`molprop-retro`

Offline retrosynthesis planning wrapper based on AiZynthFinder. This command delegates planning to AiZynthFinder’s aizynthcli and then post-processes the results into a summary CSV/JSON plus a lightweight HTML browsing site with optional route images.

calc-v4 calc-v5 prep analyze report sketch series picklists similarity featurize retro schema

Install dependencies

AiZynthFinder is intentionally an optional dependency. Install it when you want retrosynthesis:

# inside your conda env
pip install -e .[retro]

# or install AiZynthFinder directly
pip install aizynthfinder[all]

Download models + stock and create a config

AiZynthFinder provides a helper that downloads public data and writes a usable config file.

download_public_data aizynth_data

# this creates aizynth_data/config.yml

Run retrosynthesis on a results CSV

molprop-retro results.csv --config aizynth_data/config.yml --top-routes 5 --nproc 4

# If your CSV uses non-standard columns
molprop-retro results.csv --config aizynth_data/config.yml --smiles-col SMILES --id-col Compound_ID

Outputs a directory under retrosynthesis/ containing routes_summary.csv, routes_summary.json, index.html, per-target pages, and optional route PNGs.

Run retrosynthesis on a SMILES list

molprop-retro targets.smi --config aizynth_data/config.yml

The input can be a single-column SMILES file or a two-column name/SMILES file.

Notes

Retrosynthesis quality depends heavily on the chosen policy model and stock definition. The public download is a good starting point, but real project use typically requires a curated purchasables stock and tuned settings. MolProp Toolkit treats retrosynthesis outputs as a prioritization signal (route count, step count, precursors in stock), not as a guarantee of synthetic feasibility.