Package org.biojava.nbio.structure.align.ce

Class CeCPMain

java.lang.Object

org.biojava.nbio.structure.align.AbstractStructureAlignment

org.biojava.nbio.structure.align.ce.CeMain

org.biojava.nbio.structure.align.ce.CeCPMain

All Implemented Interfaces:

StructureAlignment

public class CeCPMain
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.

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
protected static class	CeCPMain.CPRange	Tiny wrapper for the disallowed regions of an alignment.

Field Summary

Fields

Modifier and Type	Field	Description
static String	algorithmName
static String	version	version history: 1.5 - Added more parameters to the command line, including -maxOptRMSD 1.4 - Added DuplicationHint parameter & default to duplicating the shorter chain 1.3 - Short CPs are now discarded 1.2 - now supports check AlignmentTools.isSequentialAlignment.

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

calculator, params

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

newline

Constructor Summary

Constructors

Constructor	Description
CeCPMain()

Method Summary

Modifier and Type	Method	Description
AFPChain	align(Atom[] ca1, Atom[] ca2, Object param)	Aligns ca1 and ca2 using a heuristic to check for CPs.
protected static CeCPMain.CPRange	calculateMinCP(int[] block, int blockLen, int ca2len, int minCPlength)	Finds the alignment index of the residues minCPlength before and after the duplication.
static AFPChain	filterDuplicateAFPs(AFPChain afpChain, CECalculator ceCalc, Atom[] ca1, Atom[] ca2duplicated)	Takes as input an AFPChain where ca2 has been artificially duplicated.
static AFPChain	filterDuplicateAFPs(AFPChain afpChain, CECalculator ceCalc, Atom[] ca1, Atom[] ca2duplicated, CECPParameters params)
String	getAlgorithmName()	Get the name of the Algorithm
String	getVersion()	Get the Version information for this Algorithm.
AFPChain	invertAlignment(AFPChain a)	Swaps the order of structures in an AFPChain
static void	main(String[] args)
static AFPChain	postProcessAlignment(AFPChain afpChain, Atom[] ca1, Atom[] ca2m, CECalculator calculator)	Circular permutation specific code to be run after the standard CE alignment
static AFPChain	postProcessAlignment(AFPChain afpChain, Atom[] ca1, Atom[] ca2m, CECalculator calculator, CECPParameters param)	Circular permutation specific code to be run after the standard CE alignment

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

align, getCECalculator, getParameters, setParameters

Methods inherited from class java.lang.Object

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

Field Detail

algorithmName

public static final String algorithmName

See Also:

Constant Field Values

version

public static final String version

version history: 1.5 - Added more parameters to the command line, including -maxOptRMSD 1.4 - Added DuplicationHint parameter & default to duplicating the shorter chain 1.3 - Short CPs are now discarded 1.2 - now supports check AlignmentTools.isSequentialAlignment. XML protocol 1.1 - skipped, (trying to avoid confusion with jfatcat in all vs. all comparisons) 1.0 - initial release

See Also:

Constant Field Values

Constructor Detail

CeCPMain

public CeCPMain()

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

main

public static void main(String[] args)
                 throws ConfigurationException

Throws:

ConfigurationException

align

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

Aligns ca1 and ca2 using a heuristic to check for CPs.

Aligns ca1 against a doubled ca2, then cleans up the alignment.

Specified by:

align in interface StructureAlignment

Overrides:

align in class CeMain

Parameters:

ca1 -

ca2 -

param -

Returns:

the alignment, possibly containing a CP.

Throws:

StructureException

postProcessAlignment

public static AFPChain postProcessAlignment(AFPChain afpChain,
                                            Atom[] ca1,
                                            Atom[] ca2m,
                                            CECalculator calculator)
                                     throws StructureException

Circular permutation specific code to be run after the standard CE alignment

Parameters:

afpChain - The finished alignment

ca1 - CA atoms of the first protein

ca2m - A duplicated copy of the second protein

calculator - The CECalculator used to create afpChain

Throws:

StructureException

postProcessAlignment

public static AFPChain postProcessAlignment(AFPChain afpChain,
                                            Atom[] ca1,
                                            Atom[] ca2m,
                                            CECalculator calculator,
                                            CECPParameters param)
                                     throws StructureException

Circular permutation specific code to be run after the standard CE alignment

Parameters:

afpChain - The finished alignment

ca1 - CA atoms of the first protein

ca2m - A duplicated copy of the second protein

calculator - The CECalculator used to create afpChain

param - Parameters

Throws:

StructureException

invertAlignment

public AFPChain invertAlignment(AFPChain a)

Swaps the order of structures in an AFPChain

Parameters:

a -

Returns:

filterDuplicateAFPs

public static AFPChain filterDuplicateAFPs(AFPChain afpChain,
                                           CECalculator ceCalc,
                                           Atom[] ca1,
                                           Atom[] ca2duplicated)
                                    throws StructureException

Takes as input an AFPChain where ca2 has been artificially duplicated. This raises the possibility that some residues of ca2 will appear in multiple AFPs. This method filters out duplicates and makes sure that all AFPs are numbered relative to the original ca2.

The current version chooses a CP site such that the length of the alignment is maximized.

This method does not update scores to reflect the filtered alignment. It does update the RMSD and superposition.

Parameters:

afpChain - The alignment between ca1 and ca2-ca2. Blindly assumes that ca2 has been duplicated.

Returns:

A new AFPChain consisting of ca1 to ca2, with each residue in at most 1 AFP.

Throws:

StructureException

filterDuplicateAFPs

public static AFPChain filterDuplicateAFPs(AFPChain afpChain,
                                           CECalculator ceCalc,
                                           Atom[] ca1,
                                           Atom[] ca2duplicated,
                                           CECPParameters params)
                                    throws StructureException

Throws:

StructureException

calculateMinCP

protected static CeCPMain.CPRange calculateMinCP(int[] block,
                                                 int blockLen,
                                                 int ca2len,
                                                 int minCPlength)

Finds the alignment index of the residues minCPlength before and after the duplication.

Parameters:

block - The permuted block being considered, generally optAln[0][1]

blockLen - The length of the block (in case extra memory was allocated in block)

ca2len - The length, in residues, of the protein specified by block

minCPlength - The minimum number of residues allowed for a CP

Returns:

a CPRange with the following components:

n

Index into block of the residue such that minCPlength residues remain to the end of ca2len, or -1 if no residue fits that criterium.

mid

Index of the first residue higher than ca2len.

c

Index of minCPlength-th residue after ca2len, or ca2len*2 if no residue fits that criterium.