toxtree.plugins.smartcyp.rules
Class SMARTCYPRuleRank1

java.lang.Object
  extended by java.util.Observable
      extended by toxTree.tree.AbstractRule
          extended by toxtree.plugins.smartcyp.rules.MetaboliteGenerator
              extended by toxtree.plugins.smartcyp.rules.SMARTCYPRuleRank1
All Implemented Interfaces:
ambit2.smarts.IAcceptable, java.io.Serializable, java.lang.Cloneable, IDecisionRule, IMetaboliteGenerator, XMLSerializable
Direct Known Subclasses:
SMARTCYPRuleHigherRank, SMARTCYPRuleRank2, SMARTCYPRuleRank3

public class SMARTCYPRuleRank1
extends MetaboliteGenerator

See Also:
Serialized Form

Field Summary
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
SMARTCYPRuleRank1()
           
SMARTCYPRuleRank1(int rank)
           
 
Method Summary
 dk.smartcyp.core.MoleculeKU calculate(org.openscience.cdk.interfaces.IAtomContainer iAtomContainerTmp)
           
 java.lang.String getHelp(RuleResult ruleresult)
           
 org.openscience.cdk.interfaces.IAtomContainerSet getProducts(org.openscience.cdk.interfaces.IAtomContainer reactant, RuleResult ruleResult)
           
 ambit2.base.interfaces.IProcessor<org.openscience.cdk.interfaces.IAtomContainer,org.openscience.cdk.renderer.selection.IChemObjectSelection> 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.base.interfaces.IProcessor<org.openscience.cdk.interfaces.IAtomContainer,org.openscience.cdk.renderer.selection.IChemObjectSelection> 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 java.lang.Exception
Specified by:
getProducts in interface IMetaboliteGenerator
Overrides:
getProducts in class MetaboliteGenerator
Throws:
java.lang.Exception

getHelp

public java.lang.String getHelp(RuleResult ruleresult)
Specified by:
getHelp in interface IMetaboliteGenerator
Overrides:
getHelp in class MetaboliteGenerator


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