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 3.8 or later
• Python packages:
  • numpy
  • pyyaml
  • msgpack

Installation

Clone repository

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

Install using pip

pip install .

For development (editable install):

pip install -e .

Quick Start

from proteindf_bridge import BioPdb, AtomGroup

# 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

pytest

License

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