ResHelp Tools

ResHelp Tools is a unified, Windows-friendly GUI application for chemical data workflows: PubChem downloads, IMPPAT data extraction, docking automation (OpenBabel + AutoDock Vina), and Vina log analysis. It ships with structured logging, retry/backoff networking, and a simple headless CLI for containers.

Highlights

• One application, four tabs: PubChem, IMPPAT, Docking, Logs
• Reliable networking with retries/backoff and progress
• Structured logs (text + JSONL) with rotating files
• Preferences: theme (dark/light) and external tool paths
• Windows .exe packaging via PyInstaller
• Optional Docker image for reproducible testing

Quick start (source)

Prerequisites:

• Windows 10/11
• Python 3.10+ installed and added to PATH

Steps:

1. Clone the repo
2. Install dependencies
3. Run the GUI

git clone https://github.com/manavc-13/ResHelp-Tools.git
cd ResHelp-Tools
python -m pip install --upgrade pip
pip install -r requirements.txt
python -m app

The main window has a menu for Preferences and About. Set paths to vina.exe, vina_split.exe, optional perl.exe, and an OpenBabel bin directory if they’re not on PATH.

Packaging a Windows .exe

Creates a distributable executable under dist/.

packaging\build_windows.ps1

Output will be at dist\ResHelpTools\ResHelpTools.exe (one-folder) or dist\ResHelpTools.exe (one-file depending on spec).

Docker (optional)

Build a minimal image that runs unit tests and supports headless CLI operations.

docker build -t reshelp-tools .
docker run --rm reshelp-tools

Example headless run to parse logs (mount a folder):

docker run --rm -v ${PWD}:/app reshelp-tools python cli.py parse-logs /app/your/log/folder

Tabs overview

• PubChem: batch CID download with concurrency and retry. Resume using logs.
• IMPPAT: scrape tables for associations/therapeutics and export to CSV/Excel.
• Docking: calls OpenBabel (obminimize/obabel), AutoDock Vina, and vina_split. Organizes output poses into folders. Paths can be set in Preferences.
• Logs: parse Vina logs to summarize best affinities sorted ascending.

Logging & monitoring

• Logs saved in logs/ rotating files; JSONL events for downstream tools.
• Status bar shows memory usage (psutil), handy for long runs.

Testing

Run tests locally (if pytest installed) or via Docker.

python -m pip install pytest ; pytest -q

Troubleshooting

• PyQt6 import errors: ensure pip install -r requirements.txt completed successfully in the active interpreter.
• OpenBabel not found: install from official releases and add to PATH, or set the bin directory in Preferences.
• Vina not found: bundle in Vina/ or set explicit paths in Preferences.
• Icon build error: Pillow is installed automatically by the build script; if you customize, ensure .ico or Pillow is present.

License

Apache License 2.0. See LICENSE.

Copyright (c) 2024 Manav Amit Choudhary