Retrosynthesis

Syndirella offers two options for retrosynthesis functionality, AiZynthFinder and Postera’s Manifold.

AiZynthFinder

Before using AiZynthFinder for retrosynthesis, you need to set it up. There are two options:

Automatic Setup (Recommended):

Run the setup command to automatically download required data and create the configuration file:

syndirella setup-aizynth

Attention

⚠️ This will download large model files (~750MB total) if run the first time (will take ~5 min). These are required to run AiZynthFinder. This will automatically download the required data to [syndirella_package_path]/aizynth directory and create the configuration file automatically.

Manual Setup (Alternative):

If you prefer to set up AiZynthFinder manually:

cd [syndirella_package_path]/aizynth
download_public_data .
# Update config.yml (if you prefer)
export AIZYNTH_CONFIG_FILE="path/to/syndirella/aizynth/config.yml"

Note

To make the environment variable permanent, add the export line to your shell profile (~/.bashrc, ~/.zshrc, etc.).

Basic usage:

from syndirella.aizynth.AiZynthManager import AiZynthManager
manager = AiZynthManager()
routes = manager.perform_route_search(smiles, matching_strategy="best_overall")
Strategies:

  • “best_overall”: Use most similar SMIRKS from whole library

  • “best_child”: Use most specific SMIRKS

  • “parent_only”: Use only original Syndirella SMIRKS

  • “all_above_threshold”: Use any SMIRKS above similarity threshold

Attention

An output file will be created in the output directory per scaffold listing all information about the routes found by AiZynthFinder.

Manifold

Syndirella can perform retrosynthesis search using Postera’s Manifold API to perform retrosynthesis searches of input scaffolds and superstructure searches of reactants. You can find more information on Manifold API access here.

Attention

A Manifold Pro account is required for API access.

Setup:

  1. Get your Manifold API key from your Postera account.

  2. Set the required environment variables:

export MANIFOLD_API_KEY=[YOUR_API_KEY]
export MANIFOLD_API_URL=[API_URL]

# Example:
# export MANIFOLD_API_KEY=your_api_key_here
# export MANIFOLD_API_URL=https://api.postera.ai

Note

To make the environment variables permanent, add the export lines to your shell profile:

  • For bash: ~/.bashrc or ~/.bash_profile

  • For zsh: ~/.zshrc

After adding, reload your shell configuration:

source ~/.bashrc  # or source ~/.zshrc for zsh