Emil_Shanaty/SciMesh
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

Document quick-start help command

Browse Source
This commit is contained in:
Emil
2026-07-13 23:05:43 +03:00
parent 5eb4b2dc1e
commit 9c3965a449
1 changed files with 17 additions and 0 deletions
Download Patch File Download Diff File Expand all files Collapse all files
README.md
+17
View File
@@ -21,6 +21,23 @@ conda install -c conda-forge rdkit
pip install -e . 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
`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. `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.