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 simplify
the 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.TemplateHandler
layout.OverlapResolver
3D
modeling.builder3d.ModelBuilder3D
similarity.DistanceMoment
3D coordinates modeling.builder3d.ModelBuilder3D
3D isomorphism
pharmacophore.PharmacophoreQueryAtom
pharmacophore.PharmacophoreBond
pharmacophore.PharmacophoreUtils
pharmacophore.PharmacophoreMatcher
pharmacophore.PharmacophoreAtom
pharmacophore.PharmacophoreAngleBond
pharmacophore.PharmacophoreQueryAngleBond
pharmacophore.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
AminoAcid
interfaces.IAminoAcid
amino acids
stuctures templates.AminoAcids
animation

1
2 KEYWORD LIST

ChemSequence
interfaces.IChemSequence
aromatic ring
bond order adjustment tools.DeAromatizationTool
aromaticity detector aromaticity.AromaticityCalculator
ASN
io.iterator.IteratingPCSubstancesXMLReader
io.iterator.IteratingPCCompoundASNReader
io.iterator.IteratingPCCompoundXMLReader
association Association
atom
Atom
Bond
interfaces.IAtom
interfaces.IBond
type
AtomType
config.TXTBasedAtomTypeConfigurator
config.AtomTypeFactory
interfaces.IAtomType
valency
tools.LonePairElectronChecker
tools.SaturationChecker
tools.SmilesValencyChecker
chemical validation validate.ValidationTest
atom coloring
partial charges renderer.color.PartialAtomicChargeColors
CPK renderer.color.CPKAtomColors
atom mapping Mapping
atom parity
AtomParity
interfaces.IAtomParity
atom type
E-state atomtype.EStateAtomTypeMatcher
mmff94 modeling.builder3d.MMFF94BasedParameterSetReader
MM2 modeling.builder3d.MM2BasedParameterSetReader
atom types
Sybyl atomtype.SybylAtomTypeMatcher
atomic
interfaces.IElement
qsar.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.IBioPolymer
interfaces.IPDBPolymer
bond
ElectronContainer
Association
Bond
LonePair
interfaces.ILonePair
interfaces.IBond
recalculation graph.rebond.RebondTool
bond count
rotatable qsar.descriptors.molecular.RotatableBondsCountDescriptor
bond creation geometry.BondTools.closeEnoughToBond()
bond order
CDKConstants
smiles.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.CASNumber
index.CASNumber.isValid()
CDK source code io.CDKSourceCodeWriter
center of mass
geometry.GeometryTools.get2DCentreOfMass()
geometry.GeometryTools.get3DCentreOfMass()
charge distribution
charges.InductivePartialCharges
charges.GasteigerMarsiliPartialCharges
charges.GasteigerPEPEPartialCharges
chemical identifier
io.INChIPlainTextReader
io.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
4 KEYWORD LIST

io.CMLWriter
io.CMLReader
io.iterator.event.EventCMLReader
libio.cml.Convertor
conformer conformation io.iterator.IteratingMDLConformerReader
connection matrix graph.matrix.ConnectionMatrix
connectivity graph.ConnectivityChecker
coordinate calculation
geometry.AtomTools.add3DCoordinates1()
modeling.builder3d.AtomTetrahedralLigandPlacer3D.add3DCoordinatesForSinglyBondedLigands()
coordinate generation
geometry.AtomTools.calculate3DCoordinatesForLigands()
modeling.builder3d.AtomTetrahedralLigandPlacer3D.get3DCoordinatesForLigands()
3D modeling.builder3d.ModelBuilder3D
CPK renderer.color.CPKAtomColors
creation tools.IDCreator
crystal
Crystal
geometry.CrystalGeometryTools
interfaces.ICrystal
DBE tools.manipulator.MolecularFormulaManipulator.getDBE()
descriptor
qsar.descriptors.molecular.RuleOfFiveDescriptor
qsar.descriptors.molecular.BCUTDescriptor
qsar.descriptors.molecular.WHIMDescriptor
qsar.descriptors.molecular.ChiChainDescriptor
qsar.descriptors.molecular.GravitationalIndexDescriptor
qsar.descriptors.molecular.XLogPDescriptor
qsar.descriptors.molecular.KappaShapeIndicesDescriptor
qsar.descriptors.molecular.RotatableBondsCountDescriptor
qsar.descriptors.molecular.ChiPathDescriptor
qsar.descriptors.molecular.ChiPathClusterDescriptor
qsar.descriptors.molecular.ChiClusterDescriptor
qsar.descriptors.molecular.ZagrebIndexDescriptor
qsar.descriptors.molecular.CarbonTypesDescriptor
qsar.descriptors.molecular.TPSADescriptor
diagonalization math.Matrix.diagonalize()
dictionary
dict.OWLFile
dict.Dictionary
dict.DictionaryDatabase
dict.Entry
dict.OWLReact
dict.EntryReact
implicit CDK references dict.CDKDictionaryReferences
double bond equivalent tools.manipulator.MolecularFormulaManipulator.getDBE()
E-state atomtype.EStateAtomTypeMatcher
 5

