fastpdb

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

fastpdb is a Rust-based drop-in replacement for Biotite's PDBFile that reads and writes PDB structure files with significantly higher performance than the original Python implementation.

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

pip install fastpdb

uv add fastpdb

poetry add fastpdb

Installing fastpdb

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.

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")

Requires biotite as a runtime dependency; does not yet support hybrid-36 PDB format.

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

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

Keywords: pdb-files

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