Package org.biojava.nbio.structure.align

Interface StructureAlignment

All Known Implementing Classes:
AbstractStructureAlignment, BioJavaStructureAlignment, CeCPMain, CeMain, CeSideChainMain, FatCatFlexible, FatCatRigid, OptimalCECPMain, SmithWaterman3Daligner
public interface StructureAlignment

  • Method Details

    • align

      AFPChain align(Atom[] ca1, Atom[] ca2) throws StructureException
      Run an alignment while specifying the atoms to be aligned. Will used default parameters for the algorithm.
      Parameters:
      ca1 -
      ca2 -
      Returns:
      the afpChain object that contains the alignment.
      Throws:
      StructureException

    • align

      AFPChain align(Atom[] ca1, Atom[] ca2, Object params) throws StructureException
      run an alignment and also send a bean containing the parameters.
      Parameters:
      ca1 -
      ca2 -
      params -
      Returns:
      the afpChain object that contains the alignment.
      Throws:
      StructureException

    • getParameters

      ConfigStrucAligParams getParameters()
      Return the paramers for this algorithm.
      Returns:
      The returned object will be a Java bean.

    • setParameters

      void setParameters(ConfigStrucAligParams parameters)
      Set the default parameters for this algorithm to use
      Parameters:
      parameters -

    • getAlgorithmName

      String getAlgorithmName()
      Get the name of the Algorithm
      Returns:
      the name of the algorithm

    • getVersion

      String getVersion()
      Get the Version information for this Algorithm.
      Returns:
      the version of the algorithm