Modifier and Type | Class and Description |
---|---|
class |
AminoAcid
A AminoAcid is Monomer which stores additional amino acid specific
informations, like the N-terminus atom.
|
class |
AtomContainer
Base class for all chemical objects that maintain a list of Atoms and
ElectronContainers.
|
class |
AtomContainerSet
A set of AtomContainers.
|
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 |
ChemFile
A Object containing a number of ChemSequences.
|
class |
ChemModel
An object containing multiple MoleculeSet and
the other lower level concepts like rings, sequences,
fragments, etc.
|
class |
ChemSequence
A sequence of ChemModels, which can, for example, be used to
store the course of a reaction.
|
class |
Crystal
Class representing a molecular crystal.
|
class |
Molecule
Represents the concept of a chemical molecule, an object composed of
atoms connected by bonds.
|
class |
MoleculeSet
A set of molecules, for example those taking part in a reaction.
|
class |
Monomer
A Monomer is an AtomContainer which stores additional monomer specific
informations for a group of Atoms.
|
class |
Polymer
Subclass of Molecule to store Polymer specific attributes that a Polymer has.
|
class |
ReactionScheme
Classes that extends the definition of reaction to a scheme.
|
class |
ReactionSet
A set of reactions, for example those taking part in a reaction.
|
class |
Ring
Class representing a ring structure in a molecule.
|
class |
RingSet
Maintains a set of Ring objects.
|
class |
Strand
A Strand is an AtomContainer which stores additional strand specific
informations for a group of Atoms.
|
Modifier and Type | Method and Description |
---|---|
void |
ChemObject.addListener(IChemObjectListener col)
Use this to add yourself to this IChemObject as a listener.
|
void |
ChemObject.removeListener(IChemObjectListener col)
Use this to remove a ChemObjectListener from the ListenerList of this
IChemObject.
|
Modifier and Type | Class and Description |
---|---|
class |
DebugAminoAcid
Debugging data class.
|
class |
DebugAtomContainer
Debugging data class.
|
class |
DebugAtomContainerSet
Debugging data class.
|
class |
DebugBioPolymer
Debugging data class.
|
class |
DebugChemFile
Debugging data class.
|
class |
DebugChemModel
Debugging data class.
|
class |
DebugChemSequence
Debugging data class.
|
class |
DebugCrystal
Debugging data class.
|
class |
DebugMolecule
Debugging data class.
|
class |
DebugMoleculeSet
Debugging data class.
|
class |
DebugMonomer
Debugging data class.
|
class |
DebugPDBMonomer
Debugging data class.
|
class |
DebugPDBPolymer
Debugging data class.
|
class |
DebugPolymer
Debugging data class.
|
class |
DebugReactionScheme
Debugging data class.
|
class |
DebugReactionSet
Debugging data class.
|
class |
DebugRing
Debugging data class.
|
class |
DebugRingSet
Debugging data class.
|
class |
DebugStrand
Debugging data class.
|
Modifier and Type | Interface and Description |
---|---|
interface |
IAminoAcid
A AminoAcid is Monomer which stores additional amino acid specific
informations, like the N-terminus atom.
|
interface |
IAtomContainer
Base class for all chemical objects that maintain a list of Atoms and
ElectronContainers.
|
interface |
IBioPolymer
A BioPolymer is a subclass of a Polymer which is supposed to store
additional informations about the Polymer which are connected to BioPolymers.
|
interface |
ICrystal
Class representing a molecular crystal.
|
interface |
IMolecule
Represents a set of Molecules.
|
interface |
IMonomer
A Monomer is an AtomContainer which stores additional monomer specific
informations for a group of Atoms.
|
interface |
IPDBMonomer
Represents the idea of an protein monomer as found in PDB files.
|
interface |
IPDBPolymer
A PDBPolymer is a subclass of a BioPolymer which is supposed to store
additional informations about the BioPolymer which are connected to BioPolymers.
|
interface |
IPolymer
Subclass of Molecule to store Polymer specific attributes that a Polymer has.
|
interface |
IRing
Class representing a ring structure in a molecule.
|
interface |
IStrand
A Strand is an AtomContainer which stores additional strand specific
informations for a group of Atoms.
|
Modifier and Type | Method and Description |
---|---|
void |
IChemObject.addListener(IChemObjectListener col)
Use this to add yourself to this IChemObject as a listener.
|
void |
IChemObject.removeListener(IChemObjectListener col)
Use this to remove a ChemObjectListener from the ListenerList of this
IChemObject.
|
Modifier and Type | Interface and Description |
---|---|
interface |
IQueryAtomContainer
General concept of a IAtomContainer aimed at doing molecular subgraph
queries using the UniversalIsomorphismTester.
|
Modifier and Type | Class and Description |
---|---|
class |
QueryAtomContainer |
Modifier and Type | Class and Description |
---|---|
class |
ChargeGroup
A ChargeGroup (CG) is a numbered collection of atoms in an MDMolecule.
|
class |
MDMolecule |
class |
Residue
A residue is a named, numbered collection of atoms in an MDMolecule.
|
Modifier and Type | Class and Description |
---|---|
class |
NNAminoAcid
Deprecated.
Use the
AminoAcid instead. |
class |
NNAtomContainer
Deprecated.
