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 Detail

      • getPDPDomainNamesForPDB

        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
        Parameters:
        pdbId - PDB ID
        Returns:
        Set of domain names, e.g. "PDP:4HHBAa"
        Throws:
        java.io.IOException
      • getDomain

        Structure getDomain​(java.lang.String pdpDomainName,
                            AtomCache cache)
                     throws java.io.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:
        java.io.IOException - For IO errors, e.g. when parsing PDP information
        StructureException - For errors creating the structure
      • getPDPDomain

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