From 26fdbab71f53ab58d463043447220d051d34dbd5 Mon Sep 17 00:00:00 2001 From: Tim Dudgeon Date: Tue, 11 Aug 2026 16:33:46 +0100 Subject: [PATCH] docs: use -i/-o in screen.py examples The usage comments in screen.py and the frag-merge walkthrough invoked screen.py with --input/--output. Those are deprecated aliases on the shared molecule I/O group and are due to be withdrawn; the Job Definitions moved to -i/-o in #27, so the examples should match. Refs InformaticsMatters/squonk2-rdkit-utilities#5 Co-Authored-By: Claude Opus 5 --- frag-merge.md | 2 +- screen.py | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/frag-merge.md b/frag-merge.md index 88fc468..57de853 100644 --- a/frag-merge.md +++ b/frag-merge.md @@ -38,7 +38,7 @@ tht mean they will be reasonably 'lead like'. ## Find similar molecules ``` -./screen.py --smiles 'CC(=O)NC1=CN=CC=C1C' 'CC(NC(=O)C)c1cccc(Cl)c1' --input frag-merge/mols.smi --output frag-merge/screened.smi --metric tversky --descriptor morgan2 --nbits 1024 --interval 10000 --sim-index 5 --threshold 0.3 +./screen.py --smiles 'CC(=O)NC1=CN=CC=C1C' 'CC(NC(=O)C)c1cccc(Cl)c1' -i frag-merge/mols.smi -o frag-merge/screened.smi --metric tversky --descriptor morgan2 --nbits 1024 --interval 10000 --sim-index 5 --threshold 0.3 ... ... 2021-11-06T13:47:09+00:00 # INFO -EVENT- Processed 4560000 records, 4362 hits diff --git a/screen.py b/screen.py index 122b096..a0fd8a8 100755 --- a/screen.py +++ b/screen.py @@ -273,9 +273,9 @@ def execute(query_smis, def main(): # Examples: - # python screen.py --smiles 'O=C(Nc1ccc(Cl)cc1)c1ccccn1' --input data/10000.smi --delimiter tab -o foo.smi\ + # python screen.py --smiles 'O=C(Nc1ccc(Cl)cc1)c1ccccn1' -i data/10000.smi --delimiter tab -o foo.smi\ # --descriptor rdkit -m tanimoto - # python screen.py --queries-file data/10.smi --input data/10000.smi --delimiter tab --id-column 1 -o foo.smi \ + # python screen.py --queries-file data/10.smi -i data/10000.smi --delimiter tab --id-column 1 -o foo.smi \ # --descriptor rdkit -m tanimoto --queries-delimiter tab --threshold 0.4 parser = argparse.ArgumentParser(description='screen')