Notes on usage

After installing the package (see Installation), BONAFIDE can be used by instantiating the AtomBondFeaturizer class. The user has the opportunity to specify a custom log file name by passing data to the log_file_name parameter. By default, the log file is called bonafide.log and is created in the current working directory.

>>> from bonafide import AtomBondFeaturizer
>>> f = AtomBondFeaturizer()

The log file will contain all messages logged during the usage of BONAFIDE.

Atom, bond, and feature indices

All indices within BONAFIDE, including those for atoms, chemical bonds, and the respective features are zero-based. This means that the first atom or bond in a molecule has index 0.

Feature vectors

In case a given atom or bond feature is not represented by a single value but is rather a vector, the datatype of this feature is str and the individual values are comma-separated within the string.