Uses of Interface
org.biojava.bio.structure.Chain
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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 -
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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 modelChain
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 modelChain
Structure. getChainByPDB(java.lang.String chainId, int modelnr)
request a chain by it's PDB code by default takes only the first modelChain
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 GroupMethods 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 Compoundjava.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 modelvoid
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)
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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.
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