Uses of Interface
org.openscience.cdk.interfaces.IAtomContainer

Packages that use IAtomContainer

Package	Description
org.openscience.cdk.hash
org.openscience.cdk.interfaces
org.openscience.cdk.io.iterator.event
org.openscience.cdk.isomorphism.matchers
org.openscience.cdk.libio.cml

Uses of IAtomContainer in org.openscience.cdk.hash

Methods in org.openscience.cdk.hash with parameters of type IAtomContainer

Modifier and Type	Method and Description
int	AtomEncoder.encode(IAtom atom, IAtomContainer container) Encode an invariant attribute of the given atom.
long	MoleculeHashGenerator.generate(IAtomContainer container) Generate invariant 64-bit hash code for a molecule.
long[]	AtomHashGenerator.generate(IAtomContainer container) Generate invariant 64-bit hash codes for the atoms of the molecule.

Method parameters in org.openscience.cdk.hash with type arguments of type IAtomContainer

Modifier and Type	Method and Description
long	EnsembleHashGenerator.generate(Set<IAtomContainer> ensemble) Generate invariant 64-bit hash code for an ensemble of molecules.

Uses of IAtomContainer in org.openscience.cdk.interfaces

Subinterfaces of IAtomContainer in org.openscience.cdk.interfaces

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	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.

Methods in org.openscience.cdk.interfaces that return IAtomContainer

Modifier and Type	Method and Description
IAtomContainer	IAtomContainer.clone() Returns a deep clone of this IChemObject.
IAtomContainer	IAtomContainerSet.getAtomContainer(int number) Returns the AtomContainer at position number in the container.
IAtomContainer	IBond.getContainer()
IAtomContainer	IAtom.getContainer() Access the IAtomContainer of which this atom is a member of.
IAtomContainer	IFragmentAtom.getFragment() Returns the fully expended form of the IFragmentAtom.
IAtomContainer	IChemObjectBuilder.newAtomContainer() Create a new atom container using the default constructor.

Methods in org.openscience.cdk.interfaces that return types with arguments of type IAtomContainer

Modifier and Type	Method and Description
Iterable<IAtomContainer>	IAtomContainerSet.atomContainers() Get an Iterable for this AtomContainerSet.

Methods in org.openscience.cdk.interfaces with parameters of type IAtomContainer

Modifier and Type	Method and Description
void	ICrystal.add(IAtomContainer container) Adds the atoms in the AtomContainer as cell content.
void	IAtomContainer.add(IAtomContainer atomContainer) Adds all atoms and electronContainers of a given atomcontainer to this container.
void	IReaction.addAgent(IAtomContainer agent) Adds an agent to this reaction.
void	IAtomContainerSet.addAtomContainer(IAtomContainer atomContainer) Adds an atomContainer to this container.
void	IAtomContainerSet.addAtomContainer(IAtomContainer atomContainer, double multiplier) Adds an atomContainer to this container with the given multiplier.
void	IReaction.addProduct(IAtomContainer product) Adds a product to this reaction.
void	IReaction.addProduct(IAtomContainer product, Double coefficient) Adds a product to this reaction.
void	IReaction.addReactant(IAtomContainer reactant) Adds a reactant to this reaction.
void	IReaction.addReactant(IAtomContainer reactant, Double coefficient) Adds a reactant to this reaction with a stoichiometry coefficient.
boolean	IRingSet.contains(IAtomContainer container) True, if this set contains the IAtomContainer.
Double	IAtomContainerSet.getMultiplier(IAtomContainer container) Returns the multiplier of the given AtomContainer.
Double	IReaction.getProductCoefficient(IAtomContainer product) Returns the stoichiometry coefficient of the given product.
Double	IReaction.getReactantCoefficient(IAtomContainer reactant) Returns the stoichiometry coefficient of the given reactant.
void	IAtomContainer.remove(IAtomContainer atomContainer) Removes all atoms and electronContainers of a given atomcontainer from this container.
void	IAtomContainerSet.removeAtomContainer(IAtomContainer atomContainer) Removes an AtomContainer from this container.
void	IAtomContainerSet.replaceAtomContainer(int position, IAtomContainer container) Replace the AtomContainer at a specific position (array has to be large enough).
void	IFragmentAtom.setFragment(IAtomContainer fragment) Sets the fully expended form of the IFragmentAtom.
boolean	IAtomContainerSet.setMultiplier(IAtomContainer container, Double multiplier) Sets the coefficient of a AtomContainer to a given value.
boolean	IReaction.setProductCoefficient(IAtomContainer product, Double coefficient) Sets the coefficient of a a product to a given value.
boolean	IReaction.setReactantCoefficient(IAtomContainer reactant, Double coefficient) Sets the coefficient of a a reactant to a given value.

Method parameters in org.openscience.cdk.interfaces with type arguments of type IAtomContainer

Modifier and Type	Method and Description
void	IAtomContainerSet.sortAtomContainers(Comparator<IAtomContainer> comparator) Sort the AtomContainers using a provided Comparator.

Uses of IAtomContainer in org.openscience.cdk.io.iterator.event

Methods in org.openscience.cdk.io.iterator.event that return IAtomContainer

Modifier and Type	Method and Description
IAtomContainer	IEventChemObjectReader.getAtomContainer()

Uses of IAtomContainer in org.openscience.cdk.isomorphism.matchers

Subinterfaces of IAtomContainer in org.openscience.cdk.isomorphism.matchers

Modifier and Type	Interface and Description
interface	IQueryAtomContainer General concept of a IAtomContainer aimed at doing molecular subgraph queries using the UniversalIsomorphismTester.

Uses of IAtomContainer in org.openscience.cdk.libio.cml

Methods in org.openscience.cdk.libio.cml with parameters of type IAtomContainer

Modifier and Type	Method and Description
void	ICMLCustomizer.customize(IAtomContainer molecule, Object nodeToAdd) Customized the nodeToAdd for the given Molecule.