Package org.biojava.nbio.structure.rcsb

Class PdbIdLists

  • public class PdbIdLists
extends java.lang.Object
    Utility classes for retrieving lists of PDB IDs.
    Since:
    4.2.0
    Author:
    Andreas Prlic

    • Field Summary

      Fields 
      Modifier and Type Field Description
      static java.lang.String SERVICELOCATION  

    • Constructor Summary

      Constructors 
      Constructor Description
      PdbIdLists()  

    • Method Summary

      All Methods Static Methods Concrete Methods 
      Modifier and Type Method Description
      static java.io.InputStream doPOST​(java.net.URL url, java.lang.String data)
      do a POST to a URL and return the response stream for further processing elsewhere.
      static java.util.Set<java.lang.String> getAllViruses()
      Get the PDB IDs of all virus structures in the current PDB
      static java.util.Set<java.lang.String> getCurrentPDBIds()
      get the list of current PDB IDs
      static java.util.Set<java.lang.String> getGagPolyproteins()
      get all PDB IDs of gag-polyproteins
      static java.util.Set<java.lang.String> getNMRStructures()
      get list of all current NMR structures
      static java.util.Set<java.lang.String> getNucleotides()  
      static java.util.Set<java.lang.String> getRibosomes()  
      static java.util.Set<java.lang.String> getTransmembraneProteins()
      get all Transmembrane proteins
      static void main​(java.lang.String[] args)  
      static java.util.Set<java.lang.String> postQuery​(java.lang.String xml)
      post am XML query (PDB XML query format) to the RESTful RCSB web service

      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

    • Field Detail

    • Constructor Detail

      • PdbIdLists

        public PdbIdLists()

    • Method Detail

      • getCurrentPDBIds

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

      • getAllViruses

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

      • getNMRStructures

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

      • getGagPolyproteins

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

      • getTransmembraneProteins

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

      • getNucleotides

        public static java.util.Set<java.lang.String> getNucleotides()
                                                      throws java.io.IOException
        Throws:
        java.io.IOException

      • getRibosomes

        public static java.util.Set<java.lang.String> getRibosomes()
                                                    throws java.io.IOException
        Throws:
        java.io.IOException

      • postQuery

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

      • doPOST

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

      • main

        public static void main​(java.lang.String[] args)