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 |
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.
|
class |
Substance
An implementation of the
ISubstance interface. |
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 |
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.
|
class |
DebugSubstance
Debugging data class.
|
Modifier and Type | Method and Description |
---|---|
void |
DebugAtom.addListener(IChemObjectListener col)
Use this to add yourself to this IChemObject as a listener.
|
void |
DebugStrand.addListener(IChemObjectListener col)
Use this to add yourself to this IChemObject as a listener.
|
void |
DebugRing.addListener(IChemObjectListener col)
Use this to add yourself to this IChemObject as a listener.
|
void |
DebugBond.addListener(IChemObjectListener col)
Use this to add yourself to this IChemObject as a listener.
|
void |
DebugChemObject.addListener(IChemObjectListener col)
Use this to add yourself to this IChemObject as a listener.
|
void |
DebugCrystal.addListener(IChemObjectListener col)
Use this to add yourself to this IChemObject as a listener.
|
void |
DebugChemSequence.addListener(IChemObjectListener col)
Use this to add yourself to this IChemObject as a listener.
|
void |
DebugPseudoAtom.addListener(IChemObjectListener col)
Use this to add yourself to this IChemObject as a listener.
|
void |
DebugAminoAcid.addListener(IChemObjectListener col)
Use this to add yourself to this IChemObject as a listener.
|
void |
DebugAtomContainerSet.addListener(IChemObjectListener col)
Use this to add yourself to this IChemObject as a listener.
|
void |
DebugSubstance.addListener(IChemObjectListener col)
Use this to add yourself to this IChemObject as a listener.
|
void |
DebugElectronContainer.addListener(IChemObjectListener col)
Use this to add yourself to this IChemObject as a listener.
|
void |
DebugLonePair.addListener(IChemObjectListener col)
Use this to add yourself to this IChemObject as a listener.
|
void |
DebugPolymer.addListener(IChemObjectListener col)
Use this to add yourself to this IChemObject as a listener.
|
void |
DebugFragmentAtom.addListener(IChemObjectListener col)
Use this to add yourself to this IChemObject as a listener.
|
void |
DebugChemModel.addListener(IChemObjectListener col)
Use this to add yourself to this IChemObject as a listener.
|
void |
DebugChemFile.addListener(IChemObjectListener col)
Use this to add yourself to this IChemObject as a listener.
|
void |
DebugReaction.addListener(IChemObjectListener col)
Use this to add yourself to this IChemObject as a listener.
|
void |
DebugBioPolymer.addListener(IChemObjectListener col)
Use this to add yourself to this IChemObject as a listener.
|
void |
DebugAtomType.addListener(IChemObjectListener col)
Use this to add yourself to this IChemObject as a listener.
|
void |
DebugMonomer.addListener(IChemObjectListener col)
Use this to add yourself to this IChemObject as a listener.
|
void |
DebugElement.addListener(IChemObjectListener col)
Use this to add yourself to this IChemObject as a listener.
|
void |
DebugReactionScheme.addListener(IChemObjectListener col)
Use this to add yourself to this IChemObject as a listener.
|
void |
DebugMapping.addListener(IChemObjectListener col)
Use this to add yourself to this IChemObject as a listener.
|
void |
DebugSingleElectron.addListener(IChemObjectListener col)
Use this to add yourself to this IChemObject as a listener.
|
void |
DebugIsotope.addListener(IChemObjectListener col)
Use this to add yourself to this IChemObject as a listener.
|
void |
DebugReactionSet.addListener(IChemObjectListener col)
Use this to add yourself to this IChemObject as a listener.
|
void |
DebugAtomContainer.addListener(IChemObjectListener col)
Use this to add yourself to this IChemObject as a listener.
|
void |
DebugAtom.removeListener(IChemObjectListener col)
Use this to remove a ChemObjectListener from the ListenerList of this
IChemObject.
|
void |
DebugStrand.removeListener(IChemObjectListener col)
Use this to remove a ChemObjectListener from the ListenerList of this
IChemObject.
|
void |
DebugRing.removeListener(IChemObjectListener col)
Use this to remove a ChemObjectListener from the ListenerList of this
IChemObject.
