xyz2mol
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jensengroup
Converts an xyz file to an RDKit mol object
The additional link to the slides and the recording of Jan Jensen's presentation of xyz2mol conveys details how the program processes the data and showcases known limitations of the implementation.
Line 56 in xyz2mol.py: `atomic_valence[8] = [2,1,3]` That will cause failure in parse some structures. I suggest remove 3 from the allowed valence list. Complain from RDkit. `[16:14:52] Explicit valence...
If the following check fails https://github.com/jensengroup/xyz2mol/blob/f51267357b250855007fd628446b3fbbed715ff2/xyz2mol.py#L507-L509 an empty list is returned by `AC2mol` and therefore `xyz2mol.py` terminates without any output whatsoever. I suggest to add an `UserWarning` in case this...
Hi all, and thanks for providing xyz2mol. Is it possible to parse multi-molecule xyz files? For example, the NCIAtlas provides geometries of pairs of molecules in xyz format. Invoking xyz2mol...
Now can also work with Tinker xyz files containing connectivity information (simply dropping it), with xyz files without title line, and with files with leading atomic number before atomic symbols.
Hello, This script was very useful but some changes were required to make it run for certain molecules, for example: - DMSO - 3-methylthiazolium - 2-thiophene carboxylic acid These changes...
Does the `--sdf` argument dump anything? I just see it's a boolean but nothing it done with it in `xyz2mol.py`
Hi all, Trying to use xyz2mol to convert xyz files to sdf, however the result is an empty file without any error whatsoever. Annexed you can find the molecule that...
