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.align.util
org.biojava.nbio.structure.basepairs
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.
org.biojava.nbio.structure.io.mmtf

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
static Chain	StructureTools.addGroupToStructure(Structure s, Group g, int model, Chain chainGuess, boolean clone) Adds a particular group to a structure.
Chain	StructureImpl.findChain(String chainId) Request a particular chain from a structure.
Chain	Structure.findChain(String authId) Deprecated.
Chain	StructureImpl.findChain(String chainName, int modelnr) Request a particular chain from a particular model
Chain	Structure.findChain(String authId, int modelnr) Deprecated.
Chain	Group.getChain() Returns the parent Chain of the Group.
Chain	HetatomImpl.getChain() Returns the parent Chain of the Group.
Chain	StructureImpl.getChain(String asymId) Retrieve a Chain (polymeric, non-polymeric or water) based on the 'internal' chain id (asymId) for the first model
Chain	Structure.getChain(String asymId) Retrieve a Chain (polymeric, non-polymeric or water) based on the 'internal' chain id (asymId) for the first model
Chain	StructureImpl.getChain(String asymId, int modelnr) Retrieve a Chain (polymeric, non-polymeric or water) based on the 'internal' chain id (asymId) for the given model index
Chain	Structure.getChain(String asymId, int modelIdx) Retrieve a Chain (polymeric, non-polymeric or water) based on the 'internal' chain id (asymId) for the given model index
Chain	StructureImpl.getChainByIndex(int number) Retrieve a chain by its index within the Structure .
Chain	Structure.getChainByIndex(int chainIndex) Retrieve a chain by its index within the Structure .
Chain	StructureImpl.getChainByIndex(int modelnr, int number) Retrieve a chain by its indices within the Structure and model.
Chain	Structure.getChainByIndex(int modelnr, int chainIndex) Retrieve a chain by its indices within the Structure and model.
Chain	StructureImpl.getChainByPDB(String chainId) Request a chain by its public id (author id) for the first model.
Chain	Structure.getChainByPDB(String authId) Deprecated. use Structure.getPolyChainByPDB(String) instead
Chain	StructureImpl.getChainByPDB(String authId, int modelnr) Request a chain by its public id (author id) for the given model index.
Chain	Structure.getChainByPDB(String authId, int modelIdx) Deprecated. use Structure.getPolyChainByPDB(String,int) instead
Chain	GroupIterator.getCurrentChain() Get the current Chain.
Chain	AtomIterator.getCurrentChain() Get the chain that contains the current atom.
Chain	StructureImpl.getNonPolyChain(String asymId)
Chain	Structure.getNonPolyChain(String asymId) Retrieve a non-polymeric Chain based on the 'internal' chain id (asymId) for the first model
Chain	StructureImpl.getNonPolyChain(String asymId, int modelIdx)
Chain	Structure.getNonPolyChain(String asymId, int modelIdx) Retrieve a non-polymeric Chain based on the 'internal' chain id (asymId) for the given model index
Chain	StructureImpl.getPolyChain(String asymId)
Chain	Structure.getPolyChain(String asymId) Retrieve a polymeric Chain based on the 'internal' chain id (asymId) for the first model See Structure.getPolyChainByPDB(String) for a similar method using the chain name (authId).
Chain	StructureImpl.getPolyChain(String asymId, int modelIdx)
Chain	Structure.getPolyChain(String asymId, int modelIdx) Retrieve a polymeric Chain based on the 'internal' chain id (asymId) for the given model index See Structure.getPolyChainByPDB(String, int) for a similar method using the chain name (authId).
Chain	StructureImpl.getPolyChainByPDB(String authId)
Chain	Structure.getPolyChainByPDB(String authId) Retrieve a polymeric Chain based on the 'public' chain name (authId) for the first model See Structure.getPolyChain(String) for a similar method using the chain id (asymId).
Chain	StructureImpl.getPolyChainByPDB(String authId, int modelIdx)
Chain	Structure.getPolyChainByPDB(String authId, int modelIdx) Retrieve a polymeric Chain based on the 'public' chain name (authId) for the given model index.
Chain	EntityInfo.getRepresentative() Get the representative Chain for this EntityInfo.
Chain	StructureImpl.getWaterChain(String asymId)
Chain	Structure.getWaterChain(String asymId) Retrieve a water Chain based on the 'internal' chain id (asymId) for the first model
Chain	StructureImpl.getWaterChain(String asymId, int modelIdx)
Chain	Structure.getWaterChain(String asymId, int modelIdx) Retrieve a water chain based on the 'internal' chain id (asymId) for the given model index
Chain	StructureImpl.getWaterChainByPDB(String authId)
Chain	Structure.getWaterChainByPDB(String authId) Retrieve a water Chain based on the 'public' chain name (authId) for the first model
Chain	StructureImpl.getWaterChainByPDB(String authId, int modelIdx)
Chain	Structure.getWaterChainByPDB(String authId, int modelIdx) Retrieve a water Chain based on the 'public' chain name (authId) for the given model index

