DDBST Validation

In this notebook, we evaluate the performance of ugropy against the DDBST fragmentation database. The database file was originally published in Simon Müller’s article [1]:

https://doi.org/10.1186/s13321-019-0382-3

and is hosted in the official repository:

https://github.com/simonmb/fragmentation_algorithm

To run these tests, the database file has been replicated in the ugropy repository. All rights to the original data are retained by the authors. Both this notebook and the database file are available at:

https://github.com/ipqa-research/ugropy/tree/main/docs/source/tests_book/against_ddbst

• DDBST fragmentation database
  • Auxiliary function
  • First-attempt success rate
  • Solution multiplicity success rate
  • Testing ugropy multi-solution filters
    • filter_mostly_polyatomic
    • filter_mostly_polarity — polar
    • filter_mostly_polarity — apolar
    • filter_bigger_polyatomics — Q
    • filter_bigger_polyatomics — R
    • filter_polarity_contribution — Q — polar
    • filter_polarity_contribution — Q — apolar
    • filter_polarity_contribution — R — polar
    • filter_polarity_contribution — R — apolar