toxTree.tree.cramer
Class RuleHasOnlySaltSulphonateSulphate

java.lang.Object
  extended by java.util.Observable
      extended by toxTree.tree.AbstractRule
          extended by toxTree.tree.AbstractRuleHilightHits
              extended by toxTree.tree.rules.RuleSubstructures
                  extended by toxTree.tree.rules.RuleOnlyAllowedSubstructures
                      extended by toxTree.tree.cramer.RuleHasOnlySaltSulphonateSulphate
All Implemented Interfaces:
java.io.Serializable, java.lang.Cloneable, IDecisionRule, IRuleSubstructures, XMLSerializable

public class RuleHasOnlySaltSulphonateSulphate
extends RuleOnlyAllowedSubstructures

Rule 4 of the Cramer scheme (see CramerRules)

Author:
Nina Jeliazkova Modified 2005-8-23
See Also:
Serialized Form

Field Summary
protected static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer aminoSulphate
           
protected static java.util.ArrayList elements
           
protected static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer hClAmine
           
protected static java.lang.String[] Me
           
protected static java.lang.String[] Me1
           
protected static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer salt
           
protected static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer salt1
           
protected static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer salt2
           
protected static org.openscience.cdk.smiles.SmilesGenerator sg
           
protected static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer sulphate
           
protected static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer sulphonate
           
 
Fields inherited from class toxTree.tree.rules.RuleSubstructures
ids, MSG_HASGROUP, 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
RuleHasOnlySaltSulphonateSulphate()
           
 
Method Summary
 boolean verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
          Calls the inherited RuleOnlyAllowedSubstructures.verifyRule(IAtomContainer) Removes sulphonate and sulphate groups if any by FunctionalGroups.detachGroup(IAtomContainer, QueryAtomContainer) and sets molflag property of a molecule to mf.setResidue(residue); This makes subsequent rules to work with the residue rather than with the original molecule If a rule needs the original structure instead, it can get it by getProperty(MolFlags.PARENT) See for example Q24 and Q33 TODO treat hydrochloride of amine as free amine
 boolean verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer selected)
           
 
Methods inherited from class toxTree.tree.rules.RuleOnlyAllowedSubstructures
isImplemented
 
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.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
 

Field Detail

sg

protected static transient org.openscience.cdk.smiles.SmilesGenerator sg

Me

protected static final transient java.lang.String[] Me

Me1

protected static final transient java.lang.String[] Me1

elements

protected static transient java.util.ArrayList elements

sulphonate

protected static transient org.openscience.cdk.isomorphism.matchers.QueryAtomContainer sulphonate

sulphate

protected static transient org.openscience.cdk.isomorphism.matchers.QueryAtomContainer sulphate

aminoSulphate

protected static transient org.openscience.cdk.isomorphism.matchers.QueryAtomContainer aminoSulphate

salt

protected static transient org.openscience.cdk.isomorphism.matchers.QueryAtomContainer salt

salt1

protected static transient org.openscience.cdk.isomorphism.matchers.QueryAtomContainer salt1

salt2

protected static transient org.openscience.cdk.isomorphism.matchers.QueryAtomContainer salt2

hClAmine

protected static transient org.openscience.cdk.isomorphism.matchers.QueryAtomContainer hClAmine
Constructor Detail

RuleHasOnlySaltSulphonateSulphate

public RuleHasOnlySaltSulphonateSulphate()
Method Detail

verifyRule

public boolean verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
                   throws DecisionMethodException
Calls the inherited RuleOnlyAllowedSubstructures.verifyRule(IAtomContainer) Removes sulphonate and sulphate groups if any by FunctionalGroups.detachGroup(IAtomContainer, QueryAtomContainer) and sets molflag property of a molecule to mf.setResidue(residue); This makes subsequent rules to work with the residue rather than with the original molecule If a rule needs the original structure instead, it can get it by getProperty(MolFlags.PARENT) See for example Q24 and Q33 TODO treat hydrochloride of amine as free amine

Specified by:
verifyRule in interface IDecisionRule
Overrides:
verifyRule in class RuleOnlyAllowedSubstructures
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 RuleOnlyAllowedSubstructures
Throws:
DecisionMethodException


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