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 Structure.findChain(java.lang.String chainId)
          request a particular chain from a structure.
 Chain StructureImpl.findChain(java.lang.String chainId)
           
 Chain Structure.findChain(java.lang.String chainId, int modelnr)
          request a particular chain from a particular model
 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 StructureImpl.getChain(int number)
          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 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 StructureImpl.getChainByPDB(java.lang.String chainId)
           
 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, 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
 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> StructureImpl.getChains()
           
 java.util.List<Chain> Compound.getChains()
          get the chains that are part of this Compound
 java.util.List<Chain> Structure.getChains(int modelnr)
          retrieve all chains of a model.
 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
 void Structure.addChain(Chain chain)
          add a new chain.
 void StructureImpl.addChain(Chain chain)
          add a new chain.
 void Compound.addChain(Chain chain)
           
 void Structure.addChain(Chain chain, int modelnr)
          add a new chain, if several models are available.
 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
 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 Structure.setChains(int modelnr, java.util.List<Chain> chains)
          set the chains for a model
 void StructureImpl.setChains(int modelnr, java.util.List<Chain> chains)
           
 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(java.util.List<Chain> chains)
           
 void Compound.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
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 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
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 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
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, 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.