76 lines
2.1 KiB
Python
76 lines
2.1 KiB
Python
"""Quick-start help workload."""
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from __future__ import annotations
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import argparse
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from textwrap import dedent
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HELP_TEXT = dedent(
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"""\
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SciMesh quick start
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===================
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SciMesh runs molecular similarity workloads locally. Input must be a ChEMBL TSV
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with chembl_id and canonical_smiles columns.
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1. Activate the project environment and create a directory for outputs:
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source .venv/bin/activate
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mkdir -p results
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2. Find molecules similar to gefitinib (CHEMBL939):
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scimesh similarity-search chembl_37_chemreps.txt \\
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--query-id CHEMBL939 \\
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--top-k 20 \\
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--max-rows 10000 \\
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--output results/gefitinib_top20.csv
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3. Search by a SMILES query instead of a ChEMBL ID:
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scimesh similarity-search chembl_37_chemreps.txt \\
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--query-smiles 'CCO' \\
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--top-k 20 \\
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--output results/smiles_search.csv
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4. Find the least similar molecules. With "less", results are ranked from
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lowest similarity upward; --threshold is an optional <= filter:
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scimesh similarity-search chembl_37_chemreps.txt \\
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--query-id CHEMBL939 \\
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--threshold-direction less \\
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--threshold 0.1 \\
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--top-k 20 \\
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--output results/least_similar.csv
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5. Build a small exact similarity graph:
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scimesh similarity-graph chembl_37_chemreps.txt \\
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--max-rows 1000 \\
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--threshold 0.7 \\
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--block-size 250 \\
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--output results/similarity_graph.csv
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Use --max-rows for quick local tests; omit it to process the full dataset.
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For all options, run:
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scimesh similarity-search --help
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scimesh similarity-graph --help
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"""
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)
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class HelpWorkload:
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"""Expose practical examples without adding special logic to the main CLI."""
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name = "help"
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help = "Show a quick start and runnable examples."
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def configure_parser(self, parser: argparse.ArgumentParser) -> None:
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parser.description = "Show SciMesh setup and usage examples."
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def run(self, args: argparse.Namespace) -> int:
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print(HELP_TEXT)
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return 0
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