toxTree.tree.cramer

Class RuleHasOnlySaltSulphonateSulphate

java.lang.Object

java.util.Observable

toxTree.tree.AbstractRule

toxTree.tree.AbstractRuleHilightHits

toxTree.tree.rules.RuleSubstructures

toxTree.tree.rules.RuleOnlyAllowedSubstructures

toxTree.tree.cramer.RuleHasOnlySaltSulphonateSulphate

All Implemented Interfaces:

Serializable, 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

Fields

Modifier and Type	Field and Description
protected static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer	aminoSulphate
protected static ArrayList<String>	elements
protected static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer	hClAmine
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

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

Constructors

Constructor and Description
RuleHasOnlySaltSulphonateSulphate()

Method Summary

Modifier and Type	Method and Description
protected String[]	initMetals()
protected String[]	initMetals1()
protected QueryAtomContainers	initQuery()
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

elements

protected static ArrayList<String> 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()
                                  throws Exception

Throws:

Exception

Method Detail

initMetals

protected String[] initMetals()

initMetals1

protected String[] initMetals1()

initQuery

protected QueryAtomContainers initQuery()
                                 throws Exception

Overrides:

initQuery in class RuleSubstructures

Throws:

Exception

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