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

Packages that use Chain
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
`class` | `ChainImpl` A Chain in a PDB file.

Methods in org.biojava.bio.structure that return Chain
`Chain` | `StructureImpl.findChain(String chainId)`
`Chain` | `Structure.findChain(String chainId)` request a particular chain from a structure.
`Chain` | `StructureImpl.findChain(String chainId, int modelnr)`
`Chain` | `Structure.findChain(String chainId, int modelnr)` request a particular chain from a particular model
`Chain` | `StructureImpl.getChain(int number)` retrieve a chain by it's position within the Structure.
`Chain` | `Structure.getChain(int pos)` 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.getChain(int pos, int modelnr)` retrieve a chain by it's position within the Structure and model number.
`Chain` | `StructureImpl.getChainByPDB(String chainId)`
`Chain` | `Structure.getChainByPDB(String chainId)` request a chain by it's PDB code by default takes only the first model
`Chain` | `StructureImpl.getChainByPDB(String chainId, int modelnr)`
`Chain` | `Structure.getChainByPDB(String chainId, int modelnr)` request a chain by it's PDB code by default takes only the first model
`Chain` | `GroupIterator.getCurrentChain()` Get the current Chain.
`Chain` | `AtomIterator.getCurrentChain()` Get the chain that contains the current atom.
`Chain` | `HetatomImpl.getParent()` Returns the parent Chain of the Group
`Chain` | `Group.getParent()` Returns the parent Chain of the Group.

Methods in org.biojava.bio.structure that return types with arguments of type Chain
`List<Chain>` | `StructureImpl.getChains()`
`List<Chain>` | `Structure.getChains()` retrieve all chains - if it is a NMR structure will return the chains of the first model.
`List<Chain>` | `Compound.getChains()` get the chains that are part of this Compound
`List<Chain>` | `StructureImpl.getChains(int modelnr)` retrieve all chains of a model.
`List<Chain>` | `Structure.getChains(int modelnr)` retrieve all chains of a model.
`List<Chain>` | `StructureImpl.getModel(int modelnr)` retrieve all Chains belonging to a model .
`List<Chain>` | `Structure.getModel(int modelnr)` retrieve all Chains belonging to a model .

Methods in org.biojava.bio.structure with parameters of type Chain
`void` | `StructureImpl.addChain(Chain chain)` add a new chain.
`void` | `Structure.addChain(Chain chain)` add a new chain.
`void` | `Compound.addChain(Chain chain)`
`void` | `StructureImpl.addChain(Chain chain, int modelnr)` add a new chain, if several models are available.
`void` | `Structure.addChain(Chain chain, int modelnr)` add a new chain, if several models are available.
`void` | `HetatomImpl.setParent(Chain parent)` Set the back-reference (to its parent Chain)
`void` | `Group.setParent(Chain parent)` Set the back-reference (to its parent Chain).

Method parameters in org.biojava.bio.structure with type arguments of type Chain
`void` | `StructureImpl.addModel(List<Chain> model)` add a new model.
`void` | `Structure.addModel(List<Chain> model)` add a new model.
`void` | `StructureImpl.setChains(int modelnr, List<Chain> chains)`
`void` | `Structure.setChains(int modelnr, List<Chain> chains)` set the chains for a model
`void` | `StructureImpl.setChains(List<Chain> chains)`
`void` | `Structure.setChains(List<Chain> chains)` set the chains of a structure, if this is a NMR structure, this will only set model 0.
`void` | `Compound.setChains(List<Chain> chains)`
`void` | `StructureImpl.setModel(int position, List<Chain> model)`
`void` | `Structure.setModel(int position, List<Chain> model)` a convenience function if one wants to edit and replace the models in a structure.

Constructors in org.biojava.bio.structure with parameters of type Chain
`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
`Chain` | `SequenceScalePanel.getChain()`

Methods in org.biojava.bio.structure.gui.util with parameters of type Chain
`void` | `SequenceScalePanel.setChain(Chain c)`
`void` | `SequenceMouseListener.setChain(Chain c)`

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

Methods in org.biojava.bio.structure.io that return Chain
`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
`static List<Chain>` | `CAConverter.getCAOnly(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
`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
`void` | `SeqRes2AtomAligner.align(Structure s, List<Chain> seqResList)`
`static List<Chain>` | `CAConverter.getCAOnly(List<Chain> chains)` Convert a List of chain objects to another List of chains, containing C-alpha atoms only.

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