OCDocker.Toolbox.Conversion module

Sets of classes and functions that are used to convert informations such as molecules.

Usage:

import OCDocker.Toolbox.Conversion as occonversion

OCDocker.Toolbox.Conversion.convert_mols(input_file: str, output_file: str, return_molecule: Literal[True], overwrite: bool = False) → int | rdkit.Chem.rdchem.Mol | _OBMol[source]
OCDocker.Toolbox.Conversion.convert_mols(input_file: str, output_file: str, return_molecule: Literal[False] = False, overwrite: bool = False) → int | str

Convert a molecule file between two extensions which obabel supports.

Parameters:

  • input_file (str) – Input file path.

  • output_file (str) – Output file path.

  • return_molecule (bool) – If True, returns the molecule object. (default is False)

  • overwrite (bool, optional) – If True, overwrites the output file if it already exists. (default is False)

Returns:

The exit code of the command (based on the Error.py code table) if fails or the extension of the input file otherwise.

Return type:

int | str | rdkit.Chem.rdchem.Mol

OCDocker.Toolbox.Conversion.convert_mols_from_string(input, output, mol=None, overwrite=False)[source]

Currently only works with smiles. TODO: Add support to other formats.

Parameters:

  • input (str) – Input file content as string.

  • output (str) – Output file name.

  • mol (rdkit.Chem.rdchem.Mol | None, optional) – The molecule object to be used to convert the input string to a file. If None, it will be created. (default is None)

  • overwrite (bool) –

Returns:

The exit code of the command (based on the Error.py code table) if fails or the extension of the input file otherwise returns the extension itself.

Return type:

int | str

OCDocker.Toolbox.Conversion.kikd_to_deltag(kikd, T=298.15, kikd_order='un', R=8.314462618)[source]

Converts Ki/Kd to deltaG.

Parameters:

  • kikd (float) – Ki/Kd value.

  • T (float, optional) – Temperature in Kelvin. (default is STANDARD_TEMPERATURE_K, 298.15 K)

  • kikd_order (str, optional) – Order of the Ki/Kd value. (default is “un”)

  • R (float, optional) – Ideal gas constant in J/(mol·K). (default is RJ, 8.314462618 J/(mol·K))

Returns:

The deltaG value.

Return type:

float

OCDocker.Toolbox.Conversion.split_and_convert(path, out_path, extension, overwrite=False)[source]

Splits a multi-molecule file then save the output in multiple single-molecule file with the desired extension. (Supported by openbabel)

Parameters:

  • path (str) – Path to the multi-molecule file.

  • out_path (str) – Path to the output folder.

  • extension (str) – Extension of the output files.

  • overwrite (bool, optional) – If True, overwrites the output files if they already exist. (default is False)

Returns:

The exit code of the command (based on the Error.py code table).

Return type:

int