Class OptimalCECPMain

Method Details

• getAlgorithmName

  public String getAlgorithmName()

  Description copied from interface: StructureAlignment

  Get the name of the Algorithm

  Specified by:

  getAlgorithmName in interface StructureAlignment

  Overrides:

  getAlgorithmName in class CeMain

  Returns:

  the name of the algorithm

• getVersion

  public String getVersion()

  Description copied from interface: StructureAlignment

  Get the Version information for this Algorithm.

  Specified by:

  getVersion in interface StructureAlignment

  Overrides:

  getVersion in class CeMain

  Returns:

  the version of the algorithm

• getParameters

  public ConfigStrucAligParams getParameters()

  Description copied from interface: StructureAlignment

  Return the paramers for this algorithm.

  Specified by:

  getParameters in interface StructureAlignment

  Overrides:

  getParameters in class CeMain

  Returns:

  an OptimalCECPParameters object

• setParameters

  public void setParameters(ConfigStrucAligParams params)

  Description copied from interface: StructureAlignment

  Set the default parameters for this algorithm to use

  Specified by:

  setParameters in interface StructureAlignment

  Overrides:

  setParameters in class CeMain

  Parameters:

  params - Should be an OptimalCECPParameters object specifying alignment options

• alignPermuted

  public AFPChain alignPermuted(Atom[] ca1, Atom[] ca2, Object param, int cp) throws StructureException

  Aligns ca1 with ca2 permuted by cp residues.

  WARNING: Modifies ca2 during the permutation. Be sure to make a copy before calling this method.

  Parameters:

  ca1 -

  ca2 -

  param -

  cp -

  Returns:

  Throws:

  StructureException

• align

  public AFPChain align(Atom[] ca1, Atom[] ca2, Object param) throws StructureException

  Finds the optimal alignment between two proteins allowing for a circular permutation (CP). The precise algorithm is controlled by the parameters. If the parameter tryAllCPs is true, all possible CP sites are tried and the optimal site is returned. Otherwise, the cpPoint parameter is used to determine the CP point, greatly reducing the computation required.

  Specified by:

  align in interface StructureAlignment

  Overrides:

  align in class CeMain

  Parameters:

  ca1 - CA atoms of the first protein

  ca2 - CA atoms of the second protein

  param - CeParameters object

  Returns:

  The best-scoring alignment

  Throws:

  StructureException

  See Also:

  • alignOptimal(Atom[], Atom[], Object, AFPChain[])

• alignOptimal

  public AFPChain alignOptimal(Atom[] ca1, Atom[] ca2, Object param, AFPChain[] alignments) throws StructureException

  Finds the optimal alignment between two proteins allowing for a circular permutation (CP). This algorithm performs a CE alignment for each possible CP site. This is quite slow. Use #alignHeuristic(Atom[], Atom[], Object) for a faster algorithm.

  Parameters:

  ca1 - CA atoms of the first protein

  ca2 - CA atoms of the second protein

  param - CeParameters object

  alignments - If not null, should be an empty array of the same length as ca2. This will be filled with the alignments from permuting ca2 by 0 to n-1 residues.

  Returns:

  The best-scoring alignment

  Throws:

  StructureException

• main

  public static void main(String[] args)