toxtree.plugins.kroes.rules
Class RuleKroesFig1Q1
java.lang.Object
java.util.Observable
toxTree.tree.AbstractRule
toxTree.tree.AbstractRuleHilightHits
toxTree.tree.rules.RuleSubstructures
toxtree.plugins.kroes.rules.RuleKroesFig1Q1
- All Implemented Interfaces:
- java.io.Serializable, java.lang.Cloneable, IDecisionRule, IRuleSubstructures, XMLSerializable
public class RuleKroesFig1Q1
- extends RuleSubstructures
TODO refactor with SMARTS
- Author:
- nina
- 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 |
Method Summary |
static org.openscience.cdk.isomorphism.matchers.IQueryAtomContainer |
createQueryContainer(org.openscience.cdk.interfaces.IAtomContainer container)
|
protected static java.io.InputStream |
getConfiguration()
|
protected void |
init()
|
boolean |
isImplemented()
|
protected void |
print(org.openscience.cdk.interfaces.IAtomContainer a)
|
protected void |
readStream(java.io.InputStream fStream,
java.lang.String format)
|
boolean |
verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
This is the core of a IDecisionRule behaviour. |
Methods inherited from class toxTree.tree.rules.RuleSubstructures |
addSubstructure, clearSubstructures, equals, getIds, getQuery, getSubstructure, getSubstructures, getSubstructuresCount, removeSubstructure, setIds, setQuery, setSubstructure, verifyRule |
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 |
halogens
public static transient java.lang.String[] halogens
me_essential
public static transient java.lang.String[] me_essential
me_nonessential
public static transient java.lang.String[] me_nonessential
config
public static transient java.lang.String config
RuleKroesFig1Q1
public RuleKroesFig1Q1()
RuleKroesFig1Q1
public RuleKroesFig1Q1(java.io.InputStream stream,
java.lang.String format)
RuleKroesFig1Q1
public RuleKroesFig1Q1(java.io.File file)
init
protected void init()
readStream
protected void readStream(java.io.InputStream fStream,
java.lang.String format)
createQueryContainer
public static org.openscience.cdk.isomorphism.matchers.IQueryAtomContainer createQueryContainer(org.openscience.cdk.interfaces.IAtomContainer container)
getConfiguration
protected static java.io.InputStream getConfiguration()
isImplemented
public boolean isImplemented()
- Specified by:
isImplemented
in interface IDecisionRule
- Overrides:
isImplemented
in class RuleSubstructures
- Returns:
- false if the rule is not implemented and true if it is
verifyRule
public boolean verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
throws DecisionMethodException
- Description copied from interface:
IDecisionRule
- This is the core of a
IDecisionRule
behaviour. The method returns true
if the answer of the rule is YES for the analyzed molecule org.openscience.cdk.interfaces.AtomContainer
and FALSE
if the answer of the rule is NO for the analyzed molecule org.openscience.cdk.interfaces.AtomContainer
??
- Parameters:
mol
- org.openscience.cdk.interfaces.AtomContainer
- Returns:
- rule result, boolean
- Throws:
DecisionMethodException
print
protected void print(org.openscience.cdk.interfaces.IAtomContainer a)
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