Document quick-start help command

2026-07-13 23:05:43 +03:00
parent 5eb4b2dc1e
commit 9c3965a449
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@@ -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.