intent

Given an input structure as .xyz file, the moderator script xyz2mol_b.py provides a representation in the .sdf format. The user is expected to describe the overall charge by flag -c (or --charge) if the molecule is not neutral. Based on Jan Jensen's work on xyz2mol¹, it depends on a recent release of RDKit (e.g., 2023.03.2). It is suggested to resolve the dependencies in an activated virtual environment for Python and a call of

pip -r install requirements.txt

and eventually use the script in a pattern like

python ./xyz2mol_b.py ./acetate.xyz --charge -1

background

Based on an algorithm by Kim and Kim², Jan Jensen implemented xyz2mol³ relying on RDKit. As presented in 2020 (recording, pdf slides), the approach works best on small molecules which do not carry organometallic bonds.

With release 2202.09.3, the functionality is available in RDKit.⁴ This allows a shorter (moderator) script to convert xyz into .sdf provided one actually has access to a version of RDKit modern enough: contrasting to Greg Landrum's blog,⁵ RDKit 2022.09.3 as so far packaged for Linux Debian does not yet include this functionality – according to repology.org,⁶ this equally applies to relatives via DebiChem (e.g. Ubuntu ecosystem). As checked, creating a virtual environment for Python and a pip based installation of RDKit 2023.03.2 (and its dependencies such as numpy) offers one successful bypass. An alternative environment not tested may be anaconda.

The script was written in an instance of Linux Debian 13/trixie (branch testing) with Python (version 3.11.4) and pip installed RDKit (2202.09.3). As inspected with openbabel and Jmol, Jan Jensen's four test structures pass the conversion.

file name	charge
acetate.xyz	-1
ethane.xyz	0
propylbenzene.xyz	1
stereogenic_center.xyz	0

Footnotes

1. https://github.com/jensengroup/xyz2mol ↩

2. Kim, Y and Kim, W. Y. Universal Structure Conversion Method for Organic Molecules: From Atomic Connectivity to Three-Dimensional Geometry. Bull. Korean Chem. Soc. 2015, 36, 1769-1777, doi 10.1002/bkcs.10334. ↩

3. https://github.com/jensengroup/xyz2mol ↩

4. https://github.com/jensengroup/xyz2mol/issues/40 ↩

5. https://greglandrum.github.io/rdkit-blog/posts/2022-12-18-introducing-rdDetermineBonds.html ↩

6. https://repology.org/project/rdkit/packages ↩