Deprecated API

Contents

• Deprecated Classes
• Deprecated Methods
• Deprecated Constructors

Deprecated Classes

Class and Description
org.openscience.cdk.graph.invariant.CanonicalLabeler this labeller uses slow data structures and has been replaced - Canon
org.openscience.cdk.math.Primes

Deprecated Methods

Method and Description
org.openscience.cdk.ringsearch.AllRingsFinder.checkTimeout() timeout not used
org.openscience.cdk.tools.manipulator.AtomContainerManipulator.createAllCarbonAllSingleNonAromaticBondAtomContainer(IAtomContainer) not all attributes are removed producing unexpected results, use AtomContainerManipulator.anonymise(org.openscience.cdk.interfaces.IAtomContainer)
org.openscience.cdk.fingerprint.Fingerprinter.findPathes(IAtomContainer, int) Use Fingerprinter.encodePaths(IAtomContainer, int, BitSet, int)
org.openscience.cdk.ringsearch.AllRingsFinder.getTimeout() timeout not used
org.openscience.cdk.geometry.GeometryUtil.has2DCoordinatesNew(IAtomContainer) use GeometryUtil.get2DCoordinateCoverage(org.openscience.cdk.interfaces.IAtomContainer) for determining partial coordinates
org.openscience.cdk.tools.manipulator.AtomContainerManipulator.removeHydrogensPreserveMultiplyBonded(IAtomContainer) AtomContainerManipulator.suppressHydrogens(org.openscience.cdk.interfaces.IAtomContainer) will now not removed bridging hydrogens by default
org.openscience.cdk.ringsearch.AllRingsFinder.setTimeout(long) use the new threshold (during construction)

Deprecated Constructors

Constructor and Description
org.openscience.cdk.ringsearch.AllRingsFinder(boolean) turn logging off by setting the level in the logger implementation