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, java.io.Serializable, java.lang.Cloneable, IDecisionRule, IMetaboliteGenerator, XMLSerializable
- Direct Known Subclasses:
- SMARTCYPRuleHigherRank, SMARTCYPRuleRank2, SMARTCYPRuleRank3
public class SMARTCYPRuleRank1
- extends MetaboliteGenerator
- See Also:
- Serialized Form
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 |
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.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 |
categoriesRenderer
protected static final CategoriesRenderer categoriesRenderer
adder
protected transient org.openscience.cdk.tools.CDKHydrogenAdder adder
SMARTCYPRuleRank1
public SMARTCYPRuleRank1()
SMARTCYPRuleRank1
public SMARTCYPRuleRank1(int rank)
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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