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Merged
josemduarte merged 5 commits into from
Oct 19, 2015
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Create a chapter for Secondary Structure package #7

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Create new chapter on SS
lafita Oct 19, 2015
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Update chapter to include SS
lafita Oct 19, 2015
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Update footer indices
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Update secstruc.md
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Finish chapter on SS
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Update secstruc.md
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lafita committed Oct 19, 2015
commit f44139b42b6b0bb527706ae720f23c9bdc84cb61
32 changes: 31 additions & 1 deletion structure/secstruc.md
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Expand Up @@ -50,14 +50,44 @@ Following the `DSSP` convention, **BioJava** defines 8 types of secondary struct
S = bend
_ = loop (any other type)

## Prediction of SS in BioJava
## Parsing Secondary Structure in BioJava

Currently there exist two alternatives to parse the secondary structure in **BioJava**: either from the PDB/mmCIF
files of deposited structures (author assignment) or from the output file of a DSSP prediction. Both file types
can be obtained from the PDB serevers, if available, so they can be automatically fetched by BioJava.

Note that the DSSP prediction output is more detailed and complete than the authors assignment.
The choice of one or the other will depend on the use case.

Below you can find some examples of how to parse and assign the SS of a `Structure`:

```java
FileParsingParameters params = new FileParsingParameters();
params.setParseSecStruc(true);

AtomCache cache = new AtomCache();
cache.setFileParsingParams(params);
cache.setUseMmCif(false);

Structure s = cache.getStructure("5pti");
```

For more examples search in the **demo** package for `DemoLoadSecStruc` and `DemoParseSecStruc`.

## Prediction of Secondary Structure in BioJava

### Algorithm

The algorithm implemented in BioJava for the prediction of SS is `DSSP`. It is described in the paper from
[Kabsch W. & Sander C. in 1983](http://onlinelibrary.wiley.com/doi/10.1002/bip.360221211/abstract)
[![pubmed](http://img.shields.io/badge/in-pubmed-blue.svg?style=flat)](http://www.ncbi.nlm.nih.gov/pubmed/6667333).

```java
GuiWrapper.display(afpChain, ca1, ca2);
// Or using the biojava-structure-gui module
StructureAlignmentDisplay.display(afpChain, ca1, ca2);
```

### Data Structures


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