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Local PDB Installations

BioJava can automatically download and install most of the data files required. Those downloads will happen only once. Future requests for the data file will re-use the local copy.

The main class that provides this functionality is the AtomCache.

It is hidden inside the StructureIO class, that we already encountered earlier.

  Structure structure = StructureIO.getStructure("4hhb");

is the same as

  AtomCache cache = new AtomCache();
  cache.getStructure("4hhb");

Where are the files getting written to?

By default the AtomCache writes all files into a temporary location (The system temp directory "java.io.tempdir").

If you already have a local PDB installation, or you want to use a more permanent location to store the files, you can configure the AtomCache by setting the PDB_DIR system property

    -DPDB_DIR=/wherever/you/want/

An alternative is to hard-code the path in this way:

			AtomCache cache = new AtomCache();

			cache.setPath("/path/to/pdb/files/");