The Biochemical Library (BCL) integrates traditional small molecule cheminformatics tools with machine learning-based quantitative structure-activity/property relationship (QSAR/QSPR) modeling. The cheminformatics toolkit contains customizable tools for the design, processing, and analysis of small molecules for computer-aided drug discovery.
This is a PR for a minor modification to the FragmentAlchemy class that enables it to perform alchemy to create undefined atoms in molecules. Undefined atoms are useful for pseudo-reaction chemistry during drug design. Previously, the allowed_element_types list included 'X' (for undefined) as a possible type; however, other logic related to choosing a correct atom type from the specified element, as well as the bits for molecule cleaning, prevented that flag from being functional. This has been corrected here.
This is a PR for a minor modification to the FragmentAlchemy class that enables it to perform alchemy to create undefined atoms in molecules. Undefined atoms are useful for pseudo-reaction chemistry during drug design. Previously, the allowed_element_types list included 'X' (for undefined) as a possible type; however, other logic related to choosing a correct atom type from the specified element, as well as the bits for molecule cleaning, prevented that flag from being functional. This has been corrected here.