toxTree.tree.rules
Class RuleSubstructures
java.lang.Object
java.util.Observable
toxTree.tree.AbstractRule
toxTree.tree.AbstractRuleHilightHits
toxTree.tree.rules.RuleSubstructures
- All Implemented Interfaces:
- java.io.Serializable, java.lang.Cloneable, IDecisionRule, IRuleSubstructures, XMLSerializable
- Direct Known Subclasses:
- RuleAliphaticWithSomeFuncGroups, RuleAllSubstructures, RuleAnySubstructure, RuleCarbohydrate, RuleIonicGroups, RuleKroesFig1Q1, RuleLactoneOrCyclicDiester, RuleOnlyAllowedSubstructures, RuleRings
public abstract class RuleSubstructures
- extends AbstractRuleHilightHits
- implements IRuleSubstructures
An abstract class to implement substructure rules
- Author:
- Nina Jeliazkova
Modified 2005-8-14
- 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.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, verifyRule |
MSG_HASGROUP
public static transient java.lang.String MSG_HASGROUP
query
protected QueryAtomContainers query
ids
protected java.util.ArrayList ids
RuleSubstructures
public RuleSubstructures()
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
addSubstructure
public void addSubstructure(org.openscience.cdk.interfaces.IAtomContainer fragment)
- The fragment will be added to the list of substructures to be searched for
- Specified by:
addSubstructure
in interface IRuleSubstructures
- Parameters:
fragment
- /* (non-Javadoc)- See Also:
addSubstructure(IAtomContainer)
clearSubstructures
public void clearSubstructures()
- Description copied from interface:
IRuleSubstructures
- removes all substructures defined for a rule
- Specified by:
clearSubstructures
in interface IRuleSubstructures
getSubstructuresCount
public int getSubstructuresCount()
- Specified by:
getSubstructuresCount
in interface IRuleSubstructures
- Returns:
- the number of substructures defined for the rule
getSubstructure
public org.openscience.cdk.interfaces.IAtomContainer getSubstructure(int index)
- Description copied from interface:
IRuleSubstructures
- Returns a substructure
AtomContainer
at a given rules
- Specified by:
getSubstructure
in interface IRuleSubstructures
- Returns:
- molecule
AtomContainer
setSubstructure
public void setSubstructure(int index,
org.openscience.cdk.interfaces.IAtomContainer atomContainer)
- Description copied from interface:
IRuleSubstructures
- sets substructure at index
- Specified by:
setSubstructure
in interface IRuleSubstructures
equals
public boolean equals(java.lang.Object obj)
- Overrides:
equals
in class AbstractRule
removeSubstructure
public org.openscience.cdk.interfaces.IAtomContainer removeSubstructure(int index)
- Description copied from interface:
IRuleSubstructures
- Removes substructure at a given index
- Specified by:
removeSubstructure
in interface IRuleSubstructures
- Returns:
AtomContainer
getSubstructures
public java.util.List getSubstructures()
- Description copied from interface:
IRuleSubstructures
- Returns a list
ArrayList
of AtomContainer
defined for the rule
- Specified by:
getSubstructures
in interface IRuleSubstructures
- Returns:
- list
List
getQuery
public QueryAtomContainers getQuery()
setQuery
public void setQuery(QueryAtomContainers query)
getIds
public java.util.ArrayList getIds()
setIds
public void setIds(java.util.ArrayList ids)
verifyRule
public boolean verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol,
org.openscience.cdk.interfaces.IAtomContainer selected)
throws DecisionMethodException
- Specified by:
verifyRule
in class AbstractRuleHilightHits
- Throws:
DecisionMethodException
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