A quick tutorial how to work with mmCIF files.
The Protein Data Bank (PDB) has been distributing its archival files as PDB files for a long time. The PDB file format is based on "punchcard"-style rules how to store data in a flat file. With the increasing complexity of macromolecules that are being resolved experimentally, this file format can not be used any more to represent some or the more complex structures. As such, the wwPDB recently announced the transition from PDB to mmCIF/PDBx as the principal deposition and dissemination file format (see here and here).
The mmCIF file format has been around for some time (see Westbrook 2000 and Westbrook 2003 ) BioJava has been supporting mmCIF already for several years. This tutorial is meant to provide a quick introduction into how to parse mmCIF files using BioJava
BioJava uses the CIFTools-java library to parse mmCIF. BioJava then has its own data model that reads PDB and mmCIF files into a biological and chemically meaningful data model (BioJava supports the Chemical Components Dictionary). If you don't want to use that data model, you can still use the CIFTools-java parser, please refer to its documentation. Let's start first with the most basic way of loading a protein structure.
The simplest way to load a PDBx/mmCIF file is by using the StructureIO class.
Structure structure = StructureIO.getStructure("4HHB");
// and let's print out how many atoms are in this structure
System.out.println(StructureTools.getNrAtoms(structure));BioJava automatically downloaded the PDB file for hemoglobin 4HHB and copied it into a temporary location. This demonstrates two things:
- BioJava can automatically download and install files locally
- BioJava by default writes those files into a temporary location (The system temp directory "java.io.tempdir").
If you already have a local PDB installation, you can configure where BioJava should read the files from by setting the PDB_DIR system property
-DPDB_DIR=/wherever/you/want/
By default BioJava is using the BCIF file format for parsing data. In order to switch it to use mmCIF, we can take control over the underlying AtomCache which manages your PDB (and btw. also SCOP, CATH) installations.
AtomCache cache = new AtomCache();
cache.setFiletype(StructureFiletype.CIF);
// if you struggled to set the PDB_DIR property correctly in the previous step,
// you could set it manually like this:
cache.setPath("/tmp/");
StructureIO.setAtomCache(cache);
Structure structure = StructureIO.getStructure("4HHB");
// and let's count how many chains are in this structure.
System.out.println(structure.getChains().size());See other supported file types in the StructureFileType enum.
StructureIO can also access files via URLs and fetch the data dynamically. E.g. the following code shows how to load a file from a remote server.
String u = "http://ftp.wwpdb.org/pub/pdb/data/biounit/mmCIF/divided/nw/4nwr-assembly1.cif.gz";
Structure s = StructureIO.getStructure(u);
System.out.println(s);BioJava can also access local files, by specifying the URL as
file:///path/to/local/file
You can load a BioJava Structure object using the ciftools-java parser with:
InputStream inStream = new FileInputStream(fileName);
// now get the protein structure.
Structure cifStructure = CifStructureConverter.fromInputStream(inStream);BioJava provides a number of algorithms and visualisation tools that you can use to further analyse the structure, or look at it. Here a couple of suggestions for further reads:
- The BioJava Cookbook for protein structures
- How does BioJava represent the content of a PDB/mmCIF file?
- How to calculate a protein structure alignment using BioJava: tutorial or cookbook
- How to work with Groups (AminoAcid, Nucleotide, Hetatom)
See the http://mmcif.rcsb.org/ site for more documentation on mmcif.
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