• 📄 3rd_party_requirements.txt – Download
• 📄 collapsible_toggle.py – Download
• 📄 compGeometry.py – Download
• 📄 convexHull3D_1_0.py – Download
• 📄 convexHull4D_2_22.py – Download
• 📄 determinants.py – Download
• 📄 dynamic_option_widget.py – Download
• 📄 dynamic_option_widget_amino_acid_selection.py – Download
• 📄 file_open.py – Download
• 📄 goFo.py – Download
• 📄 input_widgets.py – Download
• 📄 minimizeNetworks.py – Download
• 📄 pHinderSurface.py – Download
• 📄 pHinder_7_0.py – Download
• 📄 pdbFile.py – Download
• 📄 pdbFile_cif.py – Download
• 📄 phinder_command_line.py – Download
• 📄 phinder_main_gui.py – Download
• 📄 sphere.py – Download
• 📄 terminal_output_widget.py – Download
• 📄 writeFunctions.py – Download

🧬 pHinder: Structural Analysis Tools

Welcome to the pHinder codebase. This folder contains Python code used in our lab’s research for protein structural analysis, sidechain topology and spatial classification, surface calculation, and void detection in protein structures for ligand/drug binding.

⚠️ Disclaimer

This is research-grade code provided for academic and exploratory purposes only. It is not intended for professional or clinical deployment.

• The code was developed and extended over many years to support diverse use cases in computational structural biology.
• You may encounter commented sections, experimental blocks, or legacy fragments — these reflect the evolving nature of scientific coding.
• Use at your own risk. While we strive for accuracy, this code has not undergone rigorous software engineering review.

📥 Getting Started

Once you have downloaded the files in the code/ folder to a folder on your computer:

1. Ensure you have Python 3.8+ installed.
2. Install any necessary dependencies (see requirements.txt if provided).
3. Prepare your input files in .pdb or .cif format and place them in an accessible directory.

Command Line Usage

To run pHinder from the command line, use the phinder_command_line.py script:

python phinder_command_line.py path/to/your_structure.pdb --chains A B --topology-calculation --sidechain-classification --interface-classification

You can customize your run by passing additional flags. Use --help to see all available options:

python phinder_command_line.py --help

GUI Mode Usage

To run pHinder with a graphical interface, use the phinder_main_gui.py script:

python phinder_main_gui.py

This will launch the GUI, allowing you to select input files and parameters through the interface.

📄 Citation

If you use pHinder in your research or publications, please cite the relevant work from our lab. This supports continued development and scientific recognition.

Thank you for your interest in our research tools!