ambit2.smarts.processors

Class SMIRKSProcessor

java.lang.Object

ambit2.core.processors.AbstractStructureProcessor

ambit2.smarts.processors.SMIRKSProcessor

All Implemented Interfaces:

Serializable, net.idea.modbcum.i.processors.IProcessor<org.openscience.cdk.interfaces.IAtomContainer,org.openscience.cdk.interfaces.IAtomContainer>

Direct Known Subclasses:

NeutraliseProcessor

public class SMIRKSProcessor
extends AbstractStructureProcessor

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
protected boolean	loadExamples
protected SMIRKSManager	smrkMan
protected boolean	transformationasproperties
protected List<SMIRKSTransformation>	transformations

Fields inherited from class ambit2.core.processors.AbstractStructureProcessor

at_property, at_property_added, at_property_removed, atomtypeasproperties, enabled, logger, sparseproperties

Constructor Summary

Constructors

Constructor and Description
SMIRKSProcessor(File jsonFile, Logger logger)
SMIRKSProcessor(InputStream jsonFile, Logger logger)
SMIRKSProcessor(Logger logger)

Method Summary

Modifier and Type	Method and Description
void	configureReactions(SMIRKSManager smrkMan)
SMIRKSTransformation	getReactionByID(int id)
List<SMIRKSTransformation>	getTransformations()
boolean	isLoadExamples()
boolean	isTransformationasproperties() assigns performed transformations as atomcontainer properties
void	loadReactionsFromJSON(File jsonFile)
void	loadReactionsFromJSON(InputStream fin)
static SMIRKSTransformation	parseTransformation(com.fasterxml.jackson.databind.node.ObjectNode node, boolean loadExample)
org.openscience.cdk.interfaces.IAtomContainer	process(org.openscience.cdk.interfaces.IAtomContainer reactant)
void	setLoadExamples(boolean loadExamples)
void	setTransformationasproperties(boolean transformationasproperties)

Methods inherited from class ambit2.core.processors.AbstractStructureProcessor

applicable, atomtypes2properties_init, atomtypes2properties, atomtypes2property, atomtypes2property, close, getID, isAtomtypeasproperties, isEnabled, isSparseproperties, open, setAtomtypeasproperties, setEnabled, setSparseproperties

Methods inherited from class java.lang.Object

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

Field Detail

loadExamples

protected boolean loadExamples

transformationasproperties

protected boolean transformationasproperties

transformations

protected List<SMIRKSTransformation> transformations

smrkMan

protected SMIRKSManager smrkMan

Constructor Detail

SMIRKSProcessor

public SMIRKSProcessor(Logger logger)

SMIRKSProcessor

public SMIRKSProcessor(File jsonFile,
                       Logger logger)
                throws Exception

Throws:

Exception

SMIRKSProcessor

public SMIRKSProcessor(InputStream jsonFile,
                       Logger logger)
                throws Exception

Throws:

Exception

Method Detail

isLoadExamples

public boolean isLoadExamples()

setLoadExamples

public void setLoadExamples(boolean loadExamples)

isTransformationasproperties

public boolean isTransformationasproperties()

assigns performed transformations as atomcontainer properties

Returns:

setTransformationasproperties

public void setTransformationasproperties(boolean transformationasproperties)

getTransformations

public List<SMIRKSTransformation> getTransformations()

loadReactionsFromJSON

public void loadReactionsFromJSON(File jsonFile)
                           throws Exception

Throws:

Exception

loadReactionsFromJSON

public void loadReactionsFromJSON(InputStream fin)
                           throws Exception

Throws:

Exception

configureReactions

public void configureReactions(SMIRKSManager smrkMan)
                        throws Exception

Throws:

Exception

getReactionByID

public SMIRKSTransformation getReactionByID(int id)

process

public org.openscience.cdk.interfaces.IAtomContainer process(org.openscience.cdk.interfaces.IAtomContainer reactant)
                                                      throws Exception

Throws:

Exception

parseTransformation

public static SMIRKSTransformation parseTransformation(com.fasterxml.jackson.databind.node.ObjectNode node,
                                                       boolean loadExample)
                                                throws Exception

Throws:

Exception