org.biojava.nbio.structure.align.fatcat

Class 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 and Description
static String	algorithmName
static String	newline
static String	VERSION version history: 1.1 - Added more parameters to the command line 1.0 - Initial version

Constructor Summary

Constructors

Constructor and Description
FatCat()

Method Summary

Modifier and Type	Method and 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 Detail

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 Detail

FatCat

public FatCat()

Method Detail

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()