The macromolecular transmission format (MMTF) is a binary encoding of biological structures.

This repository holds the Java API, encoding and decoding libraries. Along with a description of the data in the MMTF using Java data types.

The alpha release is available on Maven central.

<artifactId>mmtf-decoder</artifactId>
<packaging>pom</packaging>
<version>0.0.1-alpha1</version>

<artifactId>mmtf-api</artifactId>
<packaging>pom</packaging>
<version>0.0.1-alpha1</version>

Or you can clone this repo and install yourself.

Quick getting started.

1. Get the data for a PDB structure and print the number of chains:

HandleIO handleIO = new HandleIO();
DataApiInterface dataApi = handleIO.getDataApiFromUrlOrFile("4cup");
System.out.println("PDB Code: "+dataApi.getPdbId()+" has "+dataApi.getNumChains()+" chains");

2. Show the charge information for the first group:

PDBGroup pdbGroup = dataApi.getGroupMap().get(0);
System.out.println("HET group "+pdbGroup.getGroupName()+" has the following atomic charges: "+pdbGroup.getAtomCharges());

3. Show how many bioassemblies it has:

System.out.println("PDB Code: "+dataApi.getPdbId()+" has "+dataApi.getBioAssembly().size()+" bioassemblies");