org.biojava.bio.structure.align.ce
Class OptimalCECPMain

java.lang.Object
  org.biojava.bio.structure.align.AbstractStructureAlignment
      org.biojava.bio.structure.align.ce.CeMain
          org.biojava.bio.structure.align.ce.OptimalCECPMain

All Implemented Interfaces:

StructureAlignment

public class OptimalCECPMain
extends CeMain

A wrapper for CeMain which sets default parameters to be appropriate for finding circular permutations.

A circular permutation consists of a single cleavage point and rearrangement between two structures, for example:

 ABCDEFG
 DEFGABC
 

Author:

Spencer Bliven.

Field Summary

static String	algorithmName
protected OptimalCECPParameters	params
static String	version

Fields inherited from class org.biojava.bio.structure.align.ce.CeMain

calculator

Fields inherited from class org.biojava.bio.structure.align.AbstractStructureAlignment

newline

Constructor Summary

OptimalCECPMain()

Method Summary

AFPChain	align(Atom[] ca1, Atom[] ca2, Object param) Finds the optimal alignment between two proteins allowing for a circular permutation (CP).
AFPChain	alignOptimal(Atom[] ca1, Atom[] ca2, Object param, AFPChain[] alignments) Finds the optimal alignment between two proteins allowing for a circular permutation (CP).
AFPChain	alignPermuted(Atom[] ca1, Atom[] ca2, Object param, int cp) Aligns ca1 with ca2 permuted by cp residues.
String	getAlgorithmName() Get the name of the Algorithm
ConfigStrucAligParams	getParameters() Return the paramers for this algorithm.
String	getVersion() Get the Version information for this Algorithm.
static void	main(String[] args)
void	setParameters(ConfigStrucAligParams params) Set the default parameters for this algorithm to use

Methods inherited from class org.biojava.bio.structure.align.ce.CeMain

align, getCECalculator

Methods inherited from class org.biojava.bio.structure.align.AbstractStructureAlignment

printHelp

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface org.biojava.bio.structure.align.StructureAlignment

printHelp

Field Detail

algorithmName

public static final String algorithmName

See Also:

Constant Field Values

version

public static final String version

See Also:

Constant Field Values

params

protected OptimalCECPParameters params

Constructor Detail

OptimalCECPMain

public OptimalCECPMain()

Method Detail

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)