fastpdb
A high performance drop-in replacement for Biotite's PDBFile.
Decision gist · record as of 2026-08-14
Yes, if you are already using biotite for PDB file I/O and performance is a concern—fastpdb is a straightforward, permissively licensed replacement with no API changes. However, the abandoned repository status means no future updates or bug fixes should be expected; install only if the current feature set meets your needs and you are comfortable maintaining a frozen dependency.AI-flagged interpretation of the facts on this page — verify before relying
Before you install
- Requires biotite as a runtime dependency; does not yet support hybrid-36 PDB format.
- Medium install friction due to compiled wheels for multiple Python versions and platforms.
- The package is marked abandoned, though the latest release is recent (2025-05-27).
License · maintenance · safety
permissive license (permissive) — Licensed under a permissive license (BSD), so there are no restrictions on commercial or proprietary use of code that depends on fastpdb.
last release 2025-05-27 (444 days) · last repo commit 2026-06-21 · 43 stars · archived
0 known vulnerabilities (OSV.dev, 2026-08-14) · 117,709 downloads/mo, #12,152 on PyPI
Alternatives
Verify before relying
import fastpdb
in_file = fastpdb.PDBFile.read("path/to/file.pdb")
atom_array = in_file.get_structure(model=1)
out_file = fastpdb.PDBFile()
out_file.set_structure(atom_array)
out_file.write("path/to/another_file.pdb")- Whether the abandoned status will affect long-term compatibility with future Python or dependency updates.
- Scope and completeness of PDB format support beyond the noted absence of hybrid-36 format.
- Real-world performance gains relative to biotite in typical bioinformatics workflows.
What it is and what it does
fastpdb is a Rust-compiled library that provides a drop-in replacement for Biotite's PDBFile class, maintaining the same API while delivering multiple times faster performance for reading and writing PDB structure files. It is designed for structural biology workflows where PDB files are a standard input format.
The package wraps Rust code to accelerate I/O operations on Protein Data Bank files, making it suitable for high-throughput structural analysis pipelines. It depends on biotite at runtime and supports Python versions from 3.7 onward across macOS, Windows, and Linux. The repository is now archived and marked abandoned, meaning no new features or maintenance should be expected, though the latest release is recent enough to support current Python versions.
Use it for
- Accelerating PDB file parsing in large-scale structural biology data pipelines.
- Replacing biotite's PDBFile in existing code without API changes to gain performance.
- Reading and writing protein structures for molecular dynamics or docking simulations.
- Batch processing of PDB files in bioinformatics workflows where I/O is a bottleneck.
Worth the install?
AI-flagged interpretation of the facts on this page. Verify before relying on it.
Yes, if you are already using biotite for PDB file I/O and performance is a concern—fastpdb is a straightforward, permissively licensed replacement with no API changes.
However, the abandoned repository status means no future updates or bug fixes should be expected; install only if the current feature set meets your needs and you are comfortable maintaining a frozen dependency.
Install
fastpdb on PyPI
Before you install
Medium install friction due to compiled wheels for multiple Python versions and platforms. The package is marked abandoned, though the latest release is recent (2025-05-27). No active maintenance should be expected going forward.
Requires biotite as a runtime dependency; does not yet support hybrid-36 PDB format.
License in practice
Licensed under a permissive license (BSD), so there are no restrictions on commercial or proprietary use of code that depends on fastpdb.
Quickstart
import fastpdb
in_file = fastpdb.PDBFile.read("path/to/file.pdb")
atom_array = in_file.get_structure(model=1)
out_file = fastpdb.PDBFile()
out_file.set_structure(atom_array)
out_file.write("path/to/another_file.pdb")Verify before relying
- Whether the abandoned status will affect long-term compatibility with future Python or dependency updates.
- Scope and completeness of PDB format support beyond the noted absence of hybrid-36 format.
- Real-world performance gains relative to biotite in typical bioinformatics workflows.
Package facts
| License | permissive license permissive |
| Python support | Supports the current Python release >=3.7 |
| Install friction | Medium. Platform-specific wheel |
| Runtime dependencies | 1 packagebiotite |
| Maintenance | Abandoned 444 days since the last release |
| Last repo commit | repository archived |
| First released | |
| Downloads | 117,709 / month, #12,152 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 :: Science/ResearchLicense :: OSI Approved :: BSD LicenseNatural Language :: EnglishOperating System :: MacOSOperating System :: Microsoft :: WindowsOperating System :: POSIX :: LinuxProgramming Language :: Python :: 3Topic :: Scientific/Engineering :: Bio-Informatics |
Evidence: fastpdb-1.3.3-cp310-cp310-macosx_11_0_arm64.whl; fastpdb-1.3.3-cp310-cp310-manylinux_2_34_x86_64.whl; fastpdb-1.3.3-cp310-cp310-win_amd64.whl; fastpdb-1.3.3-cp311-cp311-macosx_11_0_arm64.whl; fastpdb-1.3.3-cp311-cp311-manylinux_2_34_x86_64.whl; fastpdb-1.3.3-cp311-cp311-win_amd64.whl; fastpdb-1.3.3-cp312-cp312-macosx_11_0_arm64.whl; fastpdb-1.3.3-cp312-cp312-manylinux_2_34_x86_64.whl; fastpdb-1.3.3-cp312-cp312-win_amd64.whl; fastpdb-1.3.3-cp313-cp313-macosx_11_0_arm64.whl; fastpdb-1.3.3-cp313-cp313-manylinux_2_34_x86_64.whl; fastpdb-1.3.3-cp313-cp313-win_amd64.whl
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See also biotite · betterproto-rust-codec · pdb2pqr · pdbpp · pdbp · mmcif-pdbx · gemmi · rpdb · zlib-ng · biotraj