ProtoCaller.Wrappers.babelwrapper module

This is the module that is responsible for wrapping some of Open Babel’s most essential features, such as: file conversion, protonation at a certain pH and 3D coordinate generation.

ProtoCaller.Wrappers.babelwrapper.babelTransform(input_filename, output_extension='mol2', pH=None, generate_3D_coords=False)

A light wrapper of some of OpenBabel’s file conversion capabilities.

Parameters

• input_filename (str) – Name of the input file.

• output_extension (str) – Type of output extension.

• pH (float or None) – Hydrogenate the molecule for a certain pH. None means no hydrogenation.

• generate_3D_coords (bool) – Whether to generate 3D coordinates for the molecule.

Returns

filename – The absolute path to the output file.

Return type

str