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

Modifier and Type	Method and Description
List<Chain>	Model.getChains() Get all chains: polymeric, non-polymeric and water
List<Chain>	StructureImpl.getChains() Retrieve all chains for the first model.
List<Chain>	EntityInfo.getChains() Get the list of chains that are part of this EntityInfo.
List<Chain>	Structure.getChains() Retrieve all chains for the first model.
List<Chain>	StructureImpl.getChains(int modelIdx) 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 .
List<Chain>	Model.getNonPolyChains()
List<Chain>	StructureImpl.getNonPolyChains()
List<Chain>	Structure.getNonPolyChains() Return all non-polymeric chains for the first model
List<Chain>	StructureImpl.getNonPolyChains(int modelIdx)
List<Chain>	Structure.getNonPolyChains(int modelIdx) Return all non-polymeric chains for the given model index.
List<Chain>	StructureImpl.getNonPolyChainsByPDB(String authId)
List<Chain>	Structure.getNonPolyChainsByPDB(String authId) Retrieve all non-polymeric Chains corresponding to the given 'public' chain name (authId) for the first model.
List<Chain>	StructureImpl.getNonPolyChainsByPDB(String authId, int modelIdx)
List<Chain>	Structure.getNonPolyChainsByPDB(String authId, int modelIdx) Retrieve all non-polymeric Chains corresponding to the 'public' chain name (authId) and the given model index.
List<Chain>	Model.getPolyChains()
List<Chain>	StructureImpl.getPolyChains()
List<Chain>	Structure.getPolyChains() Return all polymeric chains for the first model
List<Chain>	StructureImpl.getPolyChains(int modelIdx)
List<Chain>	Structure.getPolyChains(int modelIdx) Return all polymeric chains for the given model index.
List<Chain>	Model.getWaterChains()
List<Chain>	StructureImpl.getWaterChains()
List<Chain>	Structure.getWaterChains() Return all water chains for the first model
List<Chain>	StructureImpl.getWaterChains(int modelIdx)
List<Chain>	Structure.getWaterChains(int modelIdx) Return all water chains for the given model index

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

Modifier and Type	Method and Description
void	Model.addChain(Chain c)
void	StructureImpl.addChain(Chain chain) Add a new chain to the first model
void	EntityInfo.addChain(Chain chain) Add new Chain to this EntityInfo
void	Structure.addChain(Chain chain) Add a new chain to the first model
void	StructureImpl.addChain(Chain chain, int modelnr) Add a new chain to the model specified by the given index
void	Structure.addChain(Chain chain, int modelnr) Add a new chain to the model specified by the given index
static Chain	StructureTools.addGroupToStructure(Structure s, Group g, int model, Chain chainGuess, boolean clone) Adds a particular group to a structure.
int	EntityInfo.getAlignedResIndex(Group g, Chain c) Given a Group g of Chain c (member of this EnityInfo) return the corresponding position in the alignment of all member sequences (1-based numbering), i.e. the index (1-based) in the SEQRES sequence.
static Atom[]	StructureTools.getAllAtomArray(Chain c) Returns and array of all atoms of the chain, 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 javax.vecmath.Point3d[]	StructureTools.getAllNonHCoordsArray(Chain c, boolean hetAtoms) Returns and array of all non-Hydrogen atoms coordinates 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. the contact map.
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. the contact map.
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. the contact map.
static GroupType	StructureTools.getPredominantGroupType(Chain c) Deprecated. use getPredominantGroupType() instead.
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. the contact map.
static boolean	StructureTools.isChainPureNonPolymer(Chain c) Deprecated. use isPureNonPolymer() instead.
static boolean	StructureTools.isChainWaterOnly(Chain c) Deprecated. use isWaterOnly() instead.
static boolean	StructureTools.isNucleicAcid(Chain c) Deprecated. use isNucleicAcid() instead.
static boolean	StructureTools.isProtein(Chain c) Deprecated. use isProtein() instead.
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. the vecmath library double-precision 4x4 rotation+translation matrix).
static void	Calc.translate(Chain chain, javax.vecmath.Vector3d v) Translates a chain object, given a Vector3d (i.e. the vecmath library double-precision 3-d vector)

