In the beginning, just one quick paragraph of how to get access to BioJava.
BioJava is open source and you can get the code from Github, however it might be easier this way:
BioJava uses Maven as a build and distribution system. If you are new to Maven, take a look at the Getting Started with Maven guide.
As of version 4, BioJava is available in maven central. This is all you would need to add a BioJava dependency to your projects:
<dependencies>
...
<dependency>
<!-- This imports the latest SNAPSHOT builds from the protein structure modules of BioJava.
-->
<groupId>org.biojava</groupId>
<artifactId>biojava-structure</artifactId>
<version>4.2.0</version>
</dependency>
<!-- if you want to use the visualisation tools you need also this one: -->
<dependency>
<groupId>org.biojava</groupId>
<artifactId>biojava-structure-gui</artifactId>
<version>4.2.0</version>
</dependency>
<!-- other biojava jars as needed -->
</dependencies> If you run
mvn package
on your project, the BioJava dependencies will be automatically downloaded and installed for you.
BioJava can be configured through several properties:
| Property | Description |
|---|---|
PDB_DIR |
Directory for caching structure files from the PDB. Mirrors the PDB's FTP server directory structure, with PDB_DIR equivalent to ftp://ftp.wwpdb.org/pub/pdb/. Default: temp directory |
PDB_CACHE_DIR |
Cache directory for other files related to the structure package. Default: temp directory |
These can be set either as java properties or as environmental variables. For example:
# This could be added to .bashrc
export PDB_DIR=...
# Or override for a particular execution
java -DPDB_DIR=... -cp ...
Note that your IDE may ignore .bashrc settings, but should have a preference for passing VM arguments.
Navigation: Home | Book 3: The Structure Modules | Chapter 1 : Installation
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