ambit2.core.processors.quality
Class ChemicalStructureQualityCheck

java.lang.Object
  ambit2.base.processors.DefaultAmbitProcessor<org.openscience.cdk.interfaces.IMolecule,ambit2.base.data.QLabel>
      ambit2.core.processors.quality.ChemicalStructureQualityCheck

All Implemented Interfaces:

ambit2.base.interfaces.IProcessor<org.openscience.cdk.interfaces.IMolecule,ambit2.base.data.QLabel>, java.io.Serializable

public class ChemicalStructureQualityCheck
extends ambit2.base.processors.DefaultAmbitProcessor<org.openscience.cdk.interfaces.IMolecule,ambit2.base.data.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.

See Also:

Serialized Form

Field Summary

protected org.openscience.cdk.interfaces.IMolecule	groundTruth
protected org.openscience.cdk.isomorphism.IsomorphismTester	isoTester
protected ambit2.base.data.AmbitUser	qualityVerifier

Fields inherited from class ambit2.base.processors.DefaultAmbitProcessor

enabled, logger, propertyChangeSupport

Constructor Summary

ChemicalStructureQualityCheck()

Method Summary

org.openscience.cdk.interfaces.IMolecule	getGroundTruth()
ambit2.base.data.QLabel	process(org.openscience.cdk.interfaces.IMolecule target)
void	setGroundTruth(org.openscience.cdk.interfaces.IMolecule groundTruth)

Methods inherited from class ambit2.base.processors.DefaultAmbitProcessor

addPropertyChangeListener, addPropertyChangeListener, getID, isEnabled, 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 ambit2.base.data.AmbitUser qualityVerifier

groundTruth

protected org.openscience.cdk.interfaces.IMolecule groundTruth

isoTester

protected org.openscience.cdk.isomorphism.IsomorphismTester isoTester

Constructor Detail

ChemicalStructureQualityCheck

public ChemicalStructureQualityCheck()

Method Detail

getGroundTruth

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

setGroundTruth

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

process

public ambit2.base.data.QLabel process(org.openscience.cdk.interfaces.IMolecule target)
                                throws ambit2.base.exceptions.AmbitException

Throws:

ambit2.base.exceptions.AmbitException