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CDK Keyword List

CDK Keyword List

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Published by Egon Willighagen
CDK Keyword List created for CDK 1.2.0 with LaTeX.
CDK Keyword List created for CDK 1.2.0 with LaTeX.

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Published by: Egon Willighagen on Apr 11, 2009
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02/07/2011

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Keyword List
The keyword list is an overview of CDK functionality organized by keyword. For each key-word a reference is made to the CDK class that implements that functionality. To simplifythe list, the common prefix
org.openscience.cdk
has been removed. For example, the class
org.openscience.cdk.layout.StructureDiagramGenerator
has to do with 2D coordinates.
2D
layout.StructureDiagramGenerator
2D coordinates
layout.StructureDiagramGenerator
2D-coordinates
layout.TemplateHandlerlayout.OverlapResolver
3D
modeling.builder3d.ModelBuilder3Dsimilarity.DistanceMoment
3D coordinates
modeling.builder3d.ModelBuilder3D
3D isomorphism
pharmacophore.PharmacophoreQueryAtompharmacophore.PharmacophoreBondpharmacophore.PharmacophoreUtilspharmacophore.PharmacophoreMatcherpharmacophore.PharmacophoreAtompharmacophore.PharmacophoreAngleBondpharmacophore.PharmacophoreQueryAngleBondpharmacophore.PharmacophoreQueryBond
3D model
geometry.AtomTools.add3DCoordinates1()modeling.builder3d.AtomTetrahedralLigandPlacer3D.add3DCoordinatesForSinglyBondedLigands()
3D-coordinates
modeling.forcefield.GeometricMinimizer
adding
tools.CDKHydrogenAdder.addImplicitHydrogens()tools.manipulator.AtomContainerManipulator.convertImplicitToExplicitHydrogens()
adjacency matrix
graph.matrix.AdjacencyMatrix
amino acid
AminoAcidinterfaces.IAminoAcid
amino acidsstuctures
templates.AminoAcids
animation
1
 
2
KEYWORD LIST 
ChemSequenceinterfaces.IChemSequence
aromatic ringbond order adjustment
tools.DeAromatizationTool
aromaticity detector
aromaticity.AromaticityCalculator
ASN
io.iterator.IteratingPCSubstancesXMLReaderio.iterator.IteratingPCCompoundASNReaderio.iterator.IteratingPCCompoundXMLReader
association
Association
atom
AtomBondinterfaces.IAtominterfaces.IBond
type
AtomTypeconfig.TXTBasedAtomTypeConfiguratorconfig.AtomTypeFactoryinterfaces.IAtomType
valency
tools.LonePairElectronCheckertools.SaturationCheckertools.SmilesValencyChecker
chemical validation
validate.ValidationTest
atom coloringpartial charges
renderer.color.PartialAtomicChargeColors
CPK
renderer.color.CPKAtomColors
atom mapping
Mapping
atom parity
AtomParityinterfaces.IAtomParity
atom typeE-state
atomtype.EStateAtomTypeMatcher
mmff94
modeling.builder3d.MMFF94BasedParameterSetReader
MM2
modeling.builder3d.MM2BasedParameterSetReader
atom typesSybyl
atomtype.SybylAtomTypeMatcher
atomic
interfaces.IElementqsar.descriptors.molecular.APolDescriptor
atomic number
interfaces.IElement
AtomPlacer3D
modeling.builder3d.AtomPlacer3D
BCUT
qsar.descriptors.molecular.BCUTDescriptor
Binary Space Partitioning Tree
graph.rebond.Bspt
biopolymer
BioPolymer
 
3
interfaces.IBioPolymerinterfaces.IPDBPolymer
bond
ElectronContainerAssociationBondLonePairinterfaces.ILonePairinterfaces.IBond
recalculation
graph.rebond.RebondTool
bond countrotatable
qsar.descriptors.molecular.RotatableBondsCountDescriptor
bond creation
geometry.BondTools.closeEnoughToBond()
bond order
CDKConstantssmiles.DeduceBondSystemTool
calculation
tools.SaturationChecker.newSaturate()tools.SmilesValencyChecker.saturate()
bond order adjustment
tools.DeAromatizationTool
calculation
tools.SaturationChecker.newSaturate()tools.SmilesValencyChecker.saturate()
canonicalization
graph.invariant.CanonicalLabeler
CAS number
index.CASNumberindex.CASNumber.isValid()
CDK source code
io.CDKSourceCodeWriter
center of mass
geometry.GeometryTools.get2DCentreOfMass()geometry.GeometryTools.get3DCentreOfMass()
charge distribution
charges.InductivePartialChargescharges.GasteigerMarsiliPartialChargescharges.GasteigerPEPEPartialCharges
chemical identifier
io.INChIPlainTextReaderio.INChIReader
chemical validation
validate.ValidationTest
chi chain index
qsar.descriptors.molecular.ChiChainDescriptor
chi cluster index
qsar.descriptors.molecular.ChiClusterDescriptor
chi path cluster index
qsar.descriptors.molecular.ChiPathClusterDescriptor
chi path index
qsar.descriptors.molecular.ChiPathDescriptor
CIF
io.CIFReader
class convertor
libio.cml.Convertor
classification
qsar.model.R.CNNClassificationModel
CML

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