arguments module

Dataclasses related to handling arguments, specifically arguments related to how to calculate or output the dataset.

class arguments.CalculationArgs(chembl_version: str, calculate_rdkit: bool, limit_to_literature: bool, limited_flag: str, min_nof_cpds_bf: int, min_nof_cpds_b: int)[source]

Bases: object

Collection of arguments related to how to calculate the dataset.

  • chembl_version: Version of ChEMBL for output file names

  • calculate_rdkit: True if RDKit-based compound properties should be calculated

  • limit_to_literature: Include only literature sources if True

  • limited_flag: String version of limit_to_literature used in file names

  • min_nof_cpds_bf: Minimum number of compounds per target for the BF subset

  • min_nof_cpds_b: Minimum number of compounds per target for the B subset

calculate_rdkit: bool
chembl_version: str
limit_to_literature: bool
limited_flag: str
min_nof_cpds_b: int
min_nof_cpds_bf: int
class arguments.OutputArgs(output_path: str, delimiter: str, write_to_csv: bool, write_to_excel: bool, write_full_dataset: bool, write_bf: bool, write_b: bool)[source]

Bases: object

Collection of arguments related to how to output the dataset.

  • output_path: Path to write output files to

  • delimiter: Delimiter in csv-output

  • write_to_csv: True if output should be written to csv

  • write_to_excel: True if output should be written to excel

  • write_full_dataset: True if the full dataset should be written to output

  • write_bf: True if subsets based on binding+functional data should be written to output

  • write_b: True if subsets based on binding data only should be written to output

delimiter: str
output_path: str
write_b: bool
write_bf: bool
write_full_dataset: bool
write_to_csv: bool
write_to_excel: bool
arguments.get_args() → tuple[Namespace, CalculationArgs, OutputArgs][source]

Get parsed and default arguments.

Returns:

parserd arguments, arguments related to how to calculate the dataset as CalculationArgs, arguments related to how to output the dataset as OutputArgs

Return type:

tuple[argparse.Namespace, CalculationArgs, OutputArgs]

arguments.parse_args() → Namespace[source]

Get arguments with argparse.

Returns:

Populated argparse.Namespace

Return type:

argparse.Namespace