v0.1.0-alpha

PDBQT Converter v0.1.0-alpha

Release Date: March 27, 2025
Status: Pre-release / Active Development

Summary

Initial pre-release of a PDB to PDBQT conversion tool for molecular docking preparation. This tool processes protein structures by cleaning, optimizing, and converting them to formats required by docking software.

Key Features

• Structure cleaning and binding site extraction
• Missing residue and atom completion
• Hydrogen optimization using MolProbity's reduce
• Conversion to PDBQT format via MGLTools
• Chain ID preservation throughout processing

Current Limitations

• Only accepts PDB format as input
• Limited testing on selected protein structures
• Potential bugs in complex structure handling

Getting Started

# Install dependencies
./install_all_dependencies.sh

# Basic usage
python structure_handler.py --pdb_id "2PGH" --input_file "example.pdb" --target_chains "A,C"

Feedback

This is an early release under active development. Bug reports and feedback are greatly appreciated.