid valence in the result
protected boolean	matches(MolAtom atom, MolAtom queryAtom) Matches 2 atoms
protected boolean	replace(MolAtom atom, MolAtom replaceAtom, Molecule molecule) Replaces an atom to the replace atom in the target molecule
void	setAllowValenceError(boolean allowValenceError) Sets replace should be applied even in case of invalid valence in the result
void	setQueryAtom(MolAtom queryAtom) Sets the atom to be searched for by the action (the query atom)
void	setReplaceAtom(MolAtom replaceAtom) Sets the atom to replaced with by the action
protected Changes	standardize1(Molecule molecule) This method contains the current standardization mechanism.
java.lang.String	toString()

Methods inherited from class chemaxon.standardizer.AbstractStandardizerAction

addPropertyChangeListener, addPropertyChangeListener, cloneItem, getComponents, getDescriptor, getID, isActive, isAvailable, isLicensed, isValid, propertyChange, removePropertyChangeListener, removePropertyChangeListener, setActive, setID, setLicenseEnvironment, setValid, standardize

Methods inherited from class java.lang.Object

equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

PROPERTY_KEY_QUERY_ATOM

public static final java.lang.String PROPERTY_KEY_QUERY_ATOM

Property key for serialization/deserialization an event changes for query atom (MolAtom value type)

See Also:

Constant Field Values

PROPERTY_KEY_REPLACE_ATOM

public static final java.lang.String PROPERTY_KEY_REPLACE_ATOM

Property key for serialization/deserialization an event changes for replace atom (MolAtom value type)

See Also:

Constant Field Values

PROPERTY_KEY_ALLOW_VALENCE_ERROR

public static final java.lang.String PROPERTY_KEY_ALLOW_VALENCE_ERROR

Property key for serialization/deserialization an event changes for valence check (boolean value type)

See Also:

Constant Field Values

Constructor Detail

ReplaceAtomsAction

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

Initializes a replace atom standardizer action

Parameters:

params - the parameters of the action

Method Detail

standardize1

protected final Changes standardize1(Molecule molecule)
                              throws java.lang.IllegalArgumentException

Description copied from class: AbstractStandardizerAction

This method contains the current standardization mechanism. Descendants needs to implement this method.
Special molecules containing more components (e.g. RgMolecule, RxnMolecule) are decomponented by the method AbstractStandardizerAction.getComponents(Molecule), and AbstractStandardizerAction.standardize1(Molecule) method is called on each component, before applied on the original molecule. If a descendant does not want this to occur, this method must be overridden.
Logs of standardization should be generated to a Logger, that can be collected by using StandardizerLogger.getLogger() method.

Specified by:

standardize1 in class AbstractStandardizerAction

Parameters:

molecule - the Molecule instance to be standardized

Returns:

the changes applied on the molecule during the standardization process

Throws:

java.lang.IllegalArgumentException - if the provided molecule or the provided parameters of the action are invalid

replace

protected boolean replace(MolAtom atom,
                          MolAtom replaceAtom,
                          Molecule molecule)

Replaces an atom to the replace atom in the target molecule

Parameters:

atom - the atom to be replaced

replaceAtom - the atom to replace with

molecule - the parent molecule

matches

protected boolean matches(MolAtom atom,
                          MolAtom queryAtom)

Matches 2 atoms

Parameters:

atom - the first atom

queryAtom - the second atom

Returns:

true if the atoms do match

getQueryAtom

public MolAtom getQueryAtom()

Gets the atom to be searched for by the action (the query atom)

Returns:

the atom to be searched for by the action (the query atom)

setQueryAtom

public void setQueryAtom(MolAtom queryAtom)

Sets the atom to be searched for by the action (the query atom)

Parameters:

queryAtom - the atom to be searched for by the action (the query atom)

getReplaceAtom

public MolAtom getReplaceAtom()

Gets the atom to replaced with by the action

Returns:

the atom to replaced with by the action

setReplaceAtom

public void setReplaceAtom(MolAtom replaceAtom)

Sets the atom to replaced with by the action

Parameters:

replaceAtom - the atom to replaced with by the action

isAllowValenceError

public boolean isAllowValenceError()

Gets whether replace should be applied even in case of invalid valence in the result

Returns:

whether replace should be applied even in case of invalid valence in the result

setAllowValenceError

public void setAllowValenceError(boolean allowValenceError)

Sets replace should be applied even in case of invalid valence in the result

Parameters:

allowValenceError - replace should be applied even in case of invalid valence in the result

clone

public ReplaceAtomsAction clone()
                         throws java.lang.CloneNotSupportedException

Overrides:

clone in class AbstractStandardizerAction

Throws:

java.lang.CloneNotSupportedException

toString

public java.lang.String toString()

Overrides:

toString in class AbstractStandardizerAction