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

Modifier and Type	Method and Description
void	StructureImpl.addModel(List<Chain> modelChains) 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	Model.setChains(List<Chain> modelChains)
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	EntityInfo.setChains(List<Chain> chains) Set the chains for this EntityInfo
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	StructureImpl.setModel(int position, List<Chain> modelChains) 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.align.util

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

Modifier and Type	Method and Description
static List<Chain>	AlignmentTools.getAlignedModel(Atom[] ca) get an artificial List of chains containing the Atoms and groups.

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

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

Modifier and Type	Method and Description
List<Chain>	BasePairParameters.getNucleicChains(boolean removeDups) This method reports all the nucleic acid chains and has an option to remove duplicates if you are considering an analysis of only unique DNA or RNA helices in the Structure.

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

Modifier and Type	Method and Description
List<Pair<Group>>	TertiaryBasePairParameters.findPairs(List<Chain> chains) This is an alternative implementation of findPair() that looks for anything that would fit the criteria for a base-pair, useful for the context of tertiary structure of RNA.
List<Pair<Group>>	BasePairParameters.findPairs(List<Chain> chains) This method performs a search for base pairs in the structure.
List<Pair<Group>>	MismatchedBasePairParameters.findPairs(List<Chain> chains) This is an implementation for finding non-canonical base pairs when there may be missing or overhanging bases.

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	SeqRes2AtomAligner.getMatchingAtomRes(Chain seqRes, List<Chain> atomList, boolean useChainId)
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.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	SeqRes2AtomAligner.getMatchingAtomRes(Chain seqRes, List<Chain> atomList, boolean useChainId)
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 authId, String asymId, 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 void	EntityFinder.createPurelyNonPolyEntities(List<List<Chain>> nonPolyModels, List<List<Chain>> waterModels, List<EntityInfo> entities) Given all chains of all models find entities for the nonpolymers and water chains within them, assigning entity ids, types and descriptions to them.
static void	EntityFinder.createPurelyNonPolyEntities(List<List<Chain>> nonPolyModels, List<List<Chain>> waterModels, List<EntityInfo> entities) Given all chains of all models find entities for the nonpolymers and water chains within them, assigning entity ids, types and descriptions to them.
static List<EntityInfo>	EntityFinder.findPolyEntities(List<List<Chain>> polyModels) Utility method that employs some heuristics to find the EntityInfos for the polymeric chains given in constructor.
static Chain	SeqRes2AtomAligner.getMatchingAtomRes(Chain seqRes, List<Chain> atomList, boolean useChainId)
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 authorId, String asymId) Converts a Chain into a List of AtomSite objects

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

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

Modifier and Type	Method and Description
List<Chain>	MmtfSummaryDataBean.getAllChains()

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

Modifier and Type	Method and Description
static void	MmtfUtils.addSeqRes(Chain modelChain, String sequence) Add the missing groups to the SeqResGroups.
static void	MmtfUtils.insertSeqResGroup(Chain chain, Group group, int sequenceIndexId) Insert the group in the given position in the sequence.

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

Modifier and Type	Method and Description
void	MmtfSummaryDataBean.setAllChains(List<Chain> allChains)