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.
Releases are available on Maven central.
<dependency>
<groupId>org.rcsb</groupId>
<artifactId>mmtf-codec</artifactId>
<version>1.0.7</version>
</dependency>
<dependency>
<groupId>org.rcsb</groupId>
<artifactId>mmtf-api</artifactId>
<version>1.0.7</version>
</dependency>
Quick getting started.
- Get the data for a PDB structure and print the number of chains:
StructureDataInterface dataInterface = new GenericDecoder(ReaderUtils.getDataFromUrl("4CUP"));
System.out.println("PDB Code: "+dataInterface.getStructureId()+" has "+dataInterface.getNumChains()+" chains");
- Show the charge information for the first group:
System.out.println("Group name: "+dataInterface.getGroupName(0)+" has the following atomic charges: "+dataInterface.getGroupAtomCharges(0));
- Show how many bioassemblies it has:
System.out.println("PDB Code: "+dataInterface.getStructureId()+" has "+dataInterface.getNumBioassemblies()+" bioassemblies");