Chemical Similarity Search

Goal

To programmatically find chemical analogs, alternative precursors, and structurally similar compounds for a given target molecule using PubChem's "fastsimilarity_2d" endpoint. The skill retrieves lists of similar compounds ranked by sequence alignment of their 2D molecular fingerprints, providing CIDs, molecular weights, formulas, and SMILES strings.

Instructions

1. Search by SMILES String

Search for similar compounds by providing the canonical or isomeric SMILES. Adjust the --threshold (similarity cutoff 0-100, default is 95) to widen or narrow the search radius. Higher threshold equals higher similarity. Adjust --max_records to limit the output length.