Fragmenter API

Fragmenter is pre-alpha so the API is still in flux.

Below is an outline of the API for the main functions of fragmenter See examples for details on how to use these functions.


Ionization can have a profound impact on the electronic structure and the torsion barrier which can lead to different fragmentation decisions. Therefore, it is important to enumerate reasonable ionization states at physiological pH. fragmenter provides a wrapper around OpenEye’s


The fragment module is the core of fragmenter. It provides two ways to fragment molecules:

  1. Combinatorial fragmentation

    This scheme generates all possible fragments for a molecule without fragmenting rings and selected functional groups. It is not recommended for general use. It was used to generate the benchmark set used to validate fragmenter

  2. WBO fragmentation

    This scheme uses the change in WBO in the rotatable bonds to decide if the fragment needs to continue being grown out. The threshold for this change can be provided by the user. The default and recommended threshold is 0.01.