Package | Description |
---|---|
org.openscience.cdk | |
org.openscience.cdk.debug | |
org.openscience.cdk.iupac.parser |
The core classes of the ChemNomParse project, an open source attempt
of a chemical nomenclature parser, call via generate (name).
|
org.openscience.cdk.libio.md | |
org.openscience.cdk.nonotify | |
org.openscience.cdk.protein.data | |
org.openscience.cdk.ringsearch | |
org.openscience.cdk.templates | |
org.openscience.cdk.templates.saturatedhydrocarbons |
Modifier and Type | Class and Description |
---|---|
class |
BioPolymer
A BioPolymer is a subclass of a Polymer which is supposed to store
additional informations about the Polymer which are connected to BioPolymers.
|
class |
Polymer
Subclass of Molecule to store Polymer specific attributes that a Polymer has.
|
Modifier and Type | Class and Description |
---|---|
class |
DebugBioPolymer
Debugging data class.
|
class |
DebugMolecule
Debugging data class.
|
class |
DebugPDBPolymer
Debugging data class.
|
class |
DebugPolymer
Debugging data class.
|
Modifier and Type | Method and Description |
---|---|
static Molecule |
NomParser.generate(String stringToParse)
Parses the chemical name and returns the built molecule.
|
Modifier and Type | Class and Description |
---|---|
class |
MDMolecule |
Modifier and Type | Class and Description |
---|---|
class |
NNBioPolymer
Deprecated.
Use the
BioPolymer instead. |
class |
NNMolecule
Deprecated.
Use the
Molecule instead. |
class |
NNPDBPolymer
Deprecated.
Use the
PDBPolymer instead. |
class |
NNPolymer
Deprecated.
Use the
Polymer instead. |
Modifier and Type | Class and Description |
---|---|
class |
PDBPolymer
An entry in the PDB database.
|
Modifier and Type | Method and Description |
---|---|
RingSet |
FiguerasSSSRFinder.findSSSR(Molecule mol)
Deprecated.
Finds the Smallest Set of Smallest Rings.
|
Modifier and Type | Method and Description |
---|---|
static Molecule |
MoleculeFactory.make123Triazole()
Returns 1,2,3-triazole without explicit hydrogens.
|
static Molecule |
MoleculeFactory.make124Triazole()
Returns 1,2,4-triazole without explicit hydrogens.
|
static Molecule |
MoleculeFactory.make4x3CondensedRings() |
static Molecule |
MoleculeFactory.makeAlkane(int chainLength)
Generate an Alkane (chain of carbons with no hydrogens) of a given length.
|
static Molecule |
MoleculeFactory.makeAlphaPinene() |
static Molecule |
MoleculeFactory.makeAzulene()
Returns azulene without explicit hydrogens.
|
static Molecule |
MoleculeFactory.makeBenzene() |
static Molecule |
MoleculeFactory.makeBicycloRings() |
static Molecule |
MoleculeFactory.makeBiphenyl()
Returns biphenyl without explicit hydrogens.
|
static Molecule |
MoleculeFactory.makeBranchedAliphatic() |
static Molecule |
MoleculeFactory.makeCyclobutadiene()
Returns cyclobutadiene without explicit hydrogens.
|
static Molecule |
MoleculeFactory.makeCyclobutane()
Returns cyclobutane without explicit hydrogens.
|
static Molecule |
MoleculeFactory.makeCyclohexane()
Returns cyclohexane without explicit hydrogens.
|
static Molecule |
MoleculeFactory.makeCyclohexene()
Returns cyclohexene without explicit hydrogens.
|
static Molecule |
MoleculeFactory.makeCyclopentane()
Returns cyclopentane without explicit hydrogens.
|
static Molecule |
MoleculeFactory.makeDiamantane() |
static Molecule |
MoleculeFactory.makeEthylCyclohexane() |
static Molecule |
MoleculeFactory.makeEthylPropylPhenantren() |
static Molecule |
MoleculeFactory.makeFusedRings() |
static Molecule |
MoleculeFactory.makeImidazole()
Returns imidazole without explicit hydrogens.
|
static Molecule |
MoleculeFactory.makeIndole()
Returns indole without explicit hydrogens.
|
static Molecule |
MoleculeFactory.makeIsothiazole()
Returns isothiazole without explicit hydrogens.
|
static Molecule |
MoleculeFactory.makeIsoxazole()
Returns Isoxazole without explicit hydrogens.
|
static Molecule |
MoleculeFactory.makeMethylDecaline() |
static Molecule |
MoleculeFactory.makeOxadiazole()
Returns oxadiazole without explicit hydrogens.
|
static Molecule |
MoleculeFactory.makeOxazole()
Returns Oxazole without explicit hydrogens.
|
static Molecule |
MoleculeFactory.makePhenylAmine() |
static Molecule |
MoleculeFactory.makePhenylEthylBenzene() |
static Molecule |
MoleculeFactory.makePiperidine() |
static Molecule |
MoleculeFactory.makePropylCycloPropane() |
static Molecule |
MoleculeFactory.makePyrazole()
Returns pyrazole without explicit hydrogens.
|
static Molecule |
MoleculeFactory.makePyridazine()
Returns pyridazine without explicit hydrogens.
|
static Molecule |
MoleculeFactory.makePyridine()
Returns pyridine without explicit hydrogens.
|
static Molecule |
MoleculeFactory.makePyridineOxide()
Returns pyridine oxide without explicit hydrogens.
|
static Molecule |
MoleculeFactory.makePyrimidine()
Returns pyrimidine without explicit hydrogens.
|
static Molecule |
MoleculeFactory.makePyrrole()
Returns pyrrole without explicit hydrogens.
|
static Molecule |
MoleculeFactory.makePyrroleAnion()
Returns pyrrole anion without explicit hydrogens.
|
static Molecule |
MoleculeFactory.makeQuinone() |
static Molecule |
MoleculeFactory.makeSingleRing() |
static Molecule |
MoleculeFactory.makeSpiroRings() |
static Molecule |
MoleculeFactory.makeSteran() |
static Molecule |
MoleculeFactory.makeTetrahydropyran() |
static Molecule |
MoleculeFactory.makeTetrazole()
Returns tetrazole without explicit hydrogens.
|
static Molecule |
MoleculeFactory.makeThiadiazole()
Returns thiadiazole without explicit hydrogens.
|
static Molecule |
MoleculeFactory.makeThiazole()
Returns thiazole without explicit hydrogens.
|
static Molecule |
MoleculeFactory.makeTriazine()
Returns triazine without explicit hydrogens.
|
Modifier and Type | Method and Description |
---|---|
static Molecule |
IsoAlkanes.getIsobutane() |
static Molecule |
IsoAlkanes.getIsohexane() |
static Molecule |
IsoAlkanes.getIsopentane() |