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

Class CeMain

java.lang.Object

org.biojava.nbio.structure.align.AbstractStructureAlignment

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

All Implemented Interfaces:

StructureAlignment

Direct Known Subclasses:

CeCPMain, CeSideChainMain, OptimalCECPMain

public class CeMain
extends AbstractStructureAlignment
implements StructureAlignment

The main class of the Java implementation of the Combinatorial Extension Algorithm (CE), as has been originally developed by I. Shindyalov and P.Bourne (1998). The original CE paper is available from here: http://peds.oxfordjournals.org/cgi/content/short/11/9/739 For a demo of how to use this algorithm, visit the BioJava web site: CE usage example. The BioJava CE version is based on CE version 2.3 (2003 or 2004).

Author:

Andreas Prlic.

Field Summary

Fields

Modifier and Type	Field	Description
static String	algorithmName
protected CECalculator	calculator
protected CeParameters	params
static String	version	version history: 1.2 - Added more parameters to the command line, including -maxOptRMSD 1.1 - Additional parameters 1.0 - Initial port from C code

Constructor Summary

Constructors

Constructor	Description
CeMain()

Method Summary

Modifier and Type	Method	Description
AFPChain	align(Atom[] ca1, Atom[] ca2)	Run an alignment while specifying the atoms to be aligned.
AFPChain	align(Atom[] ca1, Atom[] ca2, Object param)	Align ca2 onto ca1.
String	getAlgorithmName()	Get the name of the Algorithm
CECalculator	getCECalculator()
ConfigStrucAligParams	getParameters()	Return the paramers for this algorithm.
String	getVersion()	Get the Version information for this Algorithm.
static void	main(String[] args)	Example Parameters: -pdbFilePath /tmp -autoFetch -printCE -pdb1 1cnv -pdb2 3cna
void	setParameters(ConfigStrucAligParams params)	Set the default parameters for this algorithm to use

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: 1.2 - Added more parameters to the command line, including -maxOptRMSD 1.1 - Additional parameters 1.0 - Initial port from C code

See Also:

Constant Field Values

params

protected CeParameters params

calculator

protected CECalculator calculator

Constructor Detail

CeMain

public CeMain()

Method Detail

main

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

Example Parameters: -pdbFilePath /tmp -autoFetch -printCE -pdb1 1cnv -pdb2 3cna

Throws:

Exception

align

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

Align ca2 onto ca1.

Specified by:

align in interface StructureAlignment

Specified by:

align in class AbstractStructureAlignment

Returns:

the afpChain object that contains the alignment.

Throws:

StructureException

align

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

Description copied from interface: StructureAlignment

Run an alignment while specifying the atoms to be aligned. Will used default parameters for the algorithm.

Specified by:

align in interface StructureAlignment

Specified by:

align in class AbstractStructureAlignment

Returns:

the afpChain object that contains the alignment.

Throws:

StructureException

getAlgorithmName

public String getAlgorithmName()

Description copied from interface: StructureAlignment

Get the name of the Algorithm

Specified by:

getAlgorithmName in interface StructureAlignment

Specified by:

getAlgorithmName in class AbstractStructureAlignment

Returns:

the name of the algorithm

getParameters

public ConfigStrucAligParams getParameters()

Description copied from interface: StructureAlignment

Return the paramers for this algorithm.

Specified by:

getParameters in interface StructureAlignment

Specified by:

getParameters in class AbstractStructureAlignment

Returns:

The returned object will be a Java bean.

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

Specified by:

setParameters in class AbstractStructureAlignment

getVersion

public String getVersion()

Description copied from interface: StructureAlignment

Get the Version information for this Algorithm.

Specified by:

getVersion in interface StructureAlignment

Specified by:

getVersion in class AbstractStructureAlignment

Returns:

the version of the algorithm

getCECalculator

public CECalculator getCECalculator()