Package org.biojava.nbio.structure.domain

Interface PDPProvider

All Known Implementing Classes:
RemotePDPProvider
public interface PDPProvider
Decomposes a structure into representative PDP domains. Implementations will probably want to also implement DomainProvider, which provides a very similar set of methods for general structure domain decomposition.
Since:
3.0.2
Author:
Andreas Prlic

  • Method Details

    • getPDPDomainNamesForPDB

      SortedSet<String> getPDPDomainNamesForPDB(String pdbId) throws IOException
      Get a list of all PDP domains for a given PDB entry
      Parameters:
      pdbId - PDB ID
      Returns:
      Set of domain names, e.g. "PDP:4HHBAa"
      Throws:
      IOException

    • getDomain

      Structure getDomain(String pdpDomainName, AtomCache cache) throws IOException, StructureException
      Get the structure for a particular PDP domain
      Parameters:
      pdpDomainName - PDP identifier, e.g. "PDP:4HHBAa"
      cache - AtomCache, responsible for fetching and storing the coordinates
      Returns:
      Structure representing the PDP domain
      Throws:
      IOException - For IO errors, e.g. when parsing PDP information
      StructureException - For errors creating the structure

    • getPDPDomain

      PDPDomain getPDPDomain(String pdpDomainName) throws IOException
      Get a StructureIdentifier representing the specified PDP domain.
      Parameters:
      pdpDomainName - PDP domain name
      Returns:
      a PDPDomain representing this domain name
      Throws:
      IOException