Table 4 Available input parameters for the code to generate the dataset.

--chembl, -v

No

None

ChEMBL version. The latest available ChEMBL version is used if this is not set.

--sqlite, -s

No

None

Path to SQLite database. If this is not set, ChEMBL is downloaded as an SQLite database and handled using the chembl_downloader package.

--output, -o

Yes

—

Path to write the output files to.

--delimiter, -d

No

;

Delimiter in output csv-files.

--all_sources

No

—

Include all sources if this is set. By default, this is not set, and the dataset is calculated based on only literature sources.

--rdkit

No

—

Calculate RDKit-based compound properties if this is set.

--excel

No

—

Write the results to excel. Note: this may fail if the output is too large. The results will always be written to csv.

--BF

No

—

Write the subsets based on binding and functional assays.

--B

No

—

Write the subsets based on binding assays.

--debug

No

—

Log additional debugging information.