org.openscience.cdk.graph.Cycles.allOrVertexShort()
|
org.openscience.cdk.ringsearch.AllRingsFinder.checkTimeout()
timeout not used
|
org.openscience.cdk.tools.manipulator.AtomContainerManipulator.createAllCarbonAllSingleNonAromaticBondAtomContainer(IAtomContainer)
|
org.openscience.cdk.smiles.SmilesGenerator.createSMILES(IAtomContainer)
use #create
|
org.openscience.cdk.smiles.SmilesGenerator.createSMILES(IReaction)
use #createReactionSMILES
|
org.openscience.cdk.isomorphism.matchers.QueryAtomContainer.getBondOrderSum(IAtom)
Replaced by AtomContainerManipulator#getBondOrderSum(IAtomContainer, IAtom)
|
org.openscience.cdk.AtomContainer.getBondOrderSum(IAtom)
Replaced by AtomContainerManipulator#getBondOrderSum(IAtomContainer, IAtom)
|
org.openscience.cdk.silent.AtomContainer.getBondOrderSum(IAtom)
Replaced by AtomContainerManipulator#getBondOrderSum(IAtomContainer, IAtom)
|
org.openscience.cdk.smiles.smarts.parser.SimpleCharStream.getColumn() |
org.openscience.cdk.iupac.parser.SimpleCharStream.getColumn() |
org.openscience.cdk.isomorphism.matchers.smarts.LogicalOperatorAtom.getFlag(int) |
org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator.getHillString(IMolecularFormula)
|
org.openscience.cdk.inchi.InChIGeneratorFactory.getIgnoreAromaticBonds() |
org.openscience.cdk.isomorphism.matchers.smarts.LogicalOperatorAtom.getLeft() |
org.openscience.cdk.smiles.smarts.parser.SimpleCharStream.getLine() |
org.openscience.cdk.iupac.parser.SimpleCharStream.getLine() |
org.openscience.cdk.isomorphism.matchers.smarts.LogicalOperatorAtom.getOperator() |
org.openscience.cdk.isomorphism.matchers.smarts.LogicalOperatorAtom.getRight() |
org.openscience.cdk.graph.PathTools.getShortestPath(IAtomContainer, IAtom, IAtom)
This implementation recalculates all shortest paths from the start atom
for each method call and does not indicate if there are equally short paths
from the start to the end. Replaced by ShortestPaths.atomsTo(IAtom)
|
org.openscience.cdk.ringsearch.AllRingsFinder.getTimeout()
timeout not used
|
org.openscience.cdk.geometry.GeometryTools.has2DCoordinatesNew(IAtomContainer)
|
org.openscience.cdk.geometry.GeometryUtil.has2DCoordinatesNew(IAtomContainer)
|
org.openscience.cdk.smiles.SmilesParser.isPreservingAromaticity() |
org.openscience.cdk.modeling.builder3d.TemplateHandler3D.mapTemplates(IAtomContainer, double)
|
org.openscience.cdk.isomorphism.matchers.smarts.LogicalOperatorAtom.matches(IAtom) |
org.openscience.cdk.renderer.elements.path.PathElement.points() |
org.openscience.cdk.tools.manipulator.AtomContainerManipulator.removeHydrogensPreserveMultiplyBonded(IAtomContainer)
|
org.openscience.cdk.formula.AdductFormula.setCharge(Integer) |
org.openscience.cdk.silent.AdductFormula.setCharge(Integer) |
org.openscience.cdk.inchi.InChIGeneratorFactory.setIgnoreAromaticBonds(boolean)
"the use of aromatic bonds is strongly discouraged" - InChI
FAQ, the InChI will fail for many compounds if ignore
aromatic bonds is not enabled and the compound have aromatic
flags.
|
org.openscience.cdk.isomorphism.matchers.smarts.LogicalOperatorAtom.setLeft(IQueryAtom) |
org.openscience.cdk.isomorphism.matchers.smarts.LogicalOperatorAtom.setOperator(String)
|
org.openscience.cdk.smiles.SmilesParser.setPreservingAromaticity(boolean) |
org.openscience.cdk.io.rdf.CDKOWLReader.setReader(Reader) |
org.openscience.cdk.isomorphism.matchers.smarts.LogicalOperatorAtom.setRight(IQueryAtom) |
org.openscience.cdk.ringsearch.AllRingsFinder.setTimeout(long)
use the new threshold (during construction)
|
org.openscience.cdk.smiles.SmilesGenerator.setUseAromaticityFlag(boolean)
|