java.lang.Object
- org.biojava.nbio.structure.align.pairwise.FragmentPair

```
public class FragmentPair
extends Object
```
a pair of fragments of two protein structures

Since:

1.5

Version:

%I% %G%

Author:

Andreas Prlic

Constructor Summary

Constructors
Constructor Description

FragmentPair(int length, int p1, int p2)

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`Object`	`clone()`
`Atom`	`getCenter1()`
`Atom`	`getCenter2()`
`int`	`getCluster()`
`int`	`getContacts()`
`int`	`getCovered()`
`int`	`getLength()`
`int`	`getPos1()`
`int`	`getPos2()`
`double`	`getRms()`
`Matrix`	`getRot()`
`Atom`	`getTrans()`
`Atom`	`getUnitv()`
`int`	`getUsed()`
`void`	`setCenter1(Atom center1)`
`void`	`setCenter2(Atom center2)`
`void`	`setCluster(int cluster)`
`void`	`setContacts(int contacts)`
`void`	`setCovered(int covered)`
`void`	`setLength(int length)`
`void`	`setPos1(int pos1)`
`void`	`setPos2(int pos2)`
`void`	`setRms(double rms)`
`void`	`setRot(Matrix rot)`
`void`	`setTrans(Atom trans)`
`void`	`setUnitv(Atom unitv)`
`void`	`setUsed(int used)`
`String`	`toString()`

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

Constructor Detail

FragmentPair

public FragmentPair(int length,
                    int p1,
                    int p2)

Method Detail

clone
```
public Object clone()
```
Overrides:

clone in class Object

getCluster
```
public int getCluster()
```

setCluster

public void setCluster(int cluster)

getContacts
```
public int getContacts()
```

setContacts

public void setContacts(int contacts)

getCovered
```
public int getCovered()
```

setCovered

public void setCovered(int covered)

getLength
```
public int getLength()
```

setLength
```
public void setLength(int length)
```

getPos1
```
public int getPos1()
```

setPos1
```
public void setPos1(int pos1)
```

getPos2
```
public int getPos2()
```

setPos2
```
public void setPos2(int pos2)
```

getRms
```
public double getRms()
```

setRms
```
public void setRms(double rms)
```

getRot
```
public Matrix getRot()
```

setRot
```
public void setRot(Matrix rot)
```

getTrans
```
public Atom getTrans()
```

setTrans
```
public void setTrans(Atom trans)
```

getUnitv
```
public Atom getUnitv()
```

setUnitv
```
public void setUnitv(Atom unitv)
```

getUsed
```
public int getUsed()
```

setUsed
```
public void setUsed(int used)
```

getCenter1
```
public Atom getCenter1()
```

setCenter1

public void setCenter1(Atom center1)

getCenter2
```
public Atom getCenter2()
```

setCenter2

public void setCenter2(Atom center2)

toString
```
public String toString()
```
Overrides:

toString in class Object

Class FragmentPair

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

FragmentPair

Method Detail

clone

getCluster

setCluster

getContacts

setContacts

getCovered

setCovered

getLength

setLength

getPos1

setPos1

getPos2

setPos2

getRms

setRms

getRot

setRot

getTrans

setTrans

getUnitv

setUnitv

getUsed

setUsed

getCenter1

setCenter1

getCenter2

setCenter2

toString