EAID number graph.invariant.HuLuIndexTool.getEAIDNumber()

electron
Bond
interfaces.IElectronContainer
interfaces.IBond
unpaired
SingleElectron
interfaces.ISingleElectron
electronegativities
partial equalization of orbital
charges.GasteigerMarsiliPartialCharges
charges.GasteigerPEPEPartialCharges
electronegativity
charges.InductivePartialCharges
charges.PiElectronegativity
charges.Electronegativity
tools.PeriodicTable
element
PeriodicTableElement
Element
config.IsotopeFactory
interfaces.IElement
tools.PeriodicTable
sorting tools.ElementComparator
estate
config.fragments.EStateFragments
fingerprint.EStateFingerprinter
file format
io.SMILESWriter
io.GamessReader
INChI
io.INChIPlainTextReader
io.INChIReader
XYZ io.XYZReader
Polymorph Predictor (tm) io.PMPReader
CML
io.CMLWriter
io.CMLReader
io.iterator.event.EventCMLReader
Mol2 io.Mol2Reader
Z-matrix io.ZMatrixReader
ShelX io.ShelXWriter
HIN io.HINReader
MDL SD file io.SDFWriter
ShelXL io.ShelXReader
PDB io.PDBReader
PubChem Compound ASN
6 KEYWORD LIST

io.PCSubstanceXMLReader
io.PCCompoundASNReader
CIF io.CIFReader
mmCIF io.CIFReader
MDL RXN
io.MDLRXNReader
io.MDLRXNV2000Reader
CDK source code io.CDKSourceCodeWriter
MDL RXN file io.MDLRXNWriter
MDL molfile
io.MDLWriter
io.MDLV2000Reader
io.MDLReader
io.iterator.IteratingMDLReader
PubChem Compound XML io.PCCompoundXMLReader
SDF
io.MDLV2000Reader
io.MDLReader
io.iterator.IteratingMDLReader
SMILES
io.SMILESReader
io.iterator.IteratingSMILESReader
ASN
io.iterator.IteratingPCSubstancesXMLReader
io.iterator.IteratingPCCompoundASNReader
io.iterator.IteratingPCCompoundXMLReader
file format SDF io.iterator.IteratingMDLConformerReader
fingerprint
fingerprint.FingerprinterTool
fingerprint.MACCSFingerprinter
fingerprint.Fingerprinter
fingerprint.IFingerprinter
fingerprint.SubstructureFingerprinter
fingerprint.EStateFingerprinter
fingerprint.ExtendedFingerprinter
fingerprint.GraphOnlyFingerprinter
force field modeling.forcefield.MMFF94EnergyFunction
fractional coordinates
crystal geometry.CrystalGeometryTools
fragment config.fragments.EStateFragments
Gamess io.GamessReader
Gauss elimination math.Matrix.elimination()
Gaussian (tm)
input file io.program.GaussianInputWriter
Gaussian basis set math.qm.GaussiansBasis
generator smiles.SmilesGenerator
geometry modeling.forcefield.GeometricMinimizer
 7

