nbehrnd

@e-kwsm By the lattice vectors (a,b,c) -- accounting both for lengths and enclosed angles \alpha, \beta, \gamma -- the model is in the cubic class, i.e. a = b =...

@e-kwsm An addition: for NaCl, [this page](https://lampz.tugraz.at/~hadley/ss1/crystalstructure/structures/nacl/nacl.php) by TU Graz/Austria compiles all 192 symmetry operators of space group 225.

Openbabel does not perceive the interatomic distance C-N short enough to qualify for a C=N double bond ```shell $ obabel CH2NOH.xyz -omolreport TITLE: xyz file made by CCI FORMULA: CH3NO...

I recommend you set up a virtual environment for Python and use the attached `requirements.txt` to resolve the dependencies. Different to the file available here, it contains the entry `rdkit`...

@jhjensen2 The additional entry `rdkit` in the list of requirements of `xyz2mol` appears as necessary to work with the utility experienced as very helpful if one does not want to...

@brunocalcada If your setup allows to set up a virtual environment to fetch current RDKit 2023.03.2, the attached moderator script may be helpful for you. [xyz2mol_b.zip](https://github.com/jensengroup/xyz2mol/files/12303262/xyz2mol_b.zip)

@brunocalcada If you want RDKit to add the bonds, the first snippet of code is the show case how to interact with RDKit, i.e. ```python raw_mol = Chem.MolFromXYZFile('acetate.xyz') mol =...

@brunocalcada I agree with you on the part that the current appetizing snippet of code is a bit short. To ease the initial use, I filed PR #42 a couple...

@stnrl It seems to depend on the input. + An example where this works: Generation of a model including pyridine and diethyl ether in one data set with OpenBabel (3.1.1...

With Python 3.11.2 (as provided by Linux Debian 12/bookworm), I created a virtual environment ```shell $ python3 -m virtualenv sup $ source sup/bin/activate $ pip install -r requirements.txt $ pip...