Welcome to mmtf-python’s documentation!

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

This repository holds the Python 2 and 3 compatible API, encoding and decoding libraries.

The MMTF python API is available from pip:

pip install mmtf-python

Quick getting started.

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

    from mmtf import fetch
# Get the data for 4CUP
decoded_data = fetch("4CUP")
print("PDB Code: "+str(decoded_data.structure_id)+" has "+str(decoded_data.num_chains)+" chains")

  2. Show the charge information for the first group:

    print("Group name:"+str(decoded_data.group_list[0]["groupName"])+"has the following atomic charges: "+",".join([str(x) for x in decoded_data.group_list[0]["formalChargeList"]]))

  3. Show how many bioassemblies it has:

    print("PDB Code:"+str(decoded_data.structure_id)+" has "+str(len(decoded_data.bio_assembly))+" bioassemblies")

Indices and tables