|
void |
DebugBond.removeListener(IChemObjectListener col)
Use this to remove a ChemObjectListener from the ListenerList of this
IChemObject.
|
void |
DebugChemObject.removeListener(IChemObjectListener col)
Use this to remove a ChemObjectListener from the ListenerList of this
IChemObject.
|
void |
DebugCrystal.removeListener(IChemObjectListener col)
Use this to remove a ChemObjectListener from the ListenerList of this
IChemObject.
|
void |
DebugChemSequence.removeListener(IChemObjectListener col)
Use this to remove a ChemObjectListener from the ListenerList of this
IChemObject.
|
void |
DebugPseudoAtom.removeListener(IChemObjectListener col)
Use this to remove a ChemObjectListener from the ListenerList of this
IChemObject.
|
void |
DebugAminoAcid.removeListener(IChemObjectListener col)
Use this to remove a ChemObjectListener from the ListenerList of this
IChemObject.
|
void |
DebugAtomContainerSet.removeListener(IChemObjectListener col)
Use this to remove a ChemObjectListener from the ListenerList of this
IChemObject.
|
void |
DebugSubstance.removeListener(IChemObjectListener col)
Use this to remove a ChemObjectListener from the ListenerList of this
IChemObject.
|
void |
DebugElectronContainer.removeListener(IChemObjectListener col)
Use this to remove a ChemObjectListener from the ListenerList of this
IChemObject.
|
void |
DebugLonePair.removeListener(IChemObjectListener col)
Use this to remove a ChemObjectListener from the ListenerList of this
IChemObject.
|
void |
DebugPolymer.removeListener(IChemObjectListener col)
Use this to remove a ChemObjectListener from the ListenerList of this
IChemObject.
|
void |
DebugFragmentAtom.removeListener(IChemObjectListener col)
Use this to remove a ChemObjectListener from the ListenerList of this
IChemObject.
|
void |
DebugChemModel.removeListener(IChemObjectListener col)
Use this to remove a ChemObjectListener from the ListenerList of this
IChemObject.
|
void |
DebugChemFile.removeListener(IChemObjectListener col)
Use this to remove a ChemObjectListener from the ListenerList of this
IChemObject.
|
void |
DebugReaction.removeListener(IChemObjectListener col)
Use this to remove a ChemObjectListener from the ListenerList of this
IChemObject.
|
void |
DebugBioPolymer.removeListener(IChemObjectListener col)
Use this to remove a ChemObjectListener from the ListenerList of this
IChemObject.
|
void |
DebugAtomType.removeListener(IChemObjectListener col)
Use this to remove a ChemObjectListener from the ListenerList of this
IChemObject.
|
void |
DebugMonomer.removeListener(IChemObjectListener col)
Use this to remove a ChemObjectListener from the ListenerList of this
IChemObject.
|
void |
DebugElement.removeListener(IChemObjectListener col)
Use this to remove a ChemObjectListener from the ListenerList of this
IChemObject.
|
void |
DebugReactionScheme.removeListener(IChemObjectListener col)
Use this to remove a ChemObjectListener from the ListenerList of this
IChemObject.
|
void |
DebugMapping.removeListener(IChemObjectListener col)
Use this to remove a ChemObjectListener from the ListenerList of this
IChemObject.
|
void |
DebugSingleElectron.removeListener(IChemObjectListener col)
Use this to remove a ChemObjectListener from the ListenerList of this
IChemObject.
|
void |
DebugIsotope.removeListener(IChemObjectListener col)
Use this to remove a ChemObjectListener from the ListenerList of this
IChemObject.
|
void |
DebugReactionSet.removeListener(IChemObjectListener col)
Use this to remove a ChemObjectListener from the ListenerList of this
IChemObject.
|
void |
DebugAtomContainer.removeListener(IChemObjectListener col)
Use this to remove a ChemObjectListener from the ListenerList of this
IChemObject.
|
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 |
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 | Method and Description |
---|---|
void |
QueryChemObject.addListener(IChemObjectListener col)
Use this to add yourself to this IChemObject as a listener.
|
void |
QueryChemObject.removeListener(IChemObjectListener col)
Use this to remove a ChemObjectListener from the ListenerList of this
IChemObject.
|
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 |
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.
|
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