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jensengroup / xyz2mol

Converts an xyz file to an RDKit mol object
MIT License
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atomic valence of O atom inconsistent with RDkit #34

Open XinChenQC opened 2 years ago

XinChenQC commented 2 years ago

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 for atom # 1 O, 3, is greater than permitted

jhjensen2 commented 2 years ago

I need a specific example

XinChenQC commented 2 years ago

13 O=[C]c1ccccc1,C7H5O1 C 60.148399 7.311 88.774498 O 59.610699 6.74176 89.587196 C 60.923199 8.0155 87.707703 C 60.375198 9.24672 87.064796 C 62.044102 7.49395 86.800697 C 60.619598 9.44654 85.701401 H 59.479 9.73245 87.510902 C 62.485901 7.61041 85.430702 H 62.7295 6.5795 87.050499 C 61.491798 8.55076 85.024101 H 60.237099 10.4347 85.086403 H 63.136501 6.94037 85.061996 H 61.661701 8.82767 83.954803

This is a twisted structure from ReaxFF simulation.

python xyz2mol.py ***.xyz --no-charged-fragments --use-huckel