biotraj
Basic trajectory file format functionality for Biotite; forked from MDTraj
Decision gist · record as of 2026-08-14
Yes, if you are using Biotite or need lightweight trajectory I/O for XTC, TRR, NetCDF, or DCD files. The package is stable and dependency-light (numpy, scipy only). However, maintenance is aging (last release 650 days ago), so verify that the formats you need are fully supported and check Biotite's current requirements before installing. Not recommended as a standalone replacement for MDTraj unless you have a specific license constraint.AI-flagged interpretation of the facts on this page — verify before relying
Before you install
- Requires numpy and scipy; Python >= 3.10 is required.
- Medium install friction due to compiled wheels across multiple Python versions and platforms (3.10–3.13, macOS, Linux, Windows).
- Maintenance is aging—last release was 650 days ago, though the repository remains active and the package is a dependency for Biotite.
License · maintenance · safety
copyleft license (copyleft) — Licensed under GNU Lesser General Public License v2.1 or later (copyleft). If you distribute software that links biotraj, you must provide source code and allow recipients to modify and relink the library; proprietary applications can use it but must comply with LGPLv2+ terms.
last release 2024-11-02 (650 days) · last repo commit 2025-09-22 · 1 stars
0 known vulnerabilities (OSV.dev, 2026-08-14) · 2,207,289 downloads/mo, #3,211 on PyPI
Alternatives
Verify before relying
import biotraj
# Load a trajectory file
traj = biotraj.load('trajectory.xtc', top='topology.pdb')
# Save to a different format
biotraj.save('output.dcd', traj)- Whether biotraj can be used independently or is intended only as a Biotite dependency despite being on PyPI.
- Performance characteristics and memory efficiency for large trajectory files.
- Completeness of format support relative to the original MDTraj library.
What it is and what it does
biotraj is a minimal, standalone library for reading and writing molecular dynamics trajectory files. It is extracted from the larger MDTraj project and provides I/O functionality for XTC, TRR, NetCDF, and DCD formats—the standard file types produced by molecular dynamics simulations. The package exists primarily as a dependency for Biotite, a bioinformatics toolkit, because Biotite cannot directly integrate MDTraj due to license incompatibility.
The package depends only on numpy and scipy, making it lightweight for trajectory file operations. It is classified as Beta (Development Status 4) and targets researchers and developers working with biomolecular simulation data. The library is not intended as a general-purpose replacement for MDTraj but rather as a focused tool for trajectory I/O when Biotite's license constraints apply.
Use it for
- Load molecular dynamics simulation trajectories in XTC or TRR format for analysis within Biotite workflows.
- Convert trajectory files between supported formats (XTC, TRR, NetCDF, DCD) for compatibility with different simulation engines.
- Extract trajectory data programmatically in Python without requiring the full MDTraj installation.
- Integrate trajectory file handling into bioinformatics pipelines that use Biotite as a dependency.
Worth the install?
AI-flagged interpretation of the facts on this page. Verify before relying on it.
Yes, if you are using Biotite or need lightweight trajectory I/O for XTC, TRR, NetCDF, or DCD files.
The package is stable and dependency-light (numpy, scipy only). However, maintenance is aging (last release 650 days ago), so verify that the formats you need are fully supported and check Biotite's current requirements before installing. Not recommended as a standalone replacement for MDTraj unless you have a specific license constraint.
Install
biotraj on PyPI
Before you install
Medium install friction due to compiled wheels across multiple Python versions and platforms (3.10–3.13, macOS, Linux, Windows). Maintenance is aging—last release was 650 days ago, though the repository remains active and the package is a dependency for Biotite.
Requires numpy and scipy; Python >= 3.10 is required.
License in practice
Licensed under GNU Lesser General Public License v2.1 or later (copyleft). If you distribute software that links biotraj, you must provide source code and allow recipients to modify and relink the library; proprietary applications can use it but must comply with LGPLv2+ terms.
Quickstart
import biotraj
# Load a trajectory file
traj = biotraj.load('trajectory.xtc', top='topology.pdb')
# Save to a different format
biotraj.save('output.dcd', traj)Verify before relying
- Whether biotraj can be used independently or is intended only as a Biotite dependency despite being on PyPI.
- Performance characteristics and memory efficiency for large trajectory files.
- Completeness of format support relative to the original MDTraj library.
Package facts
| License | copyleft license copyleft |
| Python support | Supports the current Python release >=3.10 |
| Install friction | Medium. Platform-specific wheel |
| Runtime dependencies | 2 packagesnumpyscipy |
| Maintenance | Aging 650 days since the last release |
| Last repo commit | |
| First released | |
| Downloads | 2,207,289 / month, #3,211 on PyPI 30-day window, as of 2026-08-14 |
| Known vulnerabilities | None known OSV.dev, checked 2026-08-14 |
| Classifiers | Development Status :: 4 - BetaIntended Audience :: DevelopersIntended Audience :: Science/ResearchLicense :: OSI Approved :: GNU Lesser General Public License v2 or later (LGPLv2+)Natural Language :: EnglishOperating System :: MacOSOperating System :: Microsoft :: WindowsOperating System :: POSIX :: LinuxProgramming Language :: Python :: 3Programming Language :: Python :: Implementation :: CPythonTopic :: Scientific/Engineering :: Bio-Informatics |
Evidence: biotraj-1.2.2-cp310-cp310-macosx_10_9_x86_64.whl; biotraj-1.2.2-cp310-cp310-macosx_11_0_arm64.whl; biotraj-1.2.2-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl; biotraj-1.2.2-cp310-cp310-win_amd64.whl; biotraj-1.2.2-cp311-cp311-macosx_10_9_x86_64.whl; biotraj-1.2.2-cp311-cp311-macosx_11_0_arm64.whl; biotraj-1.2.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl; biotraj-1.2.2-cp311-cp311-win_amd64.whl; biotraj-1.2.2-cp312-cp312-macosx_10_9_x86_64.whl; biotraj-1.2.2-cp312-cp312-macosx_11_0_arm64.whl; biotraj-1.2.2-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl; biotraj-1.2.2-cp312-cp312-win_amd64.whl; biotraj-1.2.2-cp313-cp313-macosx_10_13_x86_64.whl; biotraj-1.2.2-cp313-cp313-macosx_11_0_arm64.whl; biotraj-1.2.2-cp313-cp313-manylinux_2_17_x86_64.manylinux2014_x86_64.whl; biotraj-1.2.2-cp313-cp313-win_amd64.whl
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