FatCat

java.lang.Object

org.biojava.nbio.structure.align.fatcat.FatCat

Direct Known Subclasses:: FatCatFlexible, FatCatRigid

public class FatCat extends Object

Field Summary

Fields

Modifier and Type

Field

Description

static final String

algorithmName

static String

newline

static final String

VERSION

version history: 1.1 - Added more parameters to the command line 1.0 - Initial version
Constructor Summary

Constructors

Constructor

Description

FatCat()
Method Summary

Modifier and Type

Method

Description

protected AFPChain

align(Atom[] ca1, Atom[] ca2, FatCatParameters params, boolean doRigid)

AFPChain

alignFlexible(Atom[] ca1, Atom[] ca2, FatCatParameters params)

AFPChain

alignRigid(Atom[] ca1, Atom[] ca2)

AFPChain

alignRigid(Atom[] ca1, Atom[] ca2, FatCatParameters params)

FatCatAligner

getFatCatAligner()

static void

main(String[] argv)

See demo/FatCatDemo.java for an example how to run.

String

toString()

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Details
- VERSION
  
  public static final String VERSION
  
  version history: 1.1 - Added more parameters to the command line 1.0 - Initial version
  See Also:
  
  Constant Field Values
- newline
  
  public static String newline
- algorithmName
  
  public static final String algorithmName
  See Also:
  
  Constant Field Values
Constructor Details
- FatCat
  
  public FatCat()
Method Details
- main
  
  public static void main(String[] argv) throws ConfigurationException
  
  See demo/FatCatDemo.java for an example how to run. Launch FatCat from command line. Parameters are:
  
  Parameters:
  
  argv -
  
  Throws:
  
  ConfigurationException
- toString
  
  public String toString()
  
  Overrides:
  
  toString in class Object
- alignRigid
  
  public AFPChain alignRigid(Atom[] ca1, Atom[] ca2) throws StructureException
  
  Throws:
  
  StructureException
- alignRigid
  
  public AFPChain alignRigid(Atom[] ca1, Atom[] ca2, FatCatParameters params) throws StructureException
  
  Throws:
  
  StructureException
- alignFlexible
  
  public AFPChain alignFlexible(Atom[] ca1, Atom[] ca2, FatCatParameters params) throws StructureException
  
  Throws:
  
  StructureException
- align
  
  protected AFPChain align(Atom[] ca1, Atom[] ca2, FatCatParameters params, boolean doRigid) throws StructureException
  
  Throws:
  
  StructureException
- getFatCatAligner
  
  public FatCatAligner getFatCatAligner()