java.lang.Object
- org.biojava.nbio.structure.align.fatcat.FatCat

Direct Known Subclasses:

FatCatFlexible, FatCatRigid
```
public class FatCat
extends java.lang.Object
```

Field Summary

Fields
Modifier and Type	Field	Description
`static java.lang.String`	`algorithmName`
`static java.lang.String`	`newline`
`static java.lang.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

All Methods Static Methods Instance Methods Concrete Methods
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(java.lang.String[] argv)`	See demo/FatCatDemo.java for an example how to run.
`java.lang.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 java.lang.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 java.lang.String newline
```
- algorithmName
```
public static final java.lang.String algorithmName
```
  See Also:
  
  Constant Field Values

Constructor Detail
- FatCat
```
public FatCat()
```

Method Detail

main
```
public static void main(java.lang.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 java.lang.String toString()
```
Overrides:

toString in class java.lang.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()

Class FatCat

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

VERSION

newline

algorithmName

Constructor Detail

FatCat

Method Detail

main

toString

alignRigid

alignRigid

alignFlexible

align

getFatCatAligner