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hjkgrp / molSimplify

molSimplify code
GNU General Public License v3.0
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Missing file "linear.dat" #235

Closed lucaslucaslucaslu closed 3 months ago

lucaslucaslucaslu commented 3 months ago

Hi, I tried to run molsimplify -cores Fe -lig '[N+](=O)([O-])[O-]' -smicat [[3, 4]] -coord 2 -ligocc 1 -spin 1 -rundir ms_dummy and get FileNotFoundError: [Errno 2] No such file or directory: '/home/usr/.conda/envs/myenv/lib/python3.11/site-packages/molSimplify/Data/linear.dat'.

I didn't find this specific file in the repo, and it doesn't really work if I simply rename li.dat to linear.dat or make a copy of li.dat

I'm just wondering if there is anything I missed, thanks!

dbkchu commented 3 months ago

Hi,

Thank you for pointing out this error. It appears that there was a typo in the list of default geometry names for the two and three coordinate geometries. This has now been fixed, but this code will still not run since molSimplify does not support attaching a bidentate ligand to a linear geometry.

If you would really like only one ligand attached, I would recommend making a tetrahedral structure with the ligand and then manually deleting the second ligand.

To make a tetrahedral structure, you could run: molsimplify -cores Fe -lig '[N+](=O)([O-])[O-]' -smicat [[3, 4]] -coord 4 -ligocc 2 -spin 1

We will look into adding the ability to attach a bidentate ligand to a linear geometry, but this may take a while.