Gram-Schmidt algorithm math.Matrix.orthonormalize()

graph
path ringsearch.Path
graph matrix
molecular graph.matrix.IGraphMatrix
gravitational index qsar.descriptors.molecular.GravitationalIndexDescriptor
HIN io.HINReader
HOSE code tools.BremserOneSphereHOSECodePredictor
spherical atom search tools.HOSECodeGenerator
hydrogen
removal
tools.manipulator.AtomContainerManipulator.removeHydrogens()
tools.manipulator.AtomContainerManipulator.removeHydrogensPreserveMultiplyBonded()
tools.manipulator.AtomContainerManipulator.getHeavyAtoms()
tools.manipulator.MolecularFormulaManipulator.getHeavyElements()
hydrogens
adding
tools.CDKHydrogenAdder.addImplicitHydrogens()
tools.manipulator.AtomContainerManipulator.convertImplicitToExplicitHydrogens()
id
creation tools.IDCreator
implicit CDK references dict.CDKDictionaryReferences
INChI
io.INChIPlainTextReader
io.INChIReader
input file io.program.GaussianInputWriter
ionization potential qsar.descriptors.molecular.IPMolecularLearningDescriptor
isomorphism isomorphism.IsomorphismTester
isotope
Isotope
config.IsotopeFactory
interfaces.IIsotope
isotope pattern formula.IsotopePatternGenerator
IUPAC name iupac.parser.NomParser
jaccard similarity.Tanimoto
Jacobi algorithm math.Matrix.diagonalize()
join-the-dots
geometry.BondTools.closeEnoughToBond()
graph.rebond.Bspt
JRI qsar.model.R2.RModel
Kappe shape index qsar.descriptors.molecular.KappaShapeIndicesDescriptor
Layout
layout.StructureDiagramGenerator
layout.TemplateHandler
layout.OverlapResolver
line search modeling.forcefield.LineSearch
linear qsar.model.R.LinearRegressionModel
8 KEYWORD LIST

linear regression qsar.model.R2.LinearRegressionModel

Lipinski qsar.descriptors.molecular.RuleOfFiveDescriptor
lipophilicity qsar.descriptors.molecular.ALOGPDescriptor
log file io.GamessReader
logP qsar.descriptors.molecular.ALOGPDescriptor
lone-pair
ElectronContainer
LonePair
interfaces.ILonePair
mass interfaces.IIsotope
molecular tools.manipulator.AtomContainerManipulator.getNaturalExactMass()
mass number interfaces.IIsotope
MDL molfile
io.MDLWriter
io.MDLV2000Reader
io.MDLReader
io.iterator.IteratingMDLReader
MDL molfile V3000 io.MDLV3000Reader
MDL RXN
io.MDLRXNReader
io.MDLRXNV2000Reader
MDL RXN file io.MDLRXNWriter
MDL SD file io.SDFWriter
MDL V3000 io.MDLRXNV3000Reader
MM2 modeling.builder3d.MM2BasedParameterSetReader
mmCIF io.CIFReader
mmff94
modeling.builder3d.MMFF94BasedParameterSetReader
modeling.forcefield.MMFF94EnergyFunction
Mol2 io.Mol2Reader
molecular
graph.matrix.IGraphMatrix
tools.manipulator.AtomContainerManipulator.getNaturalExactMass()
molecular formula
formula.MolecularFormula
formula.AdductFormula
formula.MolecularFormulaChecker
formula.MolecularFormulaRange
formula.MolecularFormulaSet
interfaces.IMolecularFormulaSet
interfaces.IAdductFormula
interfaces.IMolecularFormula
molecule
Molecule
MoleculeSet
molecular formula formula.MolecularFormulaChecker
moment of inertia qsar.descriptors.molecular.MomentOfInertiaDescriptor
 9

