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Merged
sbliven merged 6 commits into from
Dec 9, 2014
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Completing tutorial #2

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Update crystal-contacts.md
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josemduarte committed Dec 9, 2014
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Expand Up @@ -44,4 +44,17 @@ The algorithm to find all unique interfaces in the crystal works roughly like th

See [DemoCrystalInterfaces](https://github.com/biojava/biojava/blob/master/biojava3-structure/src/main/java/demo/DemoCrystalInterfaces.java) for a fully working demo of the example above.

## Clustering the interfaces
One can also cluster the interfaces based on their similarity. The similarity is measured through contact overlap: number of common contacts over average number of contact in both chains. The clustering can be done as following:

```java
List<StructureInterfaceCluster> clusters = interfaces.getClusters();
for (StructureInterfaceCluster cluster:clusters) {
System.out.print("Cluster "+cluster.getId()+" members: ");
for (StructureInterface member:cluster.getMembers()) {
System.out.print(member.getId()+" ");
}
System.out.println();
}
```