AI / Agents

Skills
llms.txt
llms-full.txt

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Adriano Rutz

Maintainer

ETH Zurich

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Contributing guide
Code of conduct
Full license MIT

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Requires: Python >=3.12

Smartclass

Smartclass classifies structures using SMARTS.

🚀 Installation

uv sync

💪 Getting Started

A mini notebook is available.

uv run quarto render notebooks/smartclass.qmd

🌟 Main steps

The main steps are briefly shown below.

Get defined chemical classes

## Run the default Wikidata class-query batch
uv run smartclass querywikidata

## Optional: run a single explicit query/output pair
uv run smartclass querywikidata -q smartclass/data/queries/classes_smarts.rq -o scratch/wikidata_classes_smarts.tsv

By default, smartclass querywikidata generates these class files:

  • scratch/wikidata_classes_cxsmiles.tsv
  • scratch/wikidata_classes_smarts.tsv
  • scratch/wikidata_classes_smiles_canonical.tsv
  • scratch/wikidata_classes_smiles_isomeric.tsv
  • scratch/wikidata_classes_taxonomy.tsv

Canonicalize them

uv run notebooks/canonicalize_smarts.py

Get some SMILES to classify

uv run smartclass querywikidata -q smartclass/data/queries/chemicals_smiles_canonical.rq -o scratch/wikidata_chemicals_smiles.tsv
uv run smartclass querywikidata -q smartclass/data/queries/classes_fake_smiles.rq -o scratch/wikidata_classes_smiles.tsv

Classify compounds

uv run smartclass searchclasses --help
## uv run smartclass searchclasses
uv run smartclass searchclasses -s "O=C1OC2CC3C(C=C(OC)C(=O)C3(C)C4C(=O)C(OC)=C(C)C(C1)C24C)C" -c scratch/wikidata_classes_smarts.tsv --verbose
uv run smartclass searchclasses -s "O=C1OC2CC3C(C=C(OC)C(=O)C3(C)C4C(=O)C(OC)=C(C)C(C1)C24C)C" -c scratch/wikidata_classes_smarts.tsv --closest-only False --verbose
uv run smartclass searchclasses -i smartclass/data/bitter_smiles.tsv -c scratch/wikidata_classes_smarts.tsv
## uv run smartclass searchclasses -i scratch/wikidata_chemicals_smiles.tsv -c scratch/wikidata_classes_smarts.tsv --all-matches

## Classify against SMARTS + SMILES + CXSMILES in one run (all matches)
uv run smartclass searchclasses-all-sources -i scratch/wikidata_chemicals_smiles.tsv --all-matches --include-hierarchy --output-dir scratch/all_sources

The searchclasses-all-sources command writes:

  • scratch/all_sources/results_all_sources_by_class.tsv
  • scratch/all_sources/results_all_sources_by_structure.tsv

🤯 Future steps (not fully available now)

Measure substructures distances

uv run python3 smartclass/measure_mhfp.py -i scratch/wikidata_classes_smarts.tsv -o scratch/distances_wikidata.tsv
uv run python3 smartclass/measure_mhfp.py -i data/mia_smarts.tsv -o scratch/distances_mia.tsv

🛠️ Wikidata maintenance

Generic maintenance

uv run smartclass querywikidata -q smartclass/data/queries/maintenance_smiles_canonical_no_formula.rq -t transform_smiles_to_formula -o scratch/formulas_canonical.csv
uv run smartclass querywikidata -q smartclass/data/queries/maintenance_no_smiles_isomeric_no_mass.rq -t transform_inchi_to_mass -o scratch/masses_inchi.csv
uv run smartclass querywikidata -q smartclass/data/queries/maintenance_smiles_isomeric_no_mass.rq -t transform_smiles_to_mass -o scratch/masses_isomeric.csv
uv run smartclass querywikidata -q smartclass/data/queries/maintenance_smiles_isomeric_no_inchi.rq -t transform_smiles_to_inchi -o scratch/inchis_isomeric.csv
uv run smartclass querywikidata -q smartclass/data/queries/maintenance_isomeric_smiles_inchi_no_stereo.rq -t transform_smiles_to_inchi -o scratch/incorrect_inchis.csv
uv run smartclass querywikidata -q smartclass/data/queries/maintenance_smiles_isomeric_no_formula.rq -t transform_smiles_to_formula -o scratch/formulas_isomeric.csv
uv run smartclass querywikidata -q smartclass/data/queries/maintenance_smiles_isomeric_no_canonical.rq -t transform_smiles_i_to_smiles_c -o scratch/smiles_isomeric.csv
uv run smartclass querywikidata -q smartclass/data/queries/maintenance_no_smiles_isomeric_inchi.rq -t transform_inchi_to_smiles_isomeric -o scratch/smiles_i_inchi.csv
uv run smartclass querywikidata -q smartclass/data/queries/maintenance_inchi_no_isomeric_smiles.rq -t transform_inchi_to_smiles_isomeric -o scratch/smiles_i_inchi_2.csv
uv run smartclass querywikidata -q smartclass/data/queries/maintenance_inchi_no_canonical_smiles.rq -t transform_inchi_to_smiles_canonical -o scratch/smiles_c_inchi.csv
uv run smartclass querywikidata -q smartclass/data/queries/maintenance_inchi_no_inchikey.rq -t transform_inchi_to_inchikey -o scratch/inchikeys.csv
uv run smartclass querywikidata -q smartclass/data/queries/maintenance_formula_malformed.rq -t transform_formula_to_formula -o scratch/formulas_malformed.csv
## WDQS is not parsing the REGEX well
## uv run smartclass querywikidata -q smartclass/data/queries/maintenance_formula_malformed.rq -t transform_formula_to_formula -o scratch/formulas_malformed.csv -u https://qlever.dev/api/wikidata
uv run smartclass querywikidata -q smartclass/data/queries/maintenance_smiles_isomeric_incorrect_mass.rq -t transform_smiles_mass_to_smiles_mass -o scratch/masses_incorrect_isomeric.csv
uv run smartclass querywikidata -q smartclass/data/queries/maintenance_no_smiles_isomeric_incorrect_mass.rq -t transform_inchi_mass_to_inchi_mass -o scratch/masses_incorrect_inchi.csv