monomer
Monomer
interfaces.IMonomer
Morgan number graph.invariant.MorganNumbersTools
Murcko fragments tools.GenerateFragments
neural network
qsar.model.R.CNNClassificationModel
qsar.model.R.CNNRegressionModel
qsar.model.R2.CNNRegressionModel
Newton-Raphson modeling.forcefield.NewtonRaphsonMethod
notional coordinates geometry.CrystalGeometryTools.notionalToCartesian()
number qsar.descriptors.molecular.PetitjeanNumberDescriptor
mass interfaces.IIsotope
atomic interfaces.IElement
orbital
ElectronContainer
Association
LonePair
interfaces.ILonePair
orthonormalization math.Matrix.orthonormalize()
output io.GamessReader
parser smiles.SmilesParser
partial atomic charges
charges.InductivePartialCharges
charges.GasteigerMarsiliPartialCharges
charges.GasteigerPEPEPartialCharges
partial charges renderer.color.PartialAtomicChargeColors
partial equalization of orbital
charges.GasteigerMarsiliPartialCharges
charges.GasteigerPEPEPartialCharges
partial least squares qsar.model.R.PLSRegressionModel
path ringsearch.Path
PDB io.PDBReader
pdbpolymer
interfaces.IPDBMonomer
interfaces.IPDBAtom
interfaces.IPDBStructure
interfaces.IPDBPolymer
PEOE charges.GasteigerMarsiliPartialCharges
PEPE charges.GasteigerPEPEPartialCharges
periodic table tools.PeriodicTable
permutation
graph.AtomContainerPermutor
graph.AtomContainerBondPermutor
graph.AtomContainerAtomPermutor
Petit-Jean
shape index qsar.descriptors.molecular.PetitjeanShapeIndexDescriptor
10 KEYWORD LIST

number qsar.descriptors.molecular.PetitjeanNumberDescriptor
pharmacophore
pharmacophore.PharmacophoreQueryAtom
pharmacophore.PharmacophoreBond
pharmacophore.PharmacophoreUtils
pharmacophore.PharmacophoreMatcher
pharmacophore.PharmacophoreAtom
pharmacophore.PharmacophoreAngleBond
pharmacophore.PharmacophoreQueryAngleBond
pharmacophore.PharmacophoreQueryBond
physical properties PhysicalConstants
PLS qsar.model.R.PLSRegressionModel
pocket protein.ProteinPocketFinder
polarizability charges.Polarizability
atomic qsar.descriptors.molecular.APolDescriptor
polymer
BioPolymer
Polymer
interfaces.IBioPolymer
interfaces.IPolymer
interfaces.IPDBPolymer
protein.data.PDBStrand
protein.data.PDBPolymer
Polymorph Predictor (tm) io.PMPReader
prime numbers math.Primes
projection in 2D geometry.Projector
protein protein.ProteinPocketFinder
PubChem
io.iterator.IteratingPCSubstancesXMLReader
io.iterator.IteratingPCCompoundASNReader
io.iterator.IteratingPCCompoundXMLReader
PubChem Compound ASN
io.PCSubstanceXMLReader
io.PCCompoundASNReader
PubChem Compound XML io.PCCompoundXMLReader
R
qsar.model.R2.CNNRegressionModel
qsar.model.R2.RModel
qsar.model.R2.LinearRegressionModel
radial distribution function geometry.RDFCalculator
radical
SingleElectron
interfaces.ISingleElectron
radius
vanderwaals tools.PeriodicTable
RDF geometry.RDFCalculator
reaction
 11

ReactionSet
ChemSequence
Reaction
ReactionScheme
MoleculeSet
interfaces.IReaction
interfaces.IChemSequence
interfaces.IReactionSet
atom mapping Mapping
rebonding
graph.rebond.RebondTool
graph.rebond.Bspt
recalculation graph.rebond.RebondTool
refractivity qsar.descriptors.molecular.ALOGPDescriptor
regression
qsar.model.R.CNNRegressionModel
qsar.model.R.PLSRegressionModel
linear qsar.model.R.LinearRegressionModel
removal
tools.manipulator.AtomContainerManipulator.removeHydrogens()
tools.manipulator.AtomContainerManipulator.removeHydrogensPreserveMultiplyBonded()
tools.manipulator.AtomContainerManipulator.getHeavyAtoms()
tools.manipulator.MolecularFormulaManipulator.getHeavyElements()
ring
Ring
interfaces.IRing
set of
RingSet
interfaces.IRingSet
ring finding graph.SpanningTree
ring search
ringsearch.FiguerasSSSRFinder
ringsearch.SSSRFinder
ringsearch.cyclebasis.SimpleCycle
rotatable qsar.descriptors.molecular.RotatableBondsCountDescriptor
RSS io.RssWriter
rule-of-five qsar.descriptors.molecular.RuleOfFiveDescriptor
saturation
tools.LonePairElectronChecker
tools.SaturationChecker
SDF
io.MDLV2000Reader
io.MDLReader
io.iterator.IteratingMDLReader
set of
RingSet
interfaces.IRingSet
12 KEYWORD LIST

