Package | Description |
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org.biojava.bio.structure |
Interfaces and classes for protein structure (PDB).
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org.biojava.bio.structure.gui.util |
Some utility classes for the protein structure GUIs.
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org.biojava.bio.structure.io |
Input and Output of Structures
|
Modifier and Type | Class and Description |
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class |
ChainImpl
A Chain in a PDB file.
|
Modifier and Type | Method and Description |
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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
|
Modifier and Type | Method and Description |
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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> |
Compound.getChains()
get the chains that are part of this Compound
|
java.util.List<Chain> |
StructureImpl.getChains() |
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 .
|
Modifier and Type | Method and Description |
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void |
Structure.addChain(Chain chain)
add a new chain.
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void |
Compound.addChain(Chain chain) |
void |
StructureImpl.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,
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)
|
Modifier and Type | Method and 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 |
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 |
Compound.setChains(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) |
Constructor and Description |
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StructureImpl(Chain c)
construct a Structure object that contains a particular chain
|
Modifier and Type | Method and Description |
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Chain |
SequenceScalePanel.getChain() |
Modifier and Type | Method and Description |
---|---|
void |
SequenceScalePanel.setChain(Chain c) |
void |
SequenceMouseListener.setChain(Chain c) |
Modifier and Type | Method and Description |
---|---|
static Chain |
CAConverter.getCAOnly(Chain chain)
Convert a Chain to a new Chain containing C-alpha atoms only.
|
Modifier and Type | Method and Description |
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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.
|
Modifier and Type | Method and Description |
---|---|
static Chain |
CAConverter.getCAOnly(Chain chain)
Convert a Chain to a new Chain containing C-alpha atoms only.
|
Modifier and Type | Method and 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.
|