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

java.lang.Object
  extended by org.biojava.bio.structure.align.AbstractStructureAlignment
      extended by org.biojava.bio.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
static String algorithmName
           
protected  CECalculator calculator
           
protected  CeParameters params
           
static String version
           
 
Fields inherited from class org.biojava.bio.structure.align.AbstractStructureAlignment
newline
 
Constructor Summary
CeMain()
           
 
Method Summary
 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 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 CeParameters params

calculator

protected CECalculator calculator
Constructor Detail

CeMain

public CeMain()
Method Detail

main

public static void main(String[] args)
Example Parameters: -pdbFilePath /tmp -autoFetch -printCE -pdb1 1cnv -pdb2 3cna


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()