shape index qsar.descriptors.molecular.PetitjeanShapeIndexDescriptor

ShelX io.ShelXWriter
ShelXL io.ShelXReader
similarity
fingerprint.MACCSFingerprinter
fingerprint.Fingerprinter
fingerprint.SubstructureFingerprinter
fingerprint.EStateFingerprinter
fingerprint.ExtendedFingerprinter
fingerprint.GraphOnlyFingerprinter
3D similarity.DistanceMoment
tanimoto similarity.Tanimoto
smallest-set-of-rings
ringsearch.FiguerasSSSRFinder
ringsearch.SSSRFinder
ringsearch.cyclebasis.SimpleCycle
SMARTS
isomorphism.matchers.smarts.RingMembershipAtom
isomorphism.matchers.smarts.HybridizationNumberAtom
isomorphism.matchers.smarts.AromaticOrSingleQueryBond
isomorphism.matchers.smarts.TotalValencyAtom
isomorphism.matchers.smarts.ChiralityAtom
isomorphism.matchers.smarts.SMARTSBond
isomorphism.matchers.smarts.AnyAtom
isomorphism.matchers.smarts.ExplicitConnectionAtom
isomorphism.matchers.smarts.AromaticAtom
isomorphism.matchers.smarts.AtomicNumberAtom
isomorphism.matchers.smarts.AnyOrderQueryBond
isomorphism.matchers.smarts.OrderQueryBond
isomorphism.matchers.smarts.RingIdentifierAtom
isomorphism.matchers.smarts.RingBond
isomorphism.matchers.smarts.TotalConnectionAtom
isomorphism.matchers.smarts.FormalChargeAtom
isomorphism.matchers.smarts.DegreeAtom
isomorphism.matchers.smarts.RecursiveSmartsAtom
isomorphism.matchers.smarts.AliphaticAtom
isomorphism.matchers.smarts.AromaticQueryBond
isomorphism.matchers.smarts.PeriodicGroupNumberAtom
isomorphism.matchers.smarts.NonCHHeavyAtom
isomorphism.matchers.smarts.TotalRingConnectionAtom
isomorphism.matchers.smarts.TotalHCountAtom
isomorphism.matchers.smarts.LogicalOperatorAtom
isomorphism.matchers.smarts.AromaticSymbolAtom
isomorphism.matchers.smarts.SmallestRingAtom
isomorphism.matchers.smarts.MassAtom
isomorphism.matchers.smarts.LogicalOperatorBond
isomorphism.matchers.smarts.AliphaticSymbolAtom
 13

