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

Packages that use Chain

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

Uses of Chain in org.biojava.nbio.protmod.structure

Methods in org.biojava.nbio.protmod.structure with parameters of type Chain

Modifier and Type	Method and Description
static List<Group>	StructureUtil.getAminoAcids(Chain chain) Get all amino acids in a chain.
void	ProteinModificationIdentifier.identify(Chain chain) Identify all registered modifications in a chain.
void	ProteinModificationIdentifier.identify(Chain chain, Set<ProteinModification> potentialModifications) Identify a set of modifications in a a chains.

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

Modifier and Type	Method and Description
void	ProteinModificationIdentifier.identify(List<Chain> chains) Identify all registered modifications in chains.
void	ProteinModificationIdentifier.identify(List<Chain> chains, Set<ProteinModification> potentialModifications) Identify a set of modifications in a a list of chains.

Uses of Chain in org.biojava.nbio.structure

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

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

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

Modifier and Type	Method and Description
Chain	StructureImpl.findChain(String chainId) Request a particular chain from a structure.
Chain	Structure.findChain(String chainId) Request a particular chain from a structure.
Chain	StructureImpl.findChain(String chainId, int modelnr) Request a particular chain from a particular model
Chain	Structure.findChain(String chainId, int modelnr) Request a particular chain from a particular model
Chain	Group.getChain() Returns the parent Chain of the Group.
Chain	HetatomImpl.getChain() Returns the parent Chain of the Group.
Chain	StructureImpl.getChain(int number) Retrieve a chain by its position within the Structure .
Chain	Structure.getChain(int pos) Retrieve a chain by its position within the Structure .
Chain	StructureImpl.getChain(int modelnr, int number) Retrieve a chain by its position within the Structure and model number.
Chain	Structure.getChain(int modelnr, int pos) Retrieve a chain by its position within the Structure and model number.
Chain	StructureImpl.getChainByPDB(String chainId) Request a chain by its PDB code by default takes only the first model
Chain	Structure.getChainByPDB(String chainId) Request a chain by its PDB code by default takes only the first model
Chain	StructureImpl.getChainByPDB(String chainId, int modelnr) Request a chain by its PDB code by default takes only the first model
Chain	Structure.getChainByPDB(String chainId, int modelnr) Request a chain by its 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	Compound.getRepresentative() Get the representative Chain for this Compound.

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

Modifier and Type	Method and Description
List<Chain>	StructureImpl.getChains() Retrieve all chains - if it is a NMR structure will return the chains of the first model.
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 list of 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.nbio.structure with parameters of type Chain

Modifier and Type	Method and Description
void	StructureImpl.addChain(Chain chain) Add a new chain.
void	Structure.addChain(Chain chain) Add a new chain.
void	Compound.addChain(Chain chain) Add new Chain to this Compound
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.
int	Compound.getAlignedResIndex(Group g, Chain c) Given a Group g of Chain c (member of this Compound) return the corresponding position in the alignment of all member sequences (1-based numbering), i.e.
static Atom[]	StructureTools.getAllAtomArray(Chain c) Returns and array of all atoms of the chain (first model), including Hydrogens (if present) and all HETATOMs.
static Atom[]	StructureTools.getAllNonHAtomArray(Chain c, boolean hetAtoms) Returns and array of all non-Hydrogen atoms in the given Chain, optionally including HET atoms or not Waters are not included.
static Atom[]	StructureTools.getAtomArray(Chain c, String[] atomNames) Returns an array of the requested Atoms from the Chain object.
static Atom[]	StructureTools.getAtomCAArray(Chain c) Returns an Atom array of the C-alpha atoms.
static AtomContactSet	StructureTools.getAtomsCAInContact(Chain chain, double cutoff) Returns the set of intra-chain contacts for the given chain for C-alpha atoms (including non-standard aminoacids appearing as HETATM groups), i.e.
static AtomContactSet	StructureTools.getAtomsInContact(Chain chain1, Chain chain2, double cutoff, boolean hetAtoms) Returns the set of inter-chain contacts between the two given chains for all non-H atoms.
static AtomContactSet	StructureTools.getAtomsInContact(Chain chain1, Chain chain2, String[] atomNames, double cutoff, boolean hetAtoms) Returns the set of inter-chain contacts between the two given chains for the given atom names.
static AtomContactSet	StructureTools.getAtomsInContact(Chain chain, double cutoff) Returns the set of intra-chain contacts for the given chain for all non-H atoms of non-hetatoms, i.e.
static AtomContactSet	StructureTools.getAtomsInContact(Chain chain, String[] atomNames, double cutoff) Returns the set of intra-chain contacts for the given chain for given atom names, i.e.
static GroupType	StructureTools.getPredominantGroupType(Chain c) Get the predominant GroupType for a given Chain, following these rules: if the ratio of number of residues of a certain GroupType to total non-water residues is above the threshold 0.95, then that GroupType is returned if there is no GroupType that is above the threshold then the GroupType with most members is chosen, logging it
static Atom[]	StructureTools.getRepresentativeAtomArray(Chain c) Gets a representative atom for each group that is part of the chain backbone.
static AtomContactSet	StructureTools.getRepresentativeAtomsInContact(Chain chain, double cutoff) Returns the set of intra-chain contacts for the given chain for C-alpha or C3' atoms (including non-standard aminoacids appearing as HETATM groups), i.e.
static boolean	StructureTools.isChainPureNonPolymer(Chain c) Returns true if the given chain is composed of non-polymeric groups only
static boolean	StructureTools.isChainWaterOnly(Chain c) Returns true if the given chain is composed of water molecules only
static boolean	StructureTools.isNucleicAcid(Chain c) Tell whether given chain is DNA or RNA
static boolean	StructureTools.isProtein(Chain c) Tell whether given chain is a protein chain
void	Group.setChain(Chain chain) Sets the back-reference to its parent Chain.
void	HetatomImpl.setChain(Chain chain) Sets the back-reference to its parent Chain.
static void	Calc.transform(Chain chain, javax.vecmath.Matrix4d m) Transforms a chain object, given a Matrix4d (i.e.
static void	Calc.translate(Chain chain, javax.vecmath.Vector3d v) Translates a chain object, given a Vector3d (i.e.

