Class PDBBioUnitDataProvider

  • All Implemented Interfaces:
    BioUnitDataProvider

    public class PDBBioUnitDataProvider
    extends java.lang.Object
    implements BioUnitDataProvider
    A BioUnitDataProvider that extracts the necessary info from PDB files
    Author:
    Andreas Prlic
    • Constructor Detail

      • PDBBioUnitDataProvider

        public PDBBioUnitDataProvider()
    • Method Detail

      • loadPDB

        public PDBHeader loadPDB​(java.lang.String pdbId)
      • getBioUnitTransformationList

        public java.util.List<BiologicalAssemblyTransformation> getBioUnitTransformationList​(java.lang.String pdbId,
                                                                                             int biolAssemblyNr)
        Description copied from interface: BioUnitDataProvider
        get the data for a particular assembly, counting starts at 1...
        Specified by:
        getBioUnitTransformationList in interface BioUnitDataProvider
        Parameters:
        pdbId - the PDB ID. E.g. 1STP
        biolAssemblyNr - the number of the assembly, the first one is nr 1. 0 refers to the asym unit
        Returns:
        list of transformations.
      • getNrBiolAssemblies

        public int getNrBiolAssemblies​(java.lang.String pdbId)
        Description copied from interface: BioUnitDataProvider
        Returns the number of available biological assemblies.
        Specified by:
        getNrBiolAssemblies in interface BioUnitDataProvider
        Parameters:
        pdbId - the PDB ID. E.g. 1STP
        Returns:
        nr of available assemblies.
      • hasBiolAssembly

        public boolean hasBiolAssembly​(java.lang.String pdbId)
        Description copied from interface: BioUnitDataProvider
        Does the PDB ID have biological assembly information?
        Specified by:
        hasBiolAssembly in interface BioUnitDataProvider
        Parameters:
        pdbId - the PDB ID. E.g. 1STP
        Returns:
        boolean flag
      • setAtomCache

        public void setAtomCache​(AtomCache cache)
        Description copied from interface: BioUnitDataProvider
        Set an AtomCache to use when fetching asymmetric units. If null, a new cache will be created with default parameters.
        Specified by:
        setAtomCache in interface BioUnitDataProvider