```
public class JointFragments
extends Object
```
A utility class that defines which set of atoms are considered to be on equivalent positions.

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`add(int p1, int p2, int start, int end)`
`List<int[]>`	`getIdxlist()`
`double`	`getRms()`
`void`	`setIdxlist(List<int[]> idxs)`	Stores the alignment between the residues of several fragments.
`void`	`setRms(double rms)`
`String`	`toString()`

setIdxlist
```
public void setIdxlist(List<int[]> idxs)
```
Stores the alignment between the residues of several fragments. Each int[] stores the residue numbers of several equivalent residues.

public void add(int p1,
                int p2,
                int start,
                int end)

Class JointFragments