Uses of Interface
org.biojava.bio.structure.Chain

Packages that use Chain

Package	Description
org.biojava.bio.structure	Interfaces and classes for protein structure (PDB).
org.biojava.bio.structure.gui.util	Some utility classes for the protein structure GUIs.
org.biojava.bio.structure.io	Input and Output of Structures

Uses of Chain in org.biojava.bio.structure

Classes in org.biojava.bio.structure that implement Chain

Modifier and Type	Class	Description
class	ChainImpl	A Chain in a PDB file.

Methods in org.biojava.bio.structure that return Chain

Modifier and Type	Method	Description
Chain	Structure.findChain(java.lang.String chainId)	request a particular chain from a structure.
Chain	Structure.findChain(java.lang.String chainId, int modelnr)	request a particular chain from a particular model
Chain	StructureImpl.findChain(java.lang.String chainId)
Chain	StructureImpl.findChain(java.lang.String chainId, int modelnr)
Chain	Structure.getChain(int pos)	retrieve a chain by it's position within the Structure .
Chain	Structure.getChain(int pos, int modelnr)	retrieve a chain by it's position within the Structure and model number.
Chain	StructureImpl.getChain(int number)	retrieve a chain by it's position within the Structure.
Chain	StructureImpl.getChain(int modelnr, int number)	retrieve a chain by it's position within the Structure and model number.
Chain	Structure.getChainByPDB(java.lang.String chainId)	request a chain by it's PDB code by default takes only the first model
Chain	Structure.getChainByPDB(java.lang.String chainId, int modelnr)	request a chain by it's PDB code by default takes only the first model
Chain	StructureImpl.getChainByPDB(java.lang.String chainId)
Chain	StructureImpl.getChainByPDB(java.lang.String chainId, int modelnr)
Chain	AtomIterator.getCurrentChain()	Get the chain that contains the current atom.
Chain	GroupIterator.getCurrentChain()	Get the current Chain.
Chain	Group.getParent()	Returns the parent Chain of the Group.
Chain	HetatomImpl.getParent()	Returns the parent Chain of the Group

Methods in org.biojava.bio.structure that return types with arguments of type Chain

Modifier and Type	Method	Description
java.util.List<Chain>	Compound.getChains()	get the chains that are part of this Compound
java.util.List<Chain>	Structure.getChains()	retrieve all chains - if it is a NMR structure will return the chains of the first model.
java.util.List<Chain>	Structure.getChains(int modelnr)	retrieve all chains of a model.
java.util.List<Chain>	StructureImpl.getChains()
java.util.List<Chain>	StructureImpl.getChains(int modelnr)	retrieve all chains of a model.
java.util.List<Chain>	Structure.getModel(int modelnr)	retrieve all Chains belonging to a model .
java.util.List<Chain>	StructureImpl.getModel(int modelnr)	retrieve all Chains belonging to a model .

Methods in org.biojava.bio.structure with parameters of type Chain

Modifier and Type	Method	Description
void	Compound.addChain(Chain chain)
void	Structure.addChain(Chain chain)	add a new chain.
void	Structure.addChain(Chain chain, int modelnr)	add a new chain, if several models are available.
void	StructureImpl.addChain(Chain chain)	add a new chain.
void	StructureImpl.addChain(Chain chain, int modelnr)	add a new chain, if several models are available.
void	Group.setParent(Chain parent)	Set the back-reference (to its parent Chain).
void	HetatomImpl.setParent(Chain parent)	Set the back-reference (to its parent Chain)

Method parameters in org.biojava.bio.structure with type arguments of type Chain

Modifier and Type	Method	Description
void	Structure.addModel(java.util.List<Chain> model)	add a new model.
void	StructureImpl.addModel(java.util.List<Chain> model)	add a new model.
void	Compound.setChains(java.util.List<Chain> chains)
void	Structure.setChains(int modelnr, java.util.List<Chain> chains)	set the chains for a model
void	Structure.setChains(java.util.List<Chain> chains)	set the chains of a structure, if this is a NMR structure, this will only set model 0.
void	StructureImpl.setChains(int modelnr, java.util.List<Chain> chains)
void	StructureImpl.setChains(java.util.List<Chain> chains)
void	Structure.setModel(int position, java.util.List<Chain> model)	a convenience function if one wants to edit and replace the models in a structure.
void	StructureImpl.setModel(int position, java.util.List<Chain> model)

Constructors in org.biojava.bio.structure with parameters of type Chain

Constructor	Description
StructureImpl(Chain c)	construct a Structure object that contains a particular chain

Uses of Chain in org.biojava.bio.structure.gui.util

Methods in org.biojava.bio.structure.gui.util that return Chain

Modifier and Type	Method	Description
Chain	SequenceScalePanel.getChain()

Methods in org.biojava.bio.structure.gui.util with parameters of type Chain

Modifier and Type	Method	Description
void	SequenceMouseListener.setChain(Chain c)
void	SequenceScalePanel.setChain(Chain c)

Uses of Chain in org.biojava.bio.structure.io

Methods in org.biojava.bio.structure.io that return Chain

Modifier and Type	Method	Description
static Chain	CAConverter.getCAOnly(Chain chain)	Convert a Chain to a new Chain containing C-alpha atoms only.

Methods in org.biojava.bio.structure.io that return types with arguments of type Chain

Modifier and Type	Method	Description
static java.util.List<Chain>	CAConverter.getCAOnly(java.util.List<Chain> chains)	Convert a List of chain objects to another List of chains, containing C-alpha atoms only.

Methods in org.biojava.bio.structure.io with parameters of type Chain

Modifier and Type	Method	Description
static Chain	CAConverter.getCAOnly(Chain chain)	Convert a Chain to a new Chain containing C-alpha atoms only.

Method parameters in org.biojava.bio.structure.io with type arguments of type Chain

Modifier and Type	Method	Description
void	SeqRes2AtomAligner.align(Structure s, java.util.List<Chain> seqResList)
static java.util.List<Chain>	CAConverter.getCAOnly(java.util.List<Chain> chains)	Convert a List of chain objects to another List of chains, containing C-alpha atoms only.