Uses of Interface
org.biojava.nbio.structure.Chain
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Packages that use Chain Package Description org.biojava.nbio.protmod.structure org.biojava.nbio.structure org.biojava.nbio.structure.align.util org.biojava.nbio.structure.basepairs org.biojava.nbio.structure.contact org.biojava.nbio.structure.gui.util org.biojava.nbio.structure.io Input and Output of Structuresorg.biojava.nbio.structure.io.mmcif Input and Output of mmcif files.org.biojava.nbio.structure.io.mmtf -
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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 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 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 Description class
ChainImpl
A Chain in a PDB file.Methods in org.biojava.nbio.structure that return Chain Modifier and Type Method Description static Chain
StructureTools. addGroupToStructure(Structure s, Group g, int model, Chain chainGuess, boolean clone)
Adds a particular group to a structure.Chain
Structure. findChain(String authId)
Deprecated.Chain
Structure. findChain(String authId, int modelnr)
Deprecated.Chain
StructureImpl. findChain(String chainId)
Request a particular chain from a structure.Chain
StructureImpl. findChain(String chainName, int modelnr)
Request a particular chain from a particular modelChain
Group. getChain()
Returns the parent Chain of the Group.Chain
HetatomImpl. getChain()
Returns the parent Chain of the Group.Chain
Structure. getChain(String asymId)
Retrieve a Chain (polymeric, non-polymeric or water) based on the 'internal' chain id (asymId) for the first modelChain
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 indexChain
StructureImpl. getChain(String asymId)
Retrieve a Chain (polymeric, non-polymeric or water) based on the 'internal' chain id (asymId) for the first modelChain
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 indexChain
Structure. getChainByIndex(int chainIndex)
Retrieve a chain by its index within the Structure .Chain
Structure. getChainByIndex(int modelnr, int chainIndex)
Retrieve a chain by its indices within the Structure and model.Chain
StructureImpl. getChainByIndex(int number)
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. getChainByPDB(String authId)
Deprecated.useStructure.getPolyChainByPDB(String)
insteadChain
Structure. getChainByPDB(String authId, int modelIdx)
Deprecated.useStructure.getPolyChainByPDB(String,int)
insteadChain
StructureImpl. getChainByPDB(String chainId)
Request a chain by its public id (author id) for the first model.Chain
StructureImpl. getChainByPDB(String authId, int modelnr)
Request a chain by its public id (author id) for the given model index.Chain
AtomIterator. getCurrentChain()
Get the chain that contains the current atom.Chain
GroupIterator. getCurrentChain()
Get the current Chain.Chain
Structure. getNonPolyChain(String asymId)
Retrieve a non-polymeric Chain based on the 'internal' chain id (asymId) for the first modelChain
Structure. getNonPolyChain(String asymId, int modelIdx)
Retrieve a non-polymeric Chain based on the 'internal' chain id (asymId) for the given model indexChain
StructureImpl. getNonPolyChain(String asymId)
Chain
StructureImpl. getNonPolyChain(String asymId, int modelIdx)
Chain
Structure. getPolyChain(String asymId)
Retrieve a polymeric Chain based on the 'internal' chain id (asymId) for the first modelChain
Structure. getPolyChain(String asymId, int modelIdx)
Retrieve a polymeric Chain based on the 'internal' chain id (asymId) for the given model indexChain
StructureImpl. getPolyChain(String asymId)
Chain
StructureImpl. getPolyChain(String asymId, int modelIdx)
Chain
Structure. getPolyChainByPDB(String authId)
Retrieve a polymeric Chain based on the 'public' chain name (authId) for the first modelChain
Structure. getPolyChainByPDB(String authId, int modelIdx)
Retrieve a polymeric Chain based on the 'public' chain name (authId) for the given model index.Chain
StructureImpl. getPolyChainByPDB(String authId)
Chain
StructureImpl. getPolyChainByPDB(String authId, int modelIdx)
Chain
EntityInfo. getRepresentative()
Get the representative Chain for this EntityInfo.Chain
Structure. getWaterChain(String asymId)
Retrieve a water Chain based on the 'internal' chain id (asymId) for the first modelChain
Structure. getWaterChain(String asymId, int modelIdx)
Retrieve a water chain based on the 'internal' chain id (asymId) for the given model indexChain
StructureImpl. getWaterChain(String asymId)
Chain
StructureImpl. getWaterChain(String asymId, int modelIdx)
Chain
Structure. getWaterChainByPDB(String authId)
Retrieve a water Chain based on the 'public' chain name (authId) for the first modelChain
Structure. getWaterChainByPDB(String authId, int modelIdx)
Retrieve a water Chain based on the 'public' chain name (authId) for the given model indexChain
StructureImpl. getWaterChainByPDB(String authId)
Chain
StructureImpl. getWaterChainByPDB(String authId, int modelIdx)
Methods in org.biojava.nbio.structure that return types with arguments of type Chain Modifier and Type Method Description List<Chain>
EntityInfo. getChains()
Get the list of chains that are part of this EntityInfo.List<Chain>
Model. getChains()
Get all chains: polymeric, non-polymeric and waterList<Chain>
Structure. getChains()
Retrieve all chains for the first model.List<Chain>
