molselector 0.1.0

A web app to quickly triage molecule files.

MolSelector

MolSelector is a lightweight web app for triaging molecular structures (.xyz, .mol, .mol2). Point the app at a folder of files, explore each molecule in an interactive 3D viewer powered by 3Dmol.js, and rapidly tag it as accept or decline. Decisions are written to selection_results.csv in the chosen folder so they can be versioned or analyzed later.

Features

• Fast folder loading with support for .xyz, .mol, and .mol2 files (non-recursive)
• Interactive 3D visualization using sticks and spheres with customizable styling
• Accept, decline, and back actions with mouse or keyboard shortcuts
• Native folder picker on macOS (AppleScript) and Tk-based picker on other platforms
• Automatic CSV logging with timestamps so you can stop and resume reviews anytime

Requirements

• Python 3.12+
• A modern browser with WebGL support (Chrome, Firefox, Safari, Edge)

Installation

Clone the repository and install the package in editable mode:

git clone https://github.com/your-account/molselector.git
cd molselector
python -m venv .venv
source .venv/bin/activate  # On Windows use .venv\Scripts\activate
pip install -e .

If you use uv:

uv sync

Running the app

Start a local server with the built-in CLI:

molselector launch

Open your browser to http://127.0.0.1:8000 and MolSelector will be ready. The CLI exposes options such as --host, --port, and --log-level; use molselector launch --help to view them. You can still start the app manually with uvicorn molselector.app:app if you prefer.

To preload a folder of molecules (skipping the manual selection step), supply the --xyz-folder option:

molselector launch --xyz-folder /path/to/molecules

The browser will automatically load that folder when the UI opens.

Usage

1. Enter an absolute path to a folder containing .xyz, .mol, or .mol2 files, or click Browse… to pick a folder using the native dialog.
2. MolSelector lists every supported file in the folder and loads the first unreviewed molecule in the embedded 3D viewer.
3. Inspect the structure, then use Accept, Decline, or Back to record your judgment. Decisions are saved instantly to selection_results.csv in the same folder.
4. Reloading the same folder restores previous decisions so you can resume where you left off.

Keyboard shortcuts

• Enter, A, or →: accept the current molecule
• D or ←: decline the current molecule
• Backspace, B, or ↑: go back to the previous molecule

Output format

The CSV file (selection_results.csv) contains three columns:

column	description
file	Relative path to the molecule inside the selected folder
decision	Either accept or decline
timestamp	UTC timestamp recorded at the decision moment

Native folder picker notes

• macOS: Uses AppleScript (osascript). Ensure AppleScript is available (installed by default). If the picker fails, you can still paste a folder path manually.
• Linux / Windows: Falls back to Python's Tkinter dialog. If Tk is missing, install the python3-tk package (Linux) or add Tk during Python installation (Windows).

Development

Install the dev tooling and run static checks:

pip install -e .
pip install ruff
ruff check .

When contributing code, consider adding tests or manual verification steps that cover your changes (e.g., folder loading edge cases, CSV persistence, keyboard shortcuts).

Contributing

Contributions are welcome! If you have ideas for improvements—batch actions, recursive search, alternate viewers—open an issue or submit a pull request describing the change.

License

MIT License

Copyright (c) 2025 Nicholas Hadler

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.