Package chemaxon.standardizer.actions
Class MapReactionAction
java.lang.Object
chemaxon.standardizer.AbstractStandardizerAction
chemaxon.standardizer.actions.MapReactionAction
- All Implemented Interfaces:
chemaxon.license.Licensable
,StandardizerAction
,PropertyChangeListener
,Cloneable
,EventListener
Map reaction standardizer action
- Since:
- 5.11
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Field Summary
Modifier and TypeFieldDescriptionstatic final String
keep mapping propertystatic final String
mapping style propertystatic final String
mark bonds propertyFields inherited from class chemaxon.standardizer.AbstractStandardizerAction
CONFIG_PATH_KEY, FORMAT_KEY, ID_KEY, support
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Constructor Summary
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Method Summary
Modifier and TypeMethodDescriptiongetComponents
(Molecule target) A recursive algorithm getting all components (reactants, agents and products of reaction molecules, R-group definitions of Rg-Molecules) of the molecule.Returns the mapping style of the underlying mapper.boolean
Returns if underlying mapper keeps existing maps should be kept when mapping.boolean
Returns if bonds are marked while mapping.void
setKeepMapping
(boolean keepMapping) Sets keep mapping for the underlying mapper.void
setMappingStyle
(Mapper.MappingStyle mappingStyle) Sets Mapping Style for the underlying mapper.void
setMarkBonds
(boolean markBonds) Sets mark bonds for the underlying mapper.protected Changes
standardize1
(Molecule molecule) This method contains the current standardization mechanism.toString()
Methods inherited from class chemaxon.standardizer.AbstractStandardizerAction
addPropertyChangeListener, addPropertyChangeListener, anyBooleanPropertyTrue, clone, cloneItem, getDescriptor, getID, isActive, isAvailable, isLicensed, isValid, propertyChange, removePropertyChangeListener, removePropertyChangeListener, setActive, setID, setLicenseEnvironment, setValid, standardize
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Field Details
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MAPPING_STYLE
mapping style property- See Also:
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MARK_BONDS
mark bonds property- See Also:
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KEEP_MAPPING
keep mapping property- See Also:
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Constructor Details
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MapReactionAction
Initializes the action- Parameters:
params
- the parameters of the action
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Method Details
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standardize1
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 methodAbstractStandardizerAction.getComponents(Molecule)
, andAbstractStandardizerAction.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 aLogger
, that can be collected by usingStandardizerLogger.getLogger()
method.- Specified by:
standardize1
in classAbstractStandardizerAction
- Parameters:
molecule
- theMolecule
instance to be standardized- Returns:
- the changes applied on the molecule during the standardization process
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getComponents
Description copied from class:AbstractStandardizerAction
A recursive algorithm getting all components (reactants, agents and products of reaction molecules, R-group definitions of Rg-Molecules) of the molecule. Used to collect all. If components must not be standardized, this method should be overridden.- Overrides:
getComponents
in classAbstractStandardizerAction
- Parameters:
target
- the target molecule- Returns:
- the resulted list of components
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setMappingStyle
Sets Mapping Style for the underlying mapper.- Parameters:
mappingStyle
- the new mapping style- Since:
- 6.1
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setKeepMapping
public void setKeepMapping(boolean keepMapping) Sets keep mapping for the underlying mapper.- Parameters:
keepMapping
-true
indicates existing maps should be kept when mapping- Since:
- 6.1
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setMarkBonds
public void setMarkBonds(boolean markBonds) Sets mark bonds for the underlying mapper.- Parameters:
markBonds
-true
indicates bond marks should be added when mapping
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getMappingStyle
Returns the mapping style of the underlying mapper.- Returns:
- the mapping style of the underlying mapper
- Since:
- 6.1
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isKeepMapping
public boolean isKeepMapping()Returns if underlying mapper keeps existing maps should be kept when mapping.- Returns:
true
if underlying mapper keeps existing maps should be kept when mapping- Since:
- 6.1
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isMarkBonds
public boolean isMarkBonds()Returns if bonds are marked while mapping.- Returns:
true
when bonds are marked while mapping- Since:
- 6.1
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toString
- Overrides:
toString
in classAbstractStandardizerAction
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