Structure. getChains(int modelnr)
Retrieve all chains of a model.List<Chain>
StructureImpl. getChains()
Retrieve all chains for the first model.List<Chain>
StructureImpl. getChains(int modelIdx)
Retrieve all chains of a model.List<Chain>
Structure. getModel(int modelnr)
Retrieve all Chains belonging to a model .List<Chain>
StructureImpl. getModel(int modelnr)
Retrieve all Chains belonging to a model .List<Chain>
Model. getNonPolyChains()
List<Chain>
Structure. getNonPolyChains()
Return all non-polymeric chains for the first modelList<Chain>
Structure. getNonPolyChains(int modelIdx)
Return all non-polymeric chains for the given model index.List<Chain>
StructureImpl. getNonPolyChains()
List<Chain>
StructureImpl. getNonPolyChains(int modelIdx)
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>
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>
StructureImpl. getNonPolyChainsByPDB(String authId)
List<Chain>
StructureImpl. getNonPolyChainsByPDB(String authId, int modelIdx)
List<Chain>
Model. getPolyChains()
List<Chain>
Structure. getPolyChains()
Return all polymeric chains for the first modelList<Chain>
Structure. getPolyChains(int modelIdx)
Return all polymeric chains for the given model index.List<Chain>
StructureImpl. getPolyChains()
List<Chain>
StructureImpl. getPolyChains(int modelIdx)
List<Chain>
Model. getWaterChains()
List<Chain>
Structure. getWaterChains()
Return all water chains for the first modelList<Chain>
Structure. getWaterChains(int modelIdx)
Return all water chains for the given model indexList<Chain>
StructureImpl. getWaterChains()
List<Chain>
StructureImpl. getWaterChains(int modelIdx)
Methods in org.biojava.nbio.structure with parameters of type Chain Modifier and Type Method Description void
EntityInfo. addChain(Chain chain)
Add new Chain to this EntityInfovoid
Model. addChain(Chain c)
void
Structure. addChain(Chain chain)
Add a new chain to the first modelvoid
Structure. addChain(Chain chain, int modelnr)
Add a new chain to the model specified by the given indexvoid
StructureImpl. addChain(Chain chain)
Add a new chain to the first modelvoid
StructureImpl. addChain(Chain chain, int modelnr)
Add a new chain to the model specified by the given indexstatic 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 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 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 GroupType
StructureTools. getPredominantGroupType(Chain c)
Deprecated.usegetPredominantGroupType()
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.useisPureNonPolymer()
instead.static boolean
StructureTools. isChainWaterOnly(Chain c)
Deprecated.useisWaterOnly()
instead.static boolean
StructureTools. isNucleicAcid(Chain c)
Deprecated.useisNucleicAcid()
instead.static boolean
StructureTools. isProtein(Chain c)
Deprecated.useisProtein()
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 Description void
Structure. addModel(List<Chain> model)
Add a new model.void
StructureImpl. addModel(List<Chain> modelChains)
Add a new model.void
EntityInfo. setChains(List<Chain> chains)
Set the chains for this EntityInfovoid
Model. setChains(List<Chain> modelChains)
void
Structure. setChains(int modelnr, List<Chain> chains)
Set the chains for a modelvoid
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. setChains(int modelnr, List<Chain> chains)
Set the chains for a modelvoid
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. setModel(int position, List<Chain> model)
A convenience function if one wants to edit and replace the models in a structure.void
StructureImpl. setModel(int position, List<Chain> modelChains)
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 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 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 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 Description 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.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. -
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 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 Description Chain
SequenceScalePanel. getChain()
Methods in org.biojava.nbio.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.nbio.structure.io
Methods in org.biojava.nbio.structure.io that return Chain Modifier and Type Method 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 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 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 representationMethod parameters in org.biojava.nbio.structure.io with type arguments of type Chain Modifier and Type Method 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 List<EntityInfo>
EntityFinder. findPolyEntities(List<List<Chain>> polyModels)
Utility method that employs some heuristics to find theEntityInfo
s 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 Description static List<AtomSite>
MMCIFFileTools. convertChainToAtomSites(Chain c, int model, String chainName, String chainId)
Converts a Chain into a List ofAtomSite
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 Description List<Chain>
MmtfSummaryDataBean. getAllChains()
Methods in org.biojava.nbio.structure.io.mmtf with parameters of type Chain Modifier and Type Method 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 Description void
MmtfSummaryDataBean. setAllChains(List<Chain> allChains)
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