tmtools
Python bindings around the TM-align code for structural alignment of proteins
Decision gist · record as of 2026-08-14
Yes, if you need to compute protein structural alignments and TM-scores in Python. The pre-built wheels make installation straightforward, numpy is a common dependency, and the underlying algorithm is well-established. However, the GPLv3 license requires your project to be open-source; the aging maintenance status (no release in 278 days) suggests limited active development, so evaluate whether you need ongoing support or bug fixes. No known security vulnerabilities.AI-flagged interpretation of the facts on this page — verify before relying
Before you install
- Requires numpy arrays with shape (N, 3) for coordinates; optional BioPython dependency for PDB file parsing must be installed separately.
- Medium install friction due to compiled C++ components; wheels are pre-built for Python 3.10–3.14 on Linux, macOS (x86_64 and ARM64), and Windows, reducing compilation burden.
- Package is aging (278 days since last release) but repository remains active with recent commits.
License · maintenance · safety
GPLv3 (copyleft) — Licensed under GPLv3 (copyleft), which requires derivative works and distributions to also be open-source under GPLv3. The bundled TM-align code is MIT-licensed but the wrapper is GPLv3, so any project using tmtools must comply with GPLv3 terms.
last release 2025-11-09 (278 days) · last repo commit 2025-11-09 · 66 stars
0 known vulnerabilities (OSV.dev, 2026-08-14) · 151,910 downloads/mo, #10,917 on PyPI
Alternatives
Verify before relying
pip install tmtools
import numpy as np
from tmtools import tm_align
coords1 = np.array([[1.2, 3.4, 1.5], [4.0, 2.8, 3.7]])
coords2 = np.array([[2.3, 7.4, 1.5], [4.0, 2.9, -1.7]])
res = tm_align(coords1, coords2, "AY", "AR")
print(res.tm_norm_chain1, res.rmsd)- Whether BioPython integration (optional, for PDB file I/O) is tested or maintained alongside the core library.
- Performance characteristics or scalability limits for large protein structures or batch alignments.
- Whether custom alignment feature is actively used or tested in production workflows.
What it is and what it does
tmtools wraps the TM-align algorithm—a widely-used structural biology tool for aligning protein coordinates—into a Python interface. It takes two sets of 3D atomic coordinates and amino acid sequences, computes the optimal structural alignment, and returns the rotation matrix, translation vector, and TM-score (a normalized similarity metric). The package ships with pre-built wheels for modern Python versions and common platforms, minimizing compilation friction.
The core use case is comparing protein structures to assess similarity or find conserved folds. It supports both automatic alignment discovery and user-supplied alignment strings with gaps, making it useful for hypothesis testing or domain-guided comparisons. Optional integration with BioPython allows direct parsing of PDB files. The package is in alpha status and has not seen a release in several months, though the underlying TM-align algorithm is mature and well-cited in structural biology.
Use it for
- Compare two protein structures to compute their TM-score and optimal superposition for structural similarity assessment.
- Validate a hypothesized protein alignment by supplying a custom alignment string and checking the resulting TM-score.
- Parse PDB files with BioPython and extract coordinates and sequences for downstream structural comparison workflows.
- Batch-compare a query protein structure against a library of known folds to identify homologous structures.
- Integrate structural alignment into a protein design or validation pipeline that requires quantitative similarity metrics.
Worth the install?
AI-flagged interpretation of the facts on this page. Verify before relying on it.
Yes, if you need to compute protein structural alignments and TM-scores in Python.
The pre-built wheels make installation straightforward, numpy is a common dependency, and the underlying algorithm is well-established. However, the GPLv3 license requires your project to be open-source; the aging maintenance status (no release in 278 days) suggests limited active development, so evaluate whether you need ongoing support or bug fixes. No known security vulnerabilities.
Install
tmtools on PyPI
Before you install
Medium install friction due to compiled C++ components; wheels are pre-built for Python 3.10–3.14 on Linux, macOS (x86_64 and ARM64), and Windows, reducing compilation burden. Package is aging (278 days since last release) but repository remains active with recent commits.
Requires numpy arrays with shape (N, 3) for coordinates; optional BioPython dependency for PDB file parsing must be installed separately.
License in practice
Licensed under GPLv3 (copyleft), which requires derivative works and distributions to also be open-source under GPLv3. The bundled TM-align code is MIT-licensed but the wrapper is GPLv3, so any project using tmtools must comply with GPLv3 terms.
Quickstart
pip install tmtools
import numpy as np
from tmtools import tm_align
coords1 = np.array([[1.2, 3.4, 1.5], [4.0, 2.8, 3.7]])
coords2 = np.array([[2.3, 7.4, 1.5], [4.0, 2.9, -1.7]])
res = tm_align(coords1, coords2, "AY", "AR")
print(res.tm_norm_chain1, res.rmsd)Verify before relying
- Whether BioPython integration (optional, for PDB file I/O) is tested or maintained alongside the core library.
- Performance characteristics or scalability limits for large protein structures or batch alignments.
- Whether custom alignment feature is actively used or tested in production workflows.
Package facts
| License | GPLv3 copyleft |
| Python support | Not specified |
| Install friction | Medium. Platform-specific wheel |
| Runtime dependencies | 1 packagenumpy |
| Maintenance | Aging 278 days since the last release |
| Last repo commit | |
| First released | |
| Downloads | 151,910 / month, #10,917 on PyPI 30-day window, as of 2026-08-14 |
| Known vulnerabilities | None known OSV.dev, checked 2026-08-14 |
| Classifiers | Development Status :: 3 - AlphaIntended Audience :: Science/ResearchLicense :: OSI Approved :: GNU General Public License v3 (GPLv3)Programming Language :: Python :: 3Programming Language :: Python :: 3.10Programming Language :: Python :: 3.11Programming Language :: Python :: 3.12Programming Language :: Python :: 3.13Programming Language :: Python :: 3.14Topic :: Scientific/Engineering |
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