Package org.biojava.nbio.structure.io.sifts

Class SiftsChainToUniprotMapping

java.lang.Object
org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMapping
public class SiftsChainToUniprotMapping extends Object
A mapping between UniProt entries and PDB chains. For example 
 SiftsChainToUniprot sifts = SiftsChainToUniprot.load();
 SiftsChainEntry entry1 = sifts.getByUniProtId("P04585");
 System.out.println(entry1.getPdbId() + "." + entry1.getChainId()); // 1hiv.A
 System.out.println(entry1.getPdbStart() + "-" + entry1.getPdbStop()); // 1-99
 SiftsChainEntry entry2 = sifts.getByChainId("1hiv", "A");
 System.out.println(entry1.equals(entry2)); // true
Since:
3.0.7
Author:
dmyersturnbull
See Also:

  • Method Details

    • load

      public static SiftsChainToUniprotMapping load() throws IOException
      Loads the SIFTS mapping. Attempts to load the mapping file in the PDB cache directory. If the file does not exist or could not be parsed, downloads and stores a GZ-compressed file.
      Returns:
      Throws:
      IOException - If the local file could not be read and could not be downloaded

    • load

      public static SiftsChainToUniprotMapping load(boolean useOnlyLocal) throws IOException
      Loads the SIFTS mapping. Attempts to load the mapping file in the PDB cache directory. If the file does not exist or could not be parsed, downloads and stores a GZ-compressed file.
      Parameters:
      useOnlyLocal - If true, will throw an IOException if the file needs to be downloaded
      Returns:
      Throws:
      IOException - If the local file could not be read and could not be downloaded (including if onlyLocal is true)

    • chainEntrySet

      public Set<Map.Entry<String,SiftsChainEntry>> chainEntrySet()

    • containsChainId

      public boolean containsChainId(String pdbId, String chainId)

    • containsUniProtId

      public boolean containsUniProtId(String uniProtId)

    • getByChainId

      public SiftsChainEntry getByChainId(String pdbId, String chainId)

    • getByUniProtId

      public SiftsChainEntry getByUniProtId(String uniProtId)

    • keySet

      public Set<String> keySet()

    • size

      public int size()
      Returns the number of mapped entries.

    • uniProtEntrySet

      public Set<Map.Entry<String,SiftsChainEntry>> uniProtEntrySet()

    • values

      public Collection<SiftsChainEntry> values()