toxTree.tree.rules
Class RuleRingSubstituents
java.lang.Object
java.util.Observable
toxTree.tree.AbstractRule
toxTree.tree.AbstractRuleHilightHits
toxTree.tree.rules.RuleSubstructures
toxTree.tree.rules.RuleRings
toxTree.tree.rules.RuleRingSubstituents
- All Implemented Interfaces:
- java.io.Serializable, java.lang.Cloneable, IDecisionRule, IRuleSubstructures, XMLSerializable
- Direct Known Subclasses:
- RuleOnlyFuncGroupsQ30, RuleRingAllowedSubstituents, RuleRingOtherThanAllowedSubstituents, SA20_nogen
public abstract class RuleRingSubstituents
- extends RuleRings
A rule to analyze ring substituents
- Author:
- Nina Jeliazkova
Modified 2005-8-17
- 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 |
Methods inherited from class toxTree.tree.rules.RuleSubstructures |
addSubstructure, clearSubstructures, equals, getIds, getQuery, getSubstructure, getSubstructures, getSubstructuresCount, isImplemented, removeSubstructure, setIds, setQuery, setSubstructure |
Methods inherited from class toxTree.tree.AbstractRule |
addPropertyChangeListener, clearFlags, clone, createRule, 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 |
Methods inherited from interface toxTree.core.IDecisionRule |
addPropertyChangeListener, clearFlags, clone, getEditor, getExampleMolecule, getExplanation, getID, getNum, getSelector, getTitle, hideResiduesID, isEditable, isResidueIDHidden, removePropertyChangeListener, setEditable, setExampleMolecule, setExplanation, setID, setNum, setTitle, toString |
ERR_PRECONDITION_FAILED
public static java.lang.String ERR_PRECONDITION_FAILED
CONDITION_FAILED
public static java.lang.String CONDITION_FAILED
CYCLIC_SUBSTITUENT
public static java.lang.String CYCLIC_SUBSTITUENT
LONGCHAIN_SUBSTITUENT
public static java.lang.String LONGCHAIN_SUBSTITUENT
flags
protected boolean[] flags
analyzeOnlyRingsWithFlagSet
protected boolean analyzeOnlyRingsWithFlagSet
RuleRingSubstituents
public RuleRingSubstituents()
analyze
protected boolean analyze(org.openscience.cdk.interfaces.IRing r)
substituentIsAllowed
public abstract boolean substituentIsAllowed(org.openscience.cdk.interfaces.IAtomContainer a,
int[] place)
throws DecisionMethodException
- returns true if the substituent is allowed and false if it is forbidden
to be implemented by the inheriting class
- Throws:
DecisionMethodException
clearFlags
public void clearFlags()
setAnalyzeHeterocyclic
public void setAnalyzeHeterocyclic(boolean flag)
setAnalyzeAromatic
public void setAnalyzeAromatic(boolean flag)
analyzeOnlyRingsWithFlagSet
public boolean analyzeOnlyRingsWithFlagSet()
- Returns:
- Returns the analyzeOnlyRingsWithFlagSet.
setAnalyzeOnlyRingsWithFlagSet
public void setAnalyzeOnlyRingsWithFlagSet(boolean analyzeOnlyRingsWithFlagSet)
- Parameters:
analyzeOnlyRingsWithFlagSet
- The analyzeOnlyRingsWithFlagSet to set.
allowedSubstituents
public java.lang.String allowedSubstituents()
verifyRule
public boolean verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
throws DecisionMethodException
IDecisionRule.verifyRule(IAtomContainer)
- Parameters:
mol
- org.openscience.cdk.interfaces.AtomContainer
- Returns:
- rule result, boolean
- Throws:
DecisionMethodException
verifyRule
public boolean verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol,
org.openscience.cdk.interfaces.IAtomContainer selected)
throws DecisionMethodException
- Overrides:
verifyRule
in class RuleSubstructures
- Throws:
DecisionMethodException
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