Package org.biojava.nbio.structure.rcsb

Class PdbIdLists

java.lang.Object
org.biojava.nbio.structure.rcsb.PdbIdLists
public class PdbIdLists extends Object
Utility classes for retrieving lists of PDB IDs.
Since:
4.2.0
Author:
Andreas Prlic

  • Field Details

  • Constructor Details

    • PdbIdLists

      public PdbIdLists()

  • Method Details

    • getCurrentPDBIds

      public static Set<String> getCurrentPDBIds() throws IOException
      get the list of current PDB IDs
      Returns:
      list of current PDB IDs
      Throws:
      IOException

    • getAllViruses

      public static Set<String> getAllViruses() throws IOException
      Get the PDB IDs of all virus structures in the current PDB
      Returns:
      list of all virus structures
      Throws:
      IOException

    • getNMRStructures

      public static Set<String> getNMRStructures() throws IOException
      get list of all current NMR structures
      Returns:
      list of NMR structures
      Throws:
      IOException

    • getGagPolyproteins

      public static Set<String> getGagPolyproteins() throws IOException
      get all PDB IDs of gag-polyproteins
      Returns:
      list of PDB IDs
      Throws:
      IOException

    • getTransmembraneProteins

      public static Set<String> getTransmembraneProteins() throws IOException
      get all Transmembrane proteins
      Returns:
      list of PDB IDs
      Throws:
      IOException

    • getNucleotides

      public static Set<String> getNucleotides() throws IOException
      Throws:
      IOException

    • getRibosomes

      public static Set<String> getRibosomes() throws IOException
      Throws:
      IOException

    • postQuery

      public static Set<String> postQuery(String xml) throws IOException
      post am XML query (PDB XML query format) to the RESTful RCSB web service
      Parameters:
      xml -
      Returns:
      a list of PDB ids.
      Throws:
      IOException

    • doPOST

      public static InputStream doPOST(URL url, String data) throws IOException
      do a POST to a URL and return the response stream for further processing elsewhere.
      Parameters:
      url -
      Returns:
      Throws:
      IOException

    • main

      public static void main(String[] args)