Class URLIdentifier

java.lang.Object
org.biojava.nbio.structure.URLIdentifier
All Implemented Interfaces:
Serializable, StructureIdentifier

public class URLIdentifier extends Object implements StructureIdentifier
Represents a structure loaded from a URL (including a file URL) A few custom query parameters are supported:
  • format=[pdb|cif] Specify the file format (will otherwise be guessed from the extension)
  • pdbId=[String] Specify the PDB ID (also guessed from the filename)
  • chainID=[String] A single chain from the structure
  • residues=[String] Residue ranges, in a form understood by SubstructureIdentifier
Author:
Spencer Bliven
See Also:
  • Field Details

  • Constructor Details

  • Method Details

    • getURL

      public URL getURL()
    • getIdentifier

      public String getIdentifier()
      Description copied from interface: StructureIdentifier
      Get the String form of this identifier. It is recommended that the
      invalid reference
      #toString()
      method also return the identifier, for consistency during serialization.
      Specified by:
      getIdentifier in interface StructureIdentifier
      Returns:
      The String form of this identifier
    • 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 without ranges (e.g. including all residues)
      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:
      • invalid reference
        StructureTools#getReducedStructure(Structure, String)
    • loadStructure

      public Structure loadStructure(AtomCache cache) throws StructureException, IOException
      Load the structure from the URL
      Specified by:
      loadStructure in interface StructureIdentifier
      Returns:
      null
      Throws:
      StructureException - For errors loading and parsing the structure
      IOException - Errors reading the structure from disk
    • guessPDBID

      public static String guessPDBID(String name)
      Recognizes PDB IDs that occur at the beginning of name followed by some delimiter.
      Parameters:
      name - Input filename
      Returns:
      A 4-character id-like string, or null if none is found