Uses of Class
org.biojava.nbio.structure.Compound

Packages that use Compound

Package	Description
org.biojava.nbio.structure	Interfaces and classes for protein structure (PDB).
org.biojava.nbio.structure.contact
org.biojava.nbio.structure.io	Input and Output of Structures

Uses of Compound in org.biojava.nbio.structure

Methods in org.biojava.nbio.structure that return Compound

Modifier and Type	Method and Description
Compound	Chain.getCompound() Returns the Compound for this chain.
Compound	ChainImpl.getCompound() Returns the Compound for this chain.
Compound	StructureImpl.getCompoundById(int molId) Request a particular compound by its molId (entity_id in mmCIF dictionary)
Compound	Structure.getCompoundById(int molId) Request a particular compound by its molId (entity_id in mmCIF dictionary)

Methods in org.biojava.nbio.structure that return types with arguments of type Compound

Modifier and Type	Method and Description
List<Compound>	StructureImpl.getCompounds() Get all the Compounds for this Structure.
List<Compound>	Structure.getCompounds() Get all the Compounds for this Structure.

Methods in org.biojava.nbio.structure with parameters of type Compound

Modifier and Type	Method and Description
void	StructureImpl.addCompound(Compound compound) Add a Compound to this Structure
void	Structure.addCompound(Compound compound) Add a Compound to this Structure
void	Chain.setCompound(Compound compound) Sets the Compound
void	ChainImpl.setCompound(Compound mol) Sets the Compound

Method parameters in org.biojava.nbio.structure with type arguments of type Compound

Modifier and Type	Method and Description
void	StructureImpl.setCompounds(List<Compound> molList) Set the Compounds
void	Structure.setCompounds(List<Compound> molList) Set the Compounds

Constructors in org.biojava.nbio.structure with parameters of type Compound

Constructor and Description
Compound(Compound c) Constructs a new Compound copying all data from the given one but not setting the Chains

Uses of Compound in org.biojava.nbio.structure.contact

Methods in org.biojava.nbio.structure.contact that return types with arguments of type Compound

Modifier and Type	Method and Description
Pair<Compound>	StructureInterface.getParentCompounds() Finds the parent compounds by looking up the references of first atom of each side of this interface

Uses of Compound in org.biojava.nbio.structure.io

Methods in org.biojava.nbio.structure.io that return types with arguments of type Compound

Modifier and Type	Method and Description
List<Compound>	CompoundFinder.findCompounds() Utility method that employs some heuristics to find the Compounds for this Structure in case the information is missing in PDB/mmCIF file