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RitS Transition State Generation App

A Streamlit web application for generating and visualizing molecular transition states using the RitS model, with optional IRC post-processing.

Usage

conda activate rits

# From the repository root
streamlit run app/app.py

Input

  • Reaction SMARTS: Atom-mapped R>>P string (with explicit hydrogens)
  • Example reactions: Built-in examples (amide hydrolysis, Diels-Alder, click chemistry, epoxidation, ester exchange, carbamate formation, E2 elimination)
  • Sampling parameters: Number of steps (5-100), number of samples (1-50), molecular charge, stereo toggle

Output

  • 2D reaction scheme (heavy atoms, no stereo annotations)
  • 3D transition-state viewer with sample selector (bonds shown = common bonds in both R and P)
  • Downloadable XYZ files (single sample or all samples)
  • IRC trajectory viewer with frame slider (reactant - TS - product)

Requirements

Model Files

  • RitS checkpoint (data/rits.ckpt)
  • RitS config (scripts/conf/rits.yaml)

Python Packages

pip install -r app/requirements.txt

IRC Post-Processing

IRC requires pysisyphus (included in requirements.txt) and xtb:

conda install -c conda-forge xtb