Database Search

Syndirella offers three options for database search functionality: Arthor, Hippo, and Postera (Manifold). All three tools support superstructure searches to find commercially available compounds that can be used as reactants in synthesis.

Arthor

Arthor is a free, publicly accessible database search tool that provides access to multiple chemical databases including ZINC, Enamine, Mcule, and stock databases.

Usage:

When running Syndirella, specify Arthor as the database search tool:

syndirella run --input input.csv --output output_dir --db_search_tool arthor

Default Vendors:

The default vendor list includes: - enamine_real - Enamine REAL Database - stock - In-Stock database - mcule - Mcule databases (includes multiple Mcule variants) - zinc - ZINC databases (includes multiple ZINC variants)

Available Vendor Options:

Arthor supports a wide range of vendor databases: check the Arthor documentation for more details.

Checking Available Databases:

You can programmatically check which databases are available:

from syndirella.database.Arthor import Arthor

arthor = Arthor()
available_dbs = arthor.get_available_databases()
print(available_dbs)

Postera (Manifold)

Postera’s Manifold API provides access to a comprehensive database of commercially available compounds. It supports superstructure searches across multiple vendor catalogs.

Setup:

Get your Manifold API key from your Postera account.
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

Attention

A Manifold Pro account is required for API access.

Usage:

When running Syndirella, specify Postera as the database search tool:

syndirella run --input input.csv --output output_dir --db_search_tool manifold

Default Vendors:

The default vendor list includes: - enamine_bb - Enamine Building Blocks - mcule - Mcule database - mcule_ultimate - Mcule Ultimate database - enamine_real - Enamine REAL database - enamine_made - Enamine Made database

Hippo

Hippo provides local database search functionality using a HIPPO database file. This option is useful when you have your own database or want to search locally without API dependencies.

Installation

HIPPO requires rdkit>=2024.9.6; AiZynthFinder declares rdkit<2024. Install in this order so pip does not pull AiZynthFinder’s RDKit:

pip install aizynthfinder --no-deps
pip install syndirella[hippo]
conda install -c conda-forge chemicalite

See the HIPPO documentation for full setup and version compatibility. To create a minimal example database (e.g. at ~/CursorProjects/HIPPO/reference_db.sqlite), run python scripts/create_hippo_example_db.py [OUTPUT_DIR].

Setup

Have a HIPPO database file available and initialize the Hippo search with the database path.

Usage

Specify Hippo as the database search tool:

syndirella run --input input.csv --output output_dir --db_search_tool hippo --reference_db /path/to/database

Default Behavior

If no database search tool is specified, Syndirella will use the default tool (Arthor).