Field Detail

• DEFAULT_SERVER

  public static final java.lang.String DEFAULT_SERVER

  See Also:

  Constant Field Values

Constructor Detail

• RemotePDPProvider

  public RemotePDPProvider()

• RemotePDPProvider

  public RemotePDPProvider​(boolean useCache)
                    throws java.io.IOException

  Parameters:

  useCache -

  Throws:

  java.io.IOException

Method Detail

• main

  public static void main​(java.lang.String[] args)
                   throws java.io.IOException,
                          StructureException

  Throws:

  java.io.IOException

  StructureException

• getServer

  public java.lang.String getServer()

• setServer

  public void setServer​(java.lang.String server)

• getDomain

  public Structure getDomain​(java.lang.String pdpDomainName,
                             AtomCache cache)
                      throws java.io.IOException,
                             StructureException

  Get the structure for a particular PDP domain

  Specified by:

  getDomain in interface PDPProvider

  Parameters:

  pdpDomainName - PDP identifier, e.g. "PDP:4HHBAa"

  cache - AtomCache, responsible for fetching and storing the coordinates

  Returns:

  Structure representing the PDP domain

  Throws:

  java.io.IOException - if the server cannot be reached

  StructureException - For errors parsing the structure

• getPDPDomain

  public PDPDomain getPDPDomain​(java.lang.String pdpDomainName)
                         throws java.io.IOException

  Get a StructureIdentifier representing the specified PDP domain.

  Specified by:

  getPDPDomain in interface PDPProvider

  Parameters:

  pdpDomainName - PDP domain name

  Returns:

  a PDPDomain representing this domain name

  Throws:

  java.io.IOException - if the server cannot be reached

• getPDPDomainNamesForPDB

  public java.util.SortedSet<java.lang.String> getPDPDomainNamesForPDB​(java.lang.String pdbId)
                                                                throws java.io.IOException

  Get a list of all PDP domains for a given PDB entry

  Specified by:

  getPDPDomainNamesForPDB in interface PDPProvider

  Parameters:

  pdbId - PDB ID

  Returns:

  Set of domain names, e.g. "PDP:4HHBAa"

  Throws:

  java.io.IOException - if the server cannot be reached