isomorphism.matchers.smarts.ImplicitHCountAtom
isomorphism.matchers.smarts.HydrogenAtom
isomorphism.matchers.smarts.SMARTSAtom
isomorphism.matchers.smarts.ConnectionCountAtom
isomorphism.matchers.smarts.StereoBond
isomorphism.matchers.smarts.RingAtom
smiles.smarts.SMARTSQueryTool
smiles.smarts.parser.SMARTSParser
smiles.smarts.parser.ASTOrExpression
smiles.smarts.parser.ASTElement
smiles.smarts.parser.ASTChirality
smiles.smarts.parser.ASTPrimitiveAtomExpression
smiles.smarts.parser.ASTAtomicMass
smiles.smarts.parser.ASTNotBond
smiles.smarts.parser.ASTCharge
smiles.smarts.parser.ASTLowAndBond
smiles.smarts.parser.ASTAtom
smiles.smarts.parser.ASTLowAndExpression
SMARTS AST
smiles.smarts.parser.ASTPeriodicGroupNumber
smiles.smarts.parser.ASTExplicitHighAndExpression
smiles.smarts.parser.ASTAtomicNumber
smiles.smarts.parser.ASTStart
smiles.smarts.parser.ASTOrBond
smiles.smarts.parser.ASTSmarts
smiles.smarts.parser.ASTImplicitHCount
smiles.smarts.parser.SimpleNode
smiles.smarts.parser.ASTAliphatic
smiles.smarts.parser.ASTHybrdizationNumber
smiles.smarts.parser.Node
smiles.smarts.parser.ASTSmallestRingSize
smiles.smarts.parser.ASTRingIdentifier
smiles.smarts.parser.ASTExplicitAtom
smiles.smarts.parser.ASTRingConnectivity
smiles.smarts.parser.ASTAromatic
smiles.smarts.parser.ASTReaction
smiles.smarts.parser.ASTTotalHCount
smiles.smarts.parser.ASTExplicitConnectivity
smiles.smarts.parser.ASTTotalConnectivity
smiles.smarts.parser.ASTSimpleBond
smiles.smarts.parser.ASTValence
smiles.smarts.parser.ASTImplicitHighAndExpression
smiles.smarts.parser.ASTGroup
smiles.smarts.parser.ASTImplicitHighAndBond
smiles.smarts.parser.ASTRecursiveSmartsExpression
smiles.smarts.parser.ASTNotExpression
smiles.smarts.parser.ASTRingMembership
14 KEYWORD LIST

smiles.smarts.parser.ASTAnyAtom
smiles.smarts.parser.ASTNonCHHeavyAtom
smiles.smarts.parser.ASTExplicitHighAndBond
smiles.smarts.parser.visitor.Smarts2MQLVisitor
smiles.smarts.parser.visitor.SmartsQueryVisitor
smiles.smarts.parser.visitor.SmartsDumpVisitor
SMILES
io.SMILESReader
io.iterator.IteratingSMILESReader
generator smiles.SmilesGenerator
parser smiles.SmilesParser
sorting tools.ElementComparator
spanning tree graph.SpanningTree
spherical atom search tools.HOSECodeGenerator
stabilization charge charges.StabilizationCharges
stack io.cml.CMLStack
steepest descent modeling.forcefield.SteepestDescentsMethod
stereochemistry
CDKConstants
AtomParity
interfaces.IAtomParity
structure diagram generation layout.TemplateHandler
Structure Diagram Generation (SDG) layout.StructureDiagramGenerator
structure generator
structgen.RandomGenerator
structgen.VicinitySampler
stuctures templates.AminoAcids
substructure search
fingerprint.FingerprinterTool.isSubset()
smiles.smarts.SMARTSQueryTool
smiles.smarts.parser.SMARTSParser
Sybyl atomtype.SybylAtomTypeMatcher
tanimoto similarity.Tanimoto
templates
templates.AminoAcids
templates.MoleculeFactory
templates.saturatedhydrocarbons.IsoAlkanes
topological bond order ctypes qsar.descriptors.molecular.CarbonTypesDescriptor
total polar surface area qsar.descriptors.molecular.TPSADescriptor
TPSA qsar.descriptors.molecular.TPSADescriptor
type
AtomType
config.TXTBasedAtomTypeConfigurator
config.AtomTypeFactory
interfaces.IAtomType
unpaired
SingleElectron
 15

interfaces.ISingleElectron
valency
tools.LonePairElectronChecker
tools.SaturationChecker
tools.SmilesValencyChecker
validation index.CASNumber.isValid()
vanderwaals tools.PeriodicTable
WHIM qsar.descriptors.molecular.WHIMDescriptor
Wiener number qsar.descriptors.molecular.WienerNumbersDescriptor
XLogP qsar.descriptors.molecular.XLogPDescriptor
XYZ io.XYZReader
Z Matrix geometry.ZMatrixTools
Z-matrix io.ZMatrixReader
Zagreb index qsar.descriptors.molecular.ZagrebIndexDescriptor