uv run smartclass querywikidata -q smartclass/data/queries/chemicals_smiles_canonical.rq -t check_smiles -o scratch/smiles_c_invalid.csv
uv run smartclass querywikidata -q smartclass/data/queries/chemicals_smiles_isomeric.rq -t check_smiles -o scratch/smiles_i_invalid.csv

uv run smartclass querywikidata -q smartclass/data/queries/chemicals_smiles_canonical_no_ref.rq -t transform_smiles_c_to_smiles_c_tauto -o scratch/smiles_c_tauto.csv
uv run smartclass querywikidata -q smartclass/data/queries/chemicals_smiles_isomeric_no_ref.rq -t transform_smiles_i_to_smiles_i -o scratch/smiles_i.csv
uv run smartclass querywikidata -q smartclass/data/queries/chemicals_smiles_isomeric_no_ref.rq -t transform_smiles_i_to_smiles_i_tauto -o scratch/smiles_i_tauto.csv
## not working for now
## uv run smartclass querywikidata -q smartclass/data/queries/stereoisomers_smiles_isomeric_inchi.rq -t transform_stereoisomers_to_entities -o scratch/stereo_i_to_entities.csv
## uv run smartclass querywikidata -q smartclass/data/queries/stereoisomers_smiles_canonical_no_isomeric.rq -t transform_stereoisomers_to_entities -o scratch/stereo_c_to_entities.csv
## uv run smartclass querywikidata -q smartclass/data/queries/chemical_entities_smiles_isomeric_inchi.rq -t transform_entities_to_stereoisomers -o scratch/entities_i_to_stereo.csv
## uv run smartclass querywikidata -q smartclass/data/queries/chemical_entities_smiles_canonical_no_isomeric.rq -t transform_entities_to_stereoisomers -o scratch/entities_c_to_stereo.csv

Improve current classes

uv run smartclass querywikidata -q smartclass/data/queries/chemicals_inchikey.rq -o scratch/wikidata_chemicals_inchikeys.tsv
uv run smartclass querywikidata -q smartclass/data/queries/chemicals_classes.rq -o scratch/wikidata_chemicals_classes.tsv
uv run smartclass querywikidata -q smartclass/data/queries/chemical_entities_smiles_isomeric_inchi.rq -o scratch/wikidata_chemical_entities_smiles_inchi.tsv
uv run smartclass querywikidata -q smartclass/data/queries/stereoisomers_smiles_isomeric_inchi.rq -o scratch/wikidata_stereoisomers_smiles_isomeric_inchi.tsv
uv run smartclass querywikidata -q smartclass/data/queries/stereoisomers_smiles_canonical_no_isomeric_inchi.rq -o scratch/wikidata_stereoisomers_smiles_canonical_inchi.tsv
uv run smartclass querywikidata -q smartclass/data/queries/chemicals_tautomer_of.rq -o scratch/wikidata_chemicals_tautomer_of.tsv
uv run python3 notebooks/improve_classes.py
uv run python3 notebooks/improve_subclasses_inchikeys.py
uv run python3 smartclass/helpers/split_csv.py

Add stereoisomers pairs

uv run smartclass querywikidata -q smartclass/data/queries/chemical_entities_inchi.rq -o scratch/wikidata_chemical_entities_inchis.tsv
uv run smartclass querywikidata -q smartclass/data/queries/chemicals_stereosiomer_of.rq -o scratch/wikidata_chemicals_stereoisomer_of.tsv
uv run python3 notebooks/pair_stereoisomers.py

🖥 Command Line Interface

The smartclass command line tool is automatically installed. It can be used from the shell with the --help flag to show all subcommands:

uv run smartclass --help

👐 Contributing

Contributions, whether filing an issue, making a pull request, or forking, are appreciated. See CONTRIBUTING.md for more information on getting involved.

👋 Attribution

A lot of inspiration and initial data has been taken by the huge work done by @rwst with YACCL.

⚖️ License

See LICENSE

🍪 Cookiecutter

This package was created with @audreyfeldroy's cookiecutter package using @cthoyt's cookiecutter-snekpack template.