cramer2.rules
Class RuleHasOnlySaltSulphonateSulphate
java.lang.Object
java.util.Observable
toxTree.tree.AbstractRule
toxTree.tree.AbstractRuleHilightHits
toxTree.tree.rules.RuleSubstructures
toxTree.tree.rules.RuleOnlyAllowedSubstructures
cramer2.rules.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 cramer2.CramerRulesExtendedExtended
)
- 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<java.lang.String> |
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 |
phosphate
|
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.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 |
Method Summary |
boolean |
verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol,
org.openscience.cdk.interfaces.IAtomContainer selected)
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 |
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 |
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<java.lang.String> elements
phosphate
protected static transient org.openscience.cdk.isomorphism.matchers.QueryAtomContainer phosphate
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
RuleHasOnlySaltSulphonateSulphate
public RuleHasOnlySaltSulphonateSulphate()
verifyRule
public boolean verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol,
org.openscience.cdk.interfaces.IAtomContainer selected)
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
- Overrides:
verifyRule
in class RuleOnlyAllowedSubstructures
- Throws:
DecisionMethodException
Copyright © 2004-2012 Ideaconsult Ltd.. All Rights Reserved.