############## Dependencies ############## ********* ALFABET ********* ``ALFABET`` is a **graph neural network model** for predicting **bond dissociation energies** and **free energies** of non-cyclic bonds in organic molecules. It was trained on a large dataset of DFT-calculated data obtained at the M06-2X/def2-TZVP level of theory. The training dataset contained neutral closed-shell molecules composed of C, H, N, and O. :footcite:`stjohn_alfabet_2020` ******** DBSTEP ******** ``DBSTEP`` is a software package for calculating **steric descriptors** from 3D molecular structures. It can be used through BONAFIDE to calculate the buried volume and buried shell volume descriptors. :footcite:`luchini_dbstep_2022` ********* DScribe ********* ``DScribe`` is a Python library that converts 3D atomic or molecular structures into **fixed-length numerical fingerprints**, *e.g.*, as input for machine learning models. :footcite:`himanen_dscribe_2020` :footcite:`laakso_dscribe_2023` Within BONAFIDE, DScribe was used to implement Atom-centered Symmetry Functions, Smooth Overlap of Atomic Positions, Local Many-body Tensor Representation, and an atomic Coulomb Matrix-based descriptor. :footcite:`surajit_atomic_coulomb_matrix_2025` ********** kallisto ********** ``kallisto`` is a command-line tool for rapidly calculating various atomic features from 3D molecular structures, that is, **coordination number**, **partial charge**, (relative) **polarizability**, the **proximity shell** descriptor, and the **van der Waals radius**. :footcite:`caldeweyher_kallisto_2021` *********** mendeleev *********** ``mendeleev`` is a Python package that provides access to an extensive database of the **properties of the chemical elements** (*e.g.*, various atomic radii or electronegativity scales), which can be accessed through BONAFIDE. :footcite:`mentel_mendeleev_2014` ********* MORFEUS ********* ``MORFEUS`` is a software package that provides a broad range of molecular as well as atom and bond descriptors calculated from 3D molecular structures. BONAFIDE implements MORFEUS' **buried volume**, **dispersion**, **local force constant**, and **solvent-accessible surface area** as well as several **angle-based** atom and bond descriptors, respectively. :footcite:`jacot_morfeus_2022` ********** Multiwfn ********** ``Multiwfn`` is a multifunctional stand-alone program for the **analysis of the electronic structure of a molecule after a quantum chemical calculation**. :footcite:`lu_multiwfn_2012` :footcite:`lu_multiwfn_2024` It provides access to a large number of atom- and bond-level features that can be calculated through BONAFIDE. For an overview of the available features, see :doc:`feature_list`. ****** Psi4 ****** ``Psi4`` is an open-source quantum chemistry software package that is used in BONAFIDE to perform **single-point energy calculations** - *e.g.*, with density functional theory (DFT), including dispersion corrections and implicit solvation models. :footcite:`turney_psi4_2012` :footcite:`parrish_psi4_2017` :footcite:`smith_psi4_2020` ******** qmdesc ******** ``qmdesc`` is a graph neural network model for predicting atom and bond property descriptors that are typically obtained through quantum chemical calculations. This includes **Hirshfeld partial charges**, **Fukui indices**, **NMR shielding constants**, as well as **bond orders** and **lengths**. The large training dataset contained neutral closed-shell molecules composed of C, H, O, N, P, S, F, Cl, Br, and I and was obtained at the B3LYP/def2-SVP level of theory. :footcite:`guan_qmdesc_2021` ******* RDKit ******* ``RDKit`` is the general cheminformatics package used in BONAFIDE. It also implements a number of atom and bond descriptors which can be calculated through BONAFIDE. For the full list, see the :doc:`feature_list`. :footcite:`rdkit` ***** xtb ***** ``xtb`` is a semi-empirical quantum chemistry software package that is used in BONAFIDE to perform **single-point energy calculations** as well as for the calculation of various **atom features** such as reactivity indices from conceptual DFT (C-DFT). :footcite:`bannwarth_xtb_2021` ---- .. footbibliography::