Use the
AtomContainer instead. |
class |
NNAtomContainerSet
Deprecated.
Use the
AtomContainerSet instead. |
class |
NNBioPolymer
Deprecated.
Use the
BioPolymer instead. |
class |
NNChemFile
Deprecated.
Use the
ChemFile instead. |
class |
NNChemModel
Deprecated.
Use the
ChemModel instead. |
class |
NNChemSequence
Deprecated.
Use the
ChemSequence instead. |
class |
NNCrystal
Deprecated.
Use the
Crystal instead. |
class |
NNMolecule
Deprecated.
Use the
Molecule instead. |
class |
NNMoleculeSet
Deprecated.
Use the
MoleculeSet instead. |
class |
NNMonomer
Deprecated.
Use the
Monomer instead. |
class |
NNPDBMonomer
Deprecated.
Use the
PDBMonomer instead. |
class |
NNPDBPolymer
Deprecated.
Use the
PDBPolymer instead. |
class |
NNPolymer
Deprecated.
Use the
Polymer instead. |
class |
NNReactionScheme
Deprecated.
Use the
ReactionScheme instead. |
class |
NNReactionSet
Deprecated.
Use the
ReactionSet instead. |
class |
NNRing
Deprecated.
Use the
Ring instead. |
class |
NNRingSet
Deprecated.
Use the
RingSet instead. |
class |
NNStrand
Deprecated.
Use the
Strand instead. |
Modifier and Type | Method and Description |
---|---|
void |
NNStrand.addListener(IChemObjectListener col)
Deprecated.
|
void |
NNSingleElectron.addListener(IChemObjectListener col)
Deprecated.
|
void |
NNRingSet.addListener(IChemObjectListener col)
Deprecated.
|
void |
NNRing.addListener(IChemObjectListener col)
Deprecated.
|
void |
NNReactionSet.addListener(IChemObjectListener col)
Deprecated.
|
void |
NNReactionScheme.addListener(IChemObjectListener col)
Deprecated.
|
void |
NNReaction.addListener(IChemObjectListener col)
Deprecated.
|
void |
NNPseudoAtom.addListener(IChemObjectListener col)
Deprecated.
|
void |
NNPolymer.addListener(IChemObjectListener col)
Deprecated.
|
void |
NNPDBStructure.addListener(IChemObjectListener col)
Deprecated.
|
void |
NNPDBPolymer.addListener(IChemObjectListener col)
Deprecated.
|
void |
NNPDBMonomer.addListener(IChemObjectListener col)
Deprecated.
|
void |
NNPDBAtom.addListener(IChemObjectListener col)
Deprecated.
|
void |
NNMonomer.addListener(IChemObjectListener col)
Deprecated.
|
void |
NNMoleculeSet.addListener(IChemObjectListener col)
Deprecated.
|
void |
NNMolecule.addListener(IChemObjectListener col)
Deprecated.
|
void |
NNMapping.addListener(IChemObjectListener col)
Deprecated.
|
void |
NNLonePair.addListener(IChemObjectListener col)
Deprecated.
|
void |
NNIsotope.addListener(IChemObjectListener col)
Deprecated.
|
void |
NNFragmentAtom.addListener(IChemObjectListener col)
Deprecated.
|
void |
NNElement.addListener(IChemObjectListener col)
Deprecated.
|
void |
NNElectronContainer.addListener(IChemObjectListener col)
Deprecated.
|
void |
NNCrystal.addListener(IChemObjectListener col)
Deprecated.
|
void |
NNChemSequence.addListener(IChemObjectListener col)
Deprecated.
|
void |
NNChemObject.addListener(IChemObjectListener col)
Deprecated.
|
void |
NNChemModel.addListener(IChemObjectListener col)
Deprecated.
|
void |
NNChemFile.addListener(IChemObjectListener col)
Deprecated.
|
void |
NNBond.addListener(IChemObjectListener col)
Deprecated.
|
void |
NNBioPolymer.addListener(IChemObjectListener col)
Deprecated.
|
void |
NNAtomType.addListener(IChemObjectListener col)
Deprecated.
|
void |
NNAtomContainerSet.addListener(IChemObjectListener col)
Deprecated.
|
void |
NNAtomContainer.addListener(IChemObjectListener col)
Deprecated.
|
void |
NNAtom.addListener(IChemObjectListener col)
Deprecated.
|
void |
NNAminoAcid.addListener(IChemObjectListener col)
Deprecated.
|
Modifier and Type | Class and Description |
---|---|
class |
PharmacophoreQuery
Represents a colleciton of pharmacophore groups and constraints.
|
Modifier and Type | Class and Description |
---|---|
class |
PDBMonomer
Represents the idea of an monomer as used in PDB files.
|
class |
PDBPolymer
An entry in the PDB database.
|
class |
PDBStrand
An entry in the PDB database.
|
Modifier and Type | Class and Description |
---|---|
class |
ReactionChain
Classes that extends the definition of reaction to a chain reaction.
|
Modifier and Type | Method and Description |
---|---|
void |
ChemObject.addListener(IChemObjectListener col)
Use this to add yourself to this IChemObject as a listener.
|
void |
ChemObject.removeListener(IChemObjectListener col)
Use this to remove a ChemObjectListener from the ListenerList of this
IChemObject.
|