mmtf-python

What it is and what it does

mmtf-python is a library for working with the macromolecular transmission format (MMTF), a binary encoding standard for biological structures maintained by the Protein Data Bank (PDB). It provides both encoding and decoding capabilities, plus a convenience API to fetch structure data directly from PDB by structure ID.

The package lets you load PDB structures into Python as decoded objects with properties like structure_id, num_chains, group_list (atomic information), and bio_assembly data. It depends only on msgpack for binary serialization. The library is stable and production-ready according to its classifier, but development has stalled since mid-2022 with no recent commits or releases.

Use it for:

• Fetch and analyze PDB protein structures programmatically by structure ID
• Extract atomic charge information and group properties from biological structures
• Count chains and bioassemblies in a protein structure for structural analysis
• Decode MMTF binary files into Python objects for computational biology workflows
• Build bioinformatics pipelines that need lightweight, standardized structure data access

Worth the install?

AI-flagged interpretation of the facts on this page — verify before relying

Decodes and encodes the macromolecular transmission format (MMTF), a binary encoding for biological structures, and provides a Python API to fetch and inspect PDB structure data.

Yes, if you need to work with PDB structures in Python and can tolerate an unmaintained package. The library is stable, has no known vulnerabilities, and a single lightweight dependency. However, be aware that it will not receive updates for Python version incompatibilities or format changes. Suitable for read-only structure analysis in established workflows, but risky for new projects expecting long-term support.

Install

mmtf-python on PyPI

pip install mmtf-python

uv add mmtf-python

poetry add mmtf-python

Installing mmtf-python

Before you install

Low install friction with a single lightweight dependency (msgpack). However, the package is abandoned—last release was 2022-07-06 and no commits since then. Not actively maintained, so security updates and compatibility fixes are unlikely.

License in practice

Licensed under Apache 2.0, a permissive license that allows commercial and private use with minimal restrictions, making it safe to use in most projects.

Quickstart

pip install mmtf-python

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

Verify before relying

• Whether msgpack dependency has known vulnerabilities or maintenance issues
• Compatibility with Python versions beyond 3.9 (classifiers list only up to 3.9)
• Whether the MMTF format specification itself has evolved since 2022

Package facts

Evidence: mmtf_python-1.1.3-py2.py3-none-any.whl

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