toxtree.plugins.smartcyp.rules

Class SMARTCYPRuleRank1

java.lang.Object

java.util.Observable

toxTree.tree.AbstractRule

toxtree.plugins.smartcyp.rules.MetaboliteGenerator

toxtree.plugins.smartcyp.rules.SMARTCYPRuleRank1

All Implemented Interfaces:

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

Direct Known Subclasses:

SMARTCYPRuleHigherRank, SMARTCYPRuleRank2, SMARTCYPRuleRank3

public class SMARTCYPRuleRank1
extends MetaboliteGenerator

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
protected org.openscience.cdk.tools.CDKHydrogenAdder	adder
protected static CategoriesRenderer	categoriesRenderer

Fields inherited from class toxtree.plugins.smartcyp.rules.MetaboliteGenerator

bundle, rank, 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
SMARTCYPRuleRank1()
SMARTCYPRuleRank1(int rank)

Method Summary

Modifier and Type	Method and Description
dk.smartcyp.core.MoleculeKU	calculate(org.openscience.cdk.interfaces.IAtomContainer iAtomContainerTmp)
String	getHelp(RuleResult ruleresult)
org.openscience.cdk.interfaces.IAtomContainerSet	getProducts(org.openscience.cdk.interfaces.IAtomContainer reactant, RuleResult ruleResult)
ambit2.rendering.IAtomContainerHighlights	getSelector()
protected boolean	hasRank(int atom_rank)
boolean	isImplemented()
boolean	verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol) returns true if at least one atom has a score assigned
boolean	verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer selected)

Methods inherited from class toxtree.plugins.smartcyp.rules.MetaboliteGenerator

accept, getRank, setRank

Methods inherited from class toxTree.tree.AbstractRule

addPropertyChangeListener, clearFlags, clone, createRule, equals, fromXML, getEditor, getExampleMolecule, getExamples, getExplanation, getID, getNum, getTitle, hideResiduesID, isEditable, 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

Field Detail

categoriesRenderer

protected static final CategoriesRenderer categoriesRenderer

adder

protected transient org.openscience.cdk.tools.CDKHydrogenAdder adder

Constructor Detail

SMARTCYPRuleRank1

public SMARTCYPRuleRank1()

SMARTCYPRuleRank1

public SMARTCYPRuleRank1(int rank)

Method Detail

verifyRule

public boolean verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
                   throws DecisionMethodException

returns true if at least one atom has a score assigned

Parameters:

mol - org.openscience.cdk.interfaces.AtomContainer

Returns:

rule result, boolean

Throws:

DecisionMethodException

hasRank

protected boolean hasRank(int atom_rank)

calculate

public dk.smartcyp.core.MoleculeKU calculate(org.openscience.cdk.interfaces.IAtomContainer iAtomContainerTmp)
                                      throws DecisionMethodException

Throws:

DecisionMethodException

getSelector

public ambit2.rendering.IAtomContainerHighlights getSelector()

Specified by:

getSelector in interface IDecisionRule

Overrides:

getSelector in class AbstractRule

verifyRule

public boolean verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol,
                          org.openscience.cdk.interfaces.IAtomContainer selected)
                   throws DecisionMethodException

Throws:

DecisionMethodException

isImplemented

public boolean isImplemented()

Specified by:

isImplemented in interface IDecisionRule

Overrides:

isImplemented in class AbstractRule

Returns:

false if the rule is not implemented and true if it is

getProducts

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

Specified by:

getProducts in interface IMetaboliteGenerator

Overrides:

getProducts in class MetaboliteGenerator

Throws:

Exception

getHelp

public String getHelp(RuleResult ruleresult)

Specified by:

getHelp in interface IMetaboliteGenerator

Overrides:

getHelp in class MetaboliteGenerator