toxTree.tree.rules
Class RuleSubstructures

java.lang.Object
  extended by java.util.Observable
      extended by toxTree.tree.AbstractRule
          extended by toxTree.tree.AbstractRuleHilightHits
              extended by 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

Field Summary
protected  java.util.ArrayList ids
           
static java.lang.String MSG_HASGROUP
           
protected  QueryAtomContainers query
           
 
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
RuleSubstructures()
           
 
Method Summary
 void addSubstructure(org.openscience.cdk.interfaces.IAtomContainer fragment)
          The fragment will be added to the list of substructures to be searched for
 void clearSubstructures()
          removes all substructures defined for a rule
 boolean equals(java.lang.Object obj)
           
 java.util.ArrayList getIds()
           
 QueryAtomContainers getQuery()
           
 org.openscience.cdk.interfaces.IAtomContainer getSubstructure(int index)
          Returns a substructure AtomContainer at a given rules
 java.util.List getSubstructures()
          Returns a list ArrayList of AtomContainer defined for the rule
 int getSubstructuresCount()
           
 boolean isImplemented()
           
 org.openscience.cdk.interfaces.IAtomContainer removeSubstructure(int index)
          Removes substructure at a given index
 void setIds(java.util.ArrayList ids)
           
 void setQuery(QueryAtomContainers query)
           
 void setSubstructure(int index, org.openscience.cdk.interfaces.IAtomContainer atomContainer)
          sets substructure at index
 boolean verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer selected)
           
 
Methods inherited from class toxTree.tree.AbstractRuleHilightHits
getSelector
 
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
 

Field Detail

MSG_HASGROUP

public static transient java.lang.String MSG_HASGROUP

query

protected QueryAtomContainers query

ids

protected java.util.ArrayList ids
Constructor Detail

RuleSubstructures

public RuleSubstructures()
Method Detail

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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