diff --git a/README.md b/README.md index 8408288..f405a32 100644 --- a/README.md +++ b/README.md @@ -21,6 +21,23 @@ conda install -c conda-forge rdkit pip install -e . ``` +## Quick start + +Run the built-in help command for copy-paste examples of both workloads: + +```bash +scimesh help +``` + +It includes environment setup, output-directory creation, similarity search by +ChEMBL ID or SMILES, and similarity-graph construction. Use the standard help +for the complete option reference: + +```bash +scimesh similarity-search --help +scimesh similarity-graph --help +``` + ## Similarity search `similarity-search` finds the top-k molecules most similar to a query. The query is supplied either by ChEMBL ID or by SMILES. It uses Morgan fingerprints with `radius=2` and `fpSize=2048`, Tanimoto similarity, streaming TSV reads, and a bounded heap. Invalid SMILES and the query molecule are skipped.