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

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

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

Uses of Chain in org.biojava.nbio.structure.contact

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

Modifier and Type	Method and Description
Pair<Chain>	StructureInterface.getParentChains() Finds the parent chains by looking up the references of first atom of each side of this interface

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

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

Modifier and Type	Method and Description
Chain	SequenceScalePanel.getChain()

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

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

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

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

Modifier and Type	Method and Description
static Chain	CAConverter.getCAOnly(Chain chain) Deprecated. Use the more generic CAConverter.getRepresentativeAtomsOnly(Chain) instead
static Chain	SeqRes2AtomAligner.getMatchingAtomRes(Chain seqRes, List<Chain> atomList)
static Chain	CAConverter.getRepresentativeAtomsOnly(Chain chain) Convert a Chain to a new Chain containing C-alpha atoms only.

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

Modifier and Type	Method and Description
static List<Chain>	CAConverter.getCAOnly(List<Chain> chains) Deprecated. Use the more generic CAConverter.getRepresentativeAtomsOnly(List) instead
static List<Chain>	CAConverter.getRepresentativeAtomsOnly(List<Chain> chains) Convert a List of chain objects to another List of chains, containing Representative atoms only.

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

Modifier and Type	Method and Description
static Chain	CAConverter.getCAOnly(Chain chain) Deprecated. Use the more generic CAConverter.getRepresentativeAtomsOnly(Chain) instead
static Chain	SeqRes2AtomAligner.getMatchingAtomRes(Chain seqRes, List<Chain> atomList)
static Chain	CAConverter.getRepresentativeAtomsOnly(Chain chain) Convert a Chain to a new Chain containing C-alpha atoms only.
void	SeqRes2AtomAligner.mapSeqresRecords(Chain atomRes, Chain seqRes) Map the seqRes groups to the atomRes chain.
static String	FileConvert.toMMCIF(Chain chain, boolean writeHeader)
static String	FileConvert.toMMCIF(Chain chain, String chainId, String internalChainId, boolean writeHeader)
static String	FileConvert.toPDB(Chain chain) Convert a Chain object to PDB representation

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

Modifier and Type	Method and Description
void	SeqRes2AtomAligner.align(Structure s, List<Chain> seqResList)
static List<Chain>	CAConverter.getCAOnly(List<Chain> chains) Deprecated. Use the more generic CAConverter.getRepresentativeAtomsOnly(List) instead
static Chain	SeqRes2AtomAligner.getMatchingAtomRes(Chain seqRes, List<Chain> atomList)
static List<Chain>	CAConverter.getRepresentativeAtomsOnly(List<Chain> chains) Convert a List of chain objects to another List of chains, containing Representative atoms only.
static void	SeqRes2AtomAligner.storeUnAlignedSeqRes(Structure structure, List<Chain> seqResChains, boolean headerOnly) Storing unaligned SEQRES groups in a Structure.

Uses of Chain in org.biojava.nbio.structure.io.mmcif

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

Modifier and Type	Method and Description
static List<AtomSite>	MMCIFFileTools.convertChainToAtomSites(Chain c, int model, String chainId, String internalChainId) Converts a Chain into a List of AtomSite objects