ambit2.core.processors.quality

Class ChemicalStructureQualityCheck

java.lang.Object

net.idea.modbcum.p.DefaultAmbitProcessor<org.openscience.cdk.interfaces.IAtomContainer,QLabel>

ambit2.core.processors.quality.ChemicalStructureQualityCheck

All Implemented Interfaces:

Serializable, net.idea.modbcum.i.processors.IProcessor<org.openscience.cdk.interfaces.IAtomContainer,QLabel>

public class ChemicalStructureQualityCheck
extends net.idea.modbcum.p.DefaultAmbitProcessor<org.openscience.cdk.interfaces.IAtomContainer,QLabel>

Verifies consistency between multiple structures, coming from different origins 2)coherence of multiple origins - compare all structures of same idchemical - assign OK if same, notOK if not same

• retrieve a chemical (by idchemical)
• retrieve structures per chemical
• calculate fingerprints per structure
• compare structure fingerprints with fingerprints from fp1024 (per chemical), if different, assign "ERROR", otherwise assign "ProbablyOK"
• (slow) select one structure and compare all other structures (same chemical) with isomrphism test; assign "ERROR" if not same.

Author:

nina

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
protected org.openscience.cdk.interfaces.IAtomContainer	groundTruth
protected org.openscience.cdk.isomorphism.IsomorphismTester	isoTester
protected AmbitUser	qualityVerifier

Fields inherited from class net.idea.modbcum.p.DefaultAmbitProcessor

enabled, logger, propertyChangeSupport

Constructor Summary

Constructors

Constructor and Description
ChemicalStructureQualityCheck()

Method Summary

Modifier and Type	Method and Description
org.openscience.cdk.interfaces.IAtomContainer	getGroundTruth()
QLabel	process(org.openscience.cdk.interfaces.IAtomContainer target)
void	setGroundTruth(org.openscience.cdk.interfaces.IAtomContainer groundTruth)

Methods inherited from class net.idea.modbcum.p.DefaultAmbitProcessor

addPropertyChangeListener, addPropertyChangeListener, close, getID, isEnabled, open, removePropertyChangeListener, removePropertyChangeListener, setEnabled, toString

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

qualityVerifier

protected AmbitUser qualityVerifier

groundTruth

protected org.openscience.cdk.interfaces.IAtomContainer groundTruth

isoTester

protected org.openscience.cdk.isomorphism.IsomorphismTester isoTester

Constructor Detail

ChemicalStructureQualityCheck

public ChemicalStructureQualityCheck()

Method Detail

getGroundTruth

public org.openscience.cdk.interfaces.IAtomContainer getGroundTruth()

setGroundTruth

public void setGroundTruth(org.openscience.cdk.interfaces.IAtomContainer groundTruth)

process

public QLabel process(org.openscience.cdk.interfaces.IAtomContainer target)
               throws net.idea.modbcum.i.exceptions.AmbitException

Throws:

net.idea.modbcum.i.exceptions.AmbitException