These are preliminary reports that have not been peer-reviewed. They should not be regarded as conclusive, guide clinical practice/health-related behavior, or be reported in news media as established information. For more information, please see our FAQs.
bond_parser.pdf (440.71 kB)

Perception of Chemical Bonds via Machine Learning

revised on 02.12.2018, 20:38 and posted on 03.12.2018, 16:49 by Christoph Loschen
An approach based on machine-learning is presented that is able to identify chemical bond types such as single, double, triple and aromatic bonds based on spatial atomic coordinates only, as provided for example from quantum chemical calculations or from crystallographic data.
The basic idea behind this work is to exploit the various chemical knowledge already assembled in molecular data files in form of connection tables and bond blocks. Rules for novel chemistry or particular functional groups can be learned automatically by training on structure data (.sd/.sdf) files with the respective bond information. Provided that the underlying database is sufficiently large and diverse, the approach is able to identify chemical bond orders in molecules with an accuracy comparable to classical bond-perception tools using hard-coded rules and cheminformatic algorithms. The workflow is implemented in Python using the open source packages RDKit, scikit-learn and pandas (


Email Address of Submitting Author


Independent Research



ORCID For Submitting Author


Declaration of Conflict of Interest

no conflict of interest

Version Notes

version 1.1 updated the Open Babel prediction accuracies