Propyl radical gives empty list of molecules

[steinmig]

I tried various options, but all of them returned an empty list for the propyl radical.

8

C     -0.3027758391    0.5794019014    1.0345046298
C      0.0425157439   -0.4399390123    0.1832077568
C      0.2724509312   -0.2796867185   -1.1600106986
H     -0.4707683461    0.4079216362    2.0816470556
H     -0.4162158143    1.5863557406    0.6730322879
H      0.1401386036   -1.4356735654    0.5989624308
H      0.5435628550   -1.1069559010   -1.7895205051
H      0.1910918658    0.6885759191   -1.6218229572

[steinmig]

As I now checked other molecules from my dataset, I noticed that I have the same behavior for all radicals. Is there no solution for those?

[nbehrnd]

With Python 3.11.2 (as provided by Linux Debian 12/bookworm), I created a virtual environment

$ python3 -m virtualenv sup
$ source sup/bin/activate
$ pip install -r requirements.txt
$ pip install rdkit
$ cat example.xyz 
8

C     -0.3027758391    0.5794019014    1.0345046298
C      0.0425157439   -0.4399390123    0.1832077568
C      0.2724509312   -0.2796867185   -1.1600106986
H     -0.4707683461    0.4079216362    2.0816470556
H     -0.4162158143    1.5863557406    0.6730322879
H      0.1401386036   -1.4356735654    0.5989624308
H      0.5435628550   -1.1069559010   -1.7895205051
H      0.1910918658    0.6885759191   -1.6218229572
$
$ python xyz2mol.py example.xyz --no-charged-fragments
[CH2]C=C
$
$ python xyz2mol.py example.xyz --no-charged-fragments -o sdf

     RDKit          3D

  8  7  0  0  0  0  0  0  0  0999 V2000
   -0.3028    0.5794    1.0345 C   0  0  0  0  0  3  0  0  0  0  0  0
    0.0425   -0.4399    0.1832 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2725   -0.2797   -1.1600 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4708    0.4079    2.0816 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4162    1.5864    0.6730 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1401   -1.4357    0.5990 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5436   -1.1070   -1.7895 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1911    0.6886   -1.6218 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  1  4  1  0
  1  5  1  0
  2  3  2  0
  2  6  1  0
  3  7  1  0
  3  8  1  0
M  RAD  1   1   2
M  END
$

The set of files I used is an old one, fetched by 2022-07-21. But running the script with -h already includes the option to process radicals.

[steinmig]

Ah great, thanks!

I never tried this option in my script, because I got lazy and tried some options only on the command line, but turns out that your cli entry point is broken?

xyz2mol h2o.xyz does not give me any output.

The installed cli entry point is

import re
import sys 

from xyz2mol import main

if __name__ == '__main__':
    sys.argv[0] = re.sub(r'(-script\.pyw?|\.exe)?$', '', sys.argv[0])
    print(sys.argv)
    sys.exit(main())

but the main function is simply

def main():

    return

[nbehrnd]

So far, I used the script only in its own virtual environment, activated only if this script is needed. My reasoning for this and against a system-wide installation is `xyz2mol` relies on functionality beyond Python's standard library. I wasn't aware (yet) that the functionality eventually was added to RDKit, a note added to `README.md` about two weeks ago; I still want to use the script as such "alone", no intent (so far) to import it into other scripts. I'm not surprised the simple input ```shell xyz2mol h2o.xyz ``` does not provide a useful result. Still in the active virtual environment (in Linux Debian), I had to add the missing shebang (`#!/usr/bin/env python3`) on top and the executable bit (`chmod +x ./xyz2mol.py`). You do not indicate the operating system accessible to you, the hint to the interpreter's location for pure Windows (no WSL), or MacOS might differ here.