Package pl.poznan.put.pdb.analysis

Class CifContainer

java.lang.Object
pl.poznan.put.pdb.analysis.CifContainer
All Implemented Interfaces:
Closeable, AutoCloseable, ModelContainer
Direct Known Subclasses:
ImmutableCifContainer
@Immutable public abstract class CifContainer extends Object implements ModelContainer
A container of one or more PDB files converted from a single mmCIF file.

  • Constructor Details

    • CifContainer

      public CifContainer()

  • Method Details

    • emptyInstance

      public static ModelContainer emptyInstance(File cifFile)
      Creates an empty instance (without any chain mapping).
      Parameters:
      cifFile - Path to the mmCIF file.
      Returns:
      An instance without any chain mapping.

    • fileChainMap

      @Parameter(order=2) public abstract Map<File,org.apache.commons.collections4.BidiMap<String,String>> fileChainMap()
      Returns:
      The mapping of chain name in PDB and mmCIF for a specific file.

    • cifFile

      @Parameter(order=1) public abstract File cifFile()
      Returns:
      The value of the cifFile attribute,

    • pdbFiles

      public final List<File> pdbFiles()
      Specified by:
      pdbFiles in interface ModelContainer
      Returns:
      A list of PDB files corresponding to this container.

    • originalCifChainName

      public final String originalCifChainName(File pdbFile, String pdbChain)
      Description copied from interface: ModelContainer
      Checks mapping of chains to get the original mmCIF chain name from the generated PDB chain name.
      Specified by:
      originalCifChainName in interface ModelContainer
      Parameters:
      pdbFile - A PDB file.
      pdbChain - Chain name in the PDB file.
      Returns:
      Original chain name in the mmCIF file.

    • convertedPdbChainName

      public final String convertedPdbChainName(File pdbFile, String cifChain)
      Description copied from interface: ModelContainer
      Checks mapping of chains to get the generated PDB chain name from the original mmCIF chain name.
      Specified by:
      convertedPdbChainName in interface ModelContainer
      Parameters:
      pdbFile - A PDB file.
      cifChain - Chain name in the mmCif file.
      Returns:
      Original chain name in the PDB file.

    • close

      public final void close()
      Deletes all files (PDB and mmCIF) maintained by this instance.
      Specified by:
      close in interface AutoCloseable
      Specified by:
      close in interface Closeable