ProteinDF_bridge -- bridge scripts between ProteinDF and molecular data formats

ProteinDF_bridge is a Python library for reading, manipulating, and converting various molecular structure formats (PDB, mmCIF, MOL2, GRO, Amber PRMTOP, etc.) for use with ProteinDF.

Requirements

• Python 3.9 or later
• Rust toolchain (cargo, rustc, latest stable) when installing from source
• Python packages:
  • numpy
  • pyyaml
  • msgpack

Installation

Pre-built Wheels (Recommended)

Pre-built wheels are available on GitHub Releases for Linux (x86_64, aarch64 with manylinux2014) and macOS (Apple Silicon). No Rust toolchain is required when installing from a wheel.

To let pip automatically select the matching wheel for your platform:

pip install proteindf_bridge --find-links https://github.com/ProteinDF/ProteinDF_bridge/releases/expanded_assets/<tag>

Note: expanded_assets/<tag> is an undocumented (non-public) GitHub web endpoint that returns the HTML fragment listing release assets. Unlike the standard releases/tag/<tag> page (where assets are loaded asynchronously via JavaScript and cannot be scraped by pip), expanded_assets allows pip to discover and select matching wheels. Because this endpoint is not an officially documented GitHub API, specifying the direct wheel URL below is also supported and recommended if you prefer a fully documented approach.

Alternatively, you can specify the direct URL to the appropriate wheel file:

pip install https://github.com/ProteinDF/ProteinDF_bridge/releases/download/<tag>/proteindf_bridge-<version>-<platform_tag>.whl

From Source

Installing from source compiles the bundled Rust extension (proteindf_bridge.rs) and requires a working Rust toolchain (rustc and cargo, latest stable).

git clone https://github.com/ProteinDF/ProteinDF_bridge.git
cd ProteinDF_bridge
pip install .

For development (editable install):

pip install -e .

Quick Start

from proteindf_bridge import BioPdb, AtomGroup
import proteindf_bridge.rs as rs

# Load structure from PDB
pdb = BioPdb()
pdb.load("protein.pdb")

# Get AtomGroup representation
ag = pdb.get_atomgroup()
print(f"Total atoms: {ag.get_number_of_all_atoms()}")

Running Tests

# Python test suite
python -m unittest discover -s tests

# Rust crate test suite
cargo test --manifest-path rust/Cargo.toml

Contributing

See CONTRIBUTING.md for the branching model (GitFlow) and release process.

License

ProteinDF_bridge is licensed under the GNU General Public License v3.0 (GPLv3).