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 final String

algorithmName

protected CECalculator

calculator

protected CeParameters

params

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

Fields inherited from class org.biojava.nbio.structure.align.AbstractStructureAlignment
newline
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 Details
- 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 Details
- CeMain
  
  public CeMain()
Method Details
- 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()

Class CeMain

Field Summary

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

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Details

algorithmName

version

params

calculator

Constructor Details

CeMain

Method Details

main

align

align

getAlgorithmName

getParameters

setParameters

getVersion

getCECalculator