toxtree.plugins.smartcyp.rules

Class MetaboliteGenerator

java.lang.Object

java.util.Observable

toxTree.tree.AbstractRule

toxtree.plugins.smartcyp.rules.MetaboliteGenerator

All Implemented Interfaces:

ambit2.smarts.IAcceptable, Serializable, Cloneable, IDecisionRule, IMetaboliteGenerator, XMLSerializable

Direct Known Subclasses:

SMARTCYPRuleRank1

public abstract class MetaboliteGenerator
extends AbstractRule
implements IMetaboliteGenerator, ambit2.smarts.IAcceptable

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
protected ResourceBundle	bundle
protected int	rank
protected ambit2.smarts.SMIRKSManager	smrkMan

Fields inherited from class toxTree.tree.AbstractRule

changes, editable, ERR_STRUCTURENOTPREPROCESSED, examples, explanation, id, logger, MSG_NO, MSG_YES, no, residueIDHidden, title

Fields inherited from interface toxTree.core.XMLSerializable

xmltag_CATEGORIES, xmltag_CATEGORY, xmltag_CATEGORYTHRESHOLD, xmltag_CLASS, xmltag_EXPLANATION, xmltag_ID, xmltag_METHOD, xmltag_METHODPARAMETER, xmltag_METHODS, xmltag_NAME, xmltag_RULE, xmltag_RULEEXAMPLE, xmltag_RULES, xmltag_TREEROOT

Constructor Summary

Constructors

Constructor and Description
MetaboliteGenerator()

Method Summary

Modifier and Type	Method and Description
boolean	accept(List<org.openscience.cdk.interfaces.IAtom> atoms)
String	getHelp(RuleResult ruleresult)
org.openscience.cdk.interfaces.IAtomContainerSet	getProducts(org.openscience.cdk.interfaces.IAtomContainer reactant, RuleResult ruleResult)
int	getRank()
void	setRank(int rank)

Methods inherited from class toxTree.tree.AbstractRule

addPropertyChangeListener, clearFlags, clone, createRule, equals, fromXML, getEditor, getExampleMolecule, getExamples, getExplanation, getID, getNum, getSelector, getTitle, hideResiduesID, isEditable, isImplemented, isResidueIDHidden, log, log, log, makeMolecule, removePropertyChangeListener, setEditable, setExampleMolecule, setExamples, setExplanation, setID, setNum, setTitle, toShallowXML, toString, toXML

Methods inherited from class java.util.Observable

addObserver, clearChanged, countObservers, deleteObserver, deleteObservers, hasChanged, notifyObservers, notifyObservers, setChanged

Methods inherited from class java.lang.Object

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

Methods inherited from interface toxTree.core.IDecisionRule

verifyRule

Field Detail

smrkMan

protected transient ambit2.smarts.SMIRKSManager smrkMan

rank

protected int rank

bundle

protected transient ResourceBundle bundle

Constructor Detail

MetaboliteGenerator

public MetaboliteGenerator()

Method Detail

getRank

public int getRank()

setRank

public void setRank(int rank)

getProducts

public org.openscience.cdk.interfaces.IAtomContainerSet getProducts(org.openscience.cdk.interfaces.IAtomContainer reactant,
                                                                    RuleResult ruleResult)
                                                             throws Exception

Specified by:

getProducts in interface IMetaboliteGenerator

Throws:

Exception

accept

public boolean accept(List<org.openscience.cdk.interfaces.IAtom> atoms)

Specified by:

accept in interface ambit2.smarts.IAcceptable

getHelp

public String getHelp(RuleResult ruleresult)

Specified by:

getHelp in interface IMetaboliteGenerator