Porting xyz2mol to the RdKit core

This project aims to construct a C++ implementation of the Python package xyz2mol from Prof. Jan H. Jensen’s research group (https://github.com/jensengroup/xyz2mol) and integrate it into the RDKit alongside wrappers. The program will be able to convert the atomic coordinates and charge of an organic molecule presented as an xyz file to an RDKit molecule object. Once the tool is equipped, RDKit users will have another way to construct a molecule. The core work of the project will involve working on reimplementation of the Python programs function's. The main two steps of the program are 1) deriving atomic connectivities from coordinates and 2) determining the most favorable bond ordering from atomic connectivities. Atomic connectivities are found using either the Huckel method or through consideration of van der Waals radii. Favorable bond ordering is determined by considering different possible valences. The project is hence split up into these subparts. Bond ordering, atomic connectivity, formal charges, and the molecule’s conformation, among a few other factors, are combined to create an RDKit mol object.