verhaar.rules
Class Rule21
java.lang.Object
java.util.Observable
toxTree.tree.AbstractRule
toxTree.tree.AbstractRuleHilightHits
toxTree.tree.rules.RuleSubstructures
toxTree.tree.rules.RuleRings
toxTree.tree.rules.RuleRingSubstituents
toxTree.tree.rules.RuleRingAllowedSubstituents
verhaar.rules.RuleRingMainStrucSubstituents
verhaar.rules.Rule21
- All Implemented Interfaces:
- java.io.Serializable, java.lang.Cloneable, IDecisionRule, IImplementationDetails, IRuleSubstructures, XMLSerializable, IAlertCounter
- Direct Known Subclasses:
- Rule22, Rule23, Rule25
public class Rule21
- extends RuleRingMainStrucSubstituents
- implements IAlertCounter
Non- or weakly acidic phenols.
- Author:
- Nina Jeliazkova jeliazkova.nina@gmail.com
Modified July 12, 2011
- 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, 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 |
alertsCounter
protected IAlertCounter alertsCounter
nitroGroupsCount
protected transient int nitroGroupsCount
halogensCount
protected transient int halogensCount
halogens
protected transient java.lang.String[] halogens
nitroIDs
protected java.util.ArrayList nitroIDs
phenolIDs
protected java.util.ArrayList phenolIDs
halogenIDs
protected java.util.ArrayList halogenIDs
maxHalogens
protected int maxHalogens
maxNitroGroups
protected int maxNitroGroups
Rule21
public Rule21()
getHalogens
protected java.lang.String[] getHalogens()
createMainStructure
protected org.openscience.cdk.isomorphism.matchers.QueryAtomContainer createMainStructure()
- Specified by:
createMainStructure
in class RuleRingMainStrucSubstituents
verifyRule
public boolean verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
throws DecisionMethodException
- Description copied from class:
RuleRingSubstituents
IDecisionRule.verifyRule(IAtomContainer)
- Specified by:
verifyRule
in interface IDecisionRule
- Overrides:
verifyRule
in class RuleRingAllowedSubstituents
- 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
- Description copied from class:
RuleRingAllowedSubstituents
- returns true if only allowed substituents are found
- Overrides:
verifyRule
in class RuleRingAllowedSubstituents
- Throws:
DecisionMethodException
substituentIsAllowed
public boolean substituentIsAllowed(org.openscience.cdk.interfaces.IAtomContainer a,
int[] place)
throws DecisionMethodException
- Description copied from class:
RuleRingSubstituents
- returns true if the substituent is allowed and false if it is forbidden
to be implemented by the inheriting class
- Overrides:
substituentIsAllowed
in class RuleRingAllowedSubstituents
- Throws:
DecisionMethodException
isImplemented
public boolean isImplemented()
- Specified by:
isImplemented
in interface IDecisionRule
- Overrides:
isImplemented
in class RuleRingAllowedSubstituents
- Returns:
- false if the rule is not implemented and true if it is
getMaxHalogens
public int getMaxHalogens()
setMaxHalogens
public void setMaxHalogens(int maxHalogens)
getMaxNitroGroups
public int getMaxNitroGroups()
setMaxNitroGroups
public void setMaxNitroGroups(int maxNitroGroups)
getImplementationDetails
public java.lang.String getImplementationDetails()
- Specified by:
getImplementationDetails
in interface IImplementationDetails
incrementCounter
public void incrementCounter(org.openscience.cdk.interfaces.IAtomContainer mol)
- Specified by:
incrementCounter
in interface IAlertCounter
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