Package org.biojava.nbio.structure.align.client

Class StructureName

java.lang.Object
org.biojava.nbio.structure.align.client.StructureName
All Implemented Interfaces:
Serializable, Comparable<StructureName>, StructureIdentifier
public class StructureName extends Object implements Comparable<StructureName>, Serializable, StructureIdentifier
A utility class that makes working with names of structures, domains and ranges easier. Accepts a wide range of identifier formats, including ScopDomain, CathDomain, PDP domains, and SubstructureIdentifier residue ranges. Where possible, data is extracted from the input string. Otherwise, range information may be loaded from one of the factory classes: CathFactory,ScopFactory, etc.
See Also:

  • Field Details

    • name

      protected String name

    • pdbId

      protected String pdbId

    • chainId

      protected String chainId

  • Constructor Details

    • StructureName

      public StructureName(String name)
      Create a new StructureName from the given identifier, which may be a domain name, a substructure identifier, etc.

      The source and PDB-Id are extracted at compile time, but fully interpreting the ID, which may require additional parsing or remote calls, is done lazily.

      The following sources are supported. Any may be prefixed by the source name followed by a colon (e.g. PDB:4HHB). In this case, that source will be used unequivocally. If no source is specified, StructureName will make a (usually reliable) guess as to which source was intended.

      • PDBPDB identifier, optionally followed by chain and/or residue ranges. Internally represented by a SubstructureIdentifier; see that class for the full format specification. Examples: 4hhb, 4hhb.A, 4hhb.A:1-50.
      • SCOP SCOP domain (or SCOPe, depending on the ScopFactory.getSCOP() version). Example: d1h6w.2
      • PDP Protein Domain Parser domain. PDP domains are not guessed, making the PDP: prefix obligatory. Example: PDP:4HHBAa
      • CATH Cath domains. Example: 1qvrC03
      • URL Arbitrary URLs. Most common protocols are handled, including http://, ftp://, and file://. Some parsing information can be passed as custom query parameters. Example: http://www.rcsb.org/pdb/files/1B8G.pdb.gz
      • FILE A file path. Supports relative paths and expands ~ to the user's home directory. Only existing files will be automatically detected; to refer to a potentially not-yet existing file, prepend the prefix. Internally represented as a URLIdentifier after path expansion. Example: ~/custom_protein.pdb
      • ECOD ECOD domain. Example: e1lyw.1
      • BIO Biological assembly. These are not guessed, making the BIO: prefix obligatory. Example: BIO:2ehz:1
      Parameters:
      name - An identifier string
      Throws:
      IllegalArgumentException - if the name has a recognizable source but is semantically invalid

  • Method Details

    • getPdbId

      public String getPdbId() throws StructureException
      Get the PDB ID for this name, if any. Equivalent to toCanonical().getPdbId()
      Returns:
      The upper-case PDB Name, or null if not applicable
      Throws:
      StructureException - Wraps errors which occur when converting to canonical form

    • getChainId

      public String getChainId()
      Gets the chain ID, for structures where it is unique and well-defined. May return '.' for multi-chain ranges, '_' for wildcard chains, or null if the information is unavailable.

      This method should only be used casually. For precise chainIds, it is better to use toCanonical() and iterate through the residue ranges.

      Returns:

    • getName

      @Deprecated public String getName()
      Deprecated.
      use getIdentifier()
      Returns:
      the identifier string

    • getIdentifier

      public String getIdentifier()
      Get the original form of the identifier
      Specified by:
      getIdentifier in interface StructureIdentifier
      Returns:
      The String form of this identifier

    • toString

      public String toString()
      Overrides:
      toString in class Object

    • isScopName

      public boolean isScopName()

    • isPDPDomain

      public boolean isPDPDomain()

    • isCathID

      public boolean isCathID()

    • isPdbId

      public boolean isPdbId()

    • isURL

      public boolean isURL()

    • isFile

      public boolean isFile()
      Indicates that the identifier was determined to correspond to a file. Note that some file identifiers may also be valid URLs; in that case, the URL source is preferred.
      Returns:

    • isEcodDomain

      public boolean isEcodDomain()

    • isBioAssembly

      public boolean isBioAssembly()

    • getSource

      public StructureName.Source getSource()

    • getBaseIdentifier

      public StructureIdentifier getBaseIdentifier() throws StructureException
      StructureName wraps another StructureIdentifier. The type of the base identifier depends on the source. Most StructureName methods deligate to the base identifier.

      It is possible that future versions of StructureName might change the return type. Except for some specialized uses, it is probably better to create the correct type of identifier directly, rather than creating a StructureName and casting the result of this method.

      Returns:
      A Str
      Throws:
      StructureException - Wraps exceptions that may be thrown by individual implementations. For example, a SCOP identifier may require that the domain definitions be available for download.

    • toCanonical

      public SubstructureIdentifier toCanonical() throws StructureException
      Description copied from interface: StructureIdentifier
      Convert to a canonical SubstructureIdentifier.

      This allows all domains to be converted to a standard format String.

      Specified by:
      toCanonical in interface StructureIdentifier
      Returns:
      A SubstructureIdentifier equivalent to this
      Throws:
      StructureException - Wraps exceptions that may be thrown by individual implementations. For example, a SCOP identifier may require that the domain definitions be available for download.

    • reduce

      public Structure reduce(Structure input) throws StructureException
      Description copied from interface: StructureIdentifier
      Takes a complete structure as input and reduces it to the substructure represented by this StructureIdentifier.

      The returned structure may be a shallow copy of the input, with shared Chains, Residues, etc.

      Specified by:
      reduce in interface StructureIdentifier
      Parameters:
      input - A full structure, e.g. as loaded from the PDB. The structure ID should match that returned by getPdbId(), if applicable.
      Returns:
      Throws:
      StructureException
      See Also:

    • loadStructure

      public Structure loadStructure(AtomCache cache) throws StructureException, IOException
      Description copied from interface: StructureIdentifier
      Loads a structure encompassing the structure identified. The Structure returned should be suitable for passing as the input to StructureIdentifier.reduce(Structure). It is recommended that the most complete structure available be returned (e.g. the full PDB) to allow processing of unselected portions where appropriate.
      Specified by:
      loadStructure in interface StructureIdentifier
      Returns:
      A Structure containing at least the atoms identified by this, or null if Structures are not applicable.
      Throws:
      StructureException - For errors loading and parsing the structure
      IOException - Errors reading the structure from disk

    • hashCode

      public int hashCode()
      Overrides:
      hashCode in class Object

    • equals

      public boolean equals(Object obj)
      Overrides:
      equals in class Object

    • compareTo

      public int compareTo(StructureName o)
      Orders identifiers lexicographically by PDB ID and then full Identifier
      Specified by:
      compareTo in interface Comparable<StructureName>

    • guessScopDomain

      public static ScopDomain guessScopDomain(String name, ScopDatabase scopDB)

      Guess a scop domain. If an exact match is found, return that.

      Otherwise, return the first scop domain found for the specified protein such that

      • The chains match, or one of the chains is '_' or '.'.
      • The domains match, or one of the domains is '_'.
      In some cases there may be several valid matches. In this case a warning will be logged.
      Parameters:
      name - SCOP domain name, or a guess thereof
      scopDB - SCOP domain provider
      Returns:
      The best match for name among the domains of scopDB, or null if none match.