This CLI can be used to predicted metabolic products and associated enzymes for a set of input compounds.
bioreactor_cli <PATH_TO_COMPOUNDS> <OUTPUT_DIRECTORY> [--neutralize=<BOOL>] [--reaction_rules=<FILE_PATH>] [--organisms=<FILE_PATH>] [--patterns_to_remove=<FILE_PATH>] [--molecules_to_remove=<FILE_PATH>] [--min_atom_count=<INT>] [--n_jobs=<INT>]| Argument | Example | Description | Default |
|---|---|---|---|
| compounds | file.tsv or "smile1;smiles2;smile3;etc" |
The path to the file containing the compounds to use as reactants. Or ;-separated SMILES strings. | |
| output_directory | output/directory/ |
The path directory to save the results to. | |
| neutralize | True or False |
Whether to neutralize the compounds before predicting the products. In this case the new products will also be neutralized. | False |
| reaction_rules | file.tsv or None |
The path to the file containing the reaction rules to use. | all_reaction_rules_forward_no_smarts_duplicates_sample.tsv |
| organisms | file.tsv or "org_id1;org_id2;org_id3;etc" or None |
The path to the file containing the organisms to use. Or ;-separated organisms identifiers. Reaction Rules will be selected accordingly (select only rules associated with enzymes encoded by genes from this organisms). | All reaction rules are used. |
| patterns_to_remove | patterns.tsv or None |
The path to the file containing the patterns to remove from the products. | patterns.tsv |
| molecules_to_remove | molecules.tsv or None |
The path to the file containing the molecules to remove from the products. | byproducts.tsv |
| min_atom_count | 4 |
The minimum number of heavy atoms a product must have. | 5 |
| n_jobs | 6 |
The number of jobs to run in parallel (-1 uses all). | 1 |
More detailed information on these arguments and possible usages can be consulted in the main README.
bioreactor_cli compounds.tsv output_directory/ --neutralize=True --reaction_rules=reaction_rules.tsv --organisms=organisms.tsv --patterns_to_remove=patterns.tsv --molecules_to_remove=molecules.tsv --min_atom_count=4 --n_jobs=6