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sbliven merged 6 commits into from
Dec 9, 2014
Merged

Completing tutorial #2

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8fbb185
Linking to new chapters
josemduarte Dec 9, 2014
e6df557
Update crystal-contacts.md
josemduarte Dec 9, 2014
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Update README.md
josemduarte Dec 9, 2014
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Adding asa chapter
josemduarte Dec 9, 2014
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Update asa.md
josemduarte Dec 9, 2014
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josemduarte Dec 9, 2014
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16 changes: 12 additions & 4 deletions structure/README.md
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Expand Up @@ -27,6 +27,7 @@ A tutorial for the protein structure modules of [BioJava](http://www.biojava.org

This tutorial is split into several chapters.


Chapter 1 - Quick [Installation](installation.md)

Chapter 2 - [First Steps](firststeps.md)
Expand All @@ -47,13 +48,20 @@ Chapter 9 - [Biological Assemblies](bioassembly.md)

Chapter 10 - [External Databases](externaldb.md) like SCOP & CATH

Chapter 11 - Protein Symmetry
Chapter 11 - [Accessible Surface Areas](asa.md)

Chapter 12 - [Contacts within a chain and between chains](contact-map.md)

Chapter 13 - Finding all interfaces in crystal: [crystal contacts](crystal-contacts.md)

Chapter 14 - Protein Symmetry

Chapter 15 - Bonds

Chapter 12 - Bonds
Chapter 16 - [Special Cases](special.md)

Chapter 13 - [Special Cases](special.md)
Chapter 17 - [Lists](lists.md) of PDB IDs and PDB [status information](lists.md).

Chapter 14 - [Lists](lists.md) of PDB IDs and PDB [status information](lists.md).

### Author:

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36 changes: 36 additions & 0 deletions structure/asa.md
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@@ -0,0 +1,36 @@
# Calculating Accessible Surface Areas

BioJava can also do calculation of Accessible Surface Areas (ASA) through an implementation of the rolling ball algorithm of Shrake and Rupley [Shrake 1973].

This code will do the ASA calculation and output the values per residue and the total:
```java
AtomCache cache = new AtomCache();
cache.setUseMmCif(true);

StructureIO.setAtomCache(cache);

Structure structure = StructureIO.getStructure("1smt");

AsaCalculator asaCalc = new AsaCalculator(structure,
AsaCalculator.DEFAULT_PROBE_SIZE,
1000, 1, false);

GroupAsa[] groupAsas = asaCalc.getGroupAsas();

double tot = 0;

for (GroupAsa groupAsa: groupAsas) {
System.out.printf("%1s\t%5s\t%3s\t%6.2f\n",
groupAsa.getGroup().getChainId(),
groupAsa.getGroup().getResidueNumber(),
groupAsa.getGroup().getPDBName(),
groupAsa.getAsaU());
tot+=groupAsa.getAsaU();
}

System.out.printf("Total area: %9.2f\n",tot);

```
See [DemoAsa](https://github.com/biojava/biojava/blob/master/biojava3-structure/src/main/java/demo/DemoAsa.java) for a fully working demo.

[Shrake 1973]: http://www.sciencedirect.com/science/article/pii/0022283673900119
13 changes: 13 additions & 0 deletions structure/crystal-contacts.md
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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();
}
```