mmtf-python
A decoding libary for the PDB mmtf format
Decision gist · record as of 2026-08-14
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.AI-flagged interpretation of the facts on this page — verify before relying
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 · maintenance · safety
Apache 2.0 (permissive) — 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.
last release 2022-07-06 (1500 days) · last repo commit 2022-07-07 · 45 stars
0 known vulnerabilities (OSV.dev, 2026-08-14) · 290,159 downloads/mo, #7,993 on PyPI
Alternatives
Verify before relying
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")- 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
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 on it.
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
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
| License | Apache 2.0 permissive |
| Python support | Not specified |
| Install friction | Low. Pure-Python wheel |
| Runtime dependencies | 1 packagemsgpack |
| Maintenance | Abandoned 1,500 days since the last release |
| Last repo commit | |
| First released | |
| Downloads | 290,159 / month, #7,993 on PyPI 30-day window, as of 2026-08-14 |
| Known vulnerabilities | None known OSV.dev, checked 2026-08-14 |
| Classifiers | Development Status :: 5 - Production/StableIntended Audience :: DevelopersLicense :: OSI Approved :: MIT LicenseProgramming Language :: Python :: 2Programming Language :: Python :: 2.6Programming Language :: Python :: 2.7Programming Language :: Python :: 3Programming Language :: Python :: 3.2Programming Language :: Python :: 3.3Programming Language :: Python :: 3.4Programming Language :: Python :: 3.5Programming Language :: Python :: 3.6Programming Language :: Python :: 3.7Programming Language :: Python :: 3.8Programming Language :: Python :: 3.9Topic :: Software Development :: Build Tools |
Evidence: mmtf_python-1.1.3-py2.py3-none-any.whl
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See also gemmi · mmcif · biotite · pdb2pqr · python-libsbml · py3Dmol · fastpdb · bech32m · pinder · databento-dbn