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Download PubChem\n```sh\npython -m biorgroup.pubchem.download \\\n    --output-pubchem-dir \u003coutput dir\u003e \\\n    --output-pubchem-db \u003coutput sql database\u003e\n```\n\n### 2 - Download Rhea\n```sh\npython -m biorgroup.rhea.download \\\n    --output-rhea-dir \u003coutput dir\u003e \\\n    --parameter-release-int \u003cint\u003e\n```\n\n### 3 - R-group search\n```sh\nsnakemake \\\n    -p \\\n    -j 48 \\\n    -c 48 \\\n    --workflow-profile template/biorgroup \\\n    -s ./src/biorgroup/rgroup/Snakefile \\\n    --use-conda \\\n    --latency-wait 5 \\\n    --rerun-incomplete \\\n    --config input_depot_str=./src/biorgroup/rgroup input_chebi_csv=rhea-chebi-smiles.csv input_pubchem_db=pubchem.db output_dir_str=chebi parameter_search_timeout_int=10\n```\n\n## Dataset overview\nThe Snakemake workflow produces a `csv.gz` file containing:  \n\n| column name | type |\n| --- | --- |\n| smiles_rhea | `str`|\n| chebi | `List[str]` |\n| num_heavy_atoms | `int` |\n| exact_mol_wt | `float` |\n| core_superstructure_smiles | `List[str]` |\n| core_superstructure_pubchem_cid | `List[List[str]]` |\n| rgroup_extended_smiles | `List[str]` |\n| rgroup_extended_pubchem_cid | `List[List[str]]` |\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbrsynth%2Fbiorgroup","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbrsynth%2Fbiorgroup","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbrsynth%2Fbiorgroup/lists"}