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Including molecular charge when converting xyz to SMILES

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Including molecular charge when converting xyz to SMILES

Jan Halborg Jensen
Here is an xyz file for a dianion (acetic acid and phenol deprotonated).  When I use obabel to convert it to SMILES I get a neural SMILES string: CC1=C(C(=O)[O])N2C(=O)[C@@H](NC(=O)[C@H](N)[C]3C=CC(=O)C=C3)[C@H]2SC1

Is there a way to tell babel what the charge of the molecule in the xyz file is?  

Thanks, Jan

40

C 5.52213434 1.04037972 -0.21344903
C 4.14979641 0.72175715 -0.69830721
C 3.80189866 -0.52425963 -1.08154369
C 4.78871811 -1.68677308 -1.05759866
O 5.36429884 -2.04393713 -2.11706225
O 5.03693689 -2.29596182 0.01240530
N 2.51806460 -0.85539957 -1.61704756
C 1.64167506 -1.93529681 -1.15665342
O 1.88177128 -3.07223781 -0.84570314
C 0.38699419 -1.03686728 -1.32089715
N -0.41565976 -0.86210634 -0.11436302
C -1.66887913 -1.46088079 0.07935917
O -2.09867013 -2.21556101 -0.79159436
C -2.40390187 -1.11435255 1.38179379
N -3.06409980 -2.33433580 1.91663587
C -3.34449137 0.03011170 1.13460705
C -3.11007081 1.26081850 1.75945915
C -3.96380542 2.32604802 1.57980687
C -5.12121413 2.20613682 0.74548299
O -5.91738469 3.18260604 0.57039672
C -5.33939968 0.93922701 0.11479753
C -4.46681404 -0.10791309 0.30923656
C 1.36558728 0.12602707 -1.70431718
S 1.46343831 1.59347592 -0.62371327
C 3.25516512 1.91176976 -0.73152740
H 5.91873564 1.92738209 -0.72779341
H 5.50359059 1.26015205 0.86445216
H 6.23407818 0.21925530 -0.37250852
H -0.25881445 -1.35000434 -2.17604312
H -0.05932105 -0.22394045 0.56886590
H -1.65835450 -0.81869359 2.16704349
H -3.76017540 -2.65505578 1.27336878
H -3.51292278 -2.09527374 2.77673377
H -2.22902428 1.37760460 2.40323164
H -3.76223158 3.27884336 2.07870878
H -6.21306056 0.80894499 -0.53040533
H -4.65218800 -1.06319493 -0.19870556
H 1.23324582 0.46603150 -2.75552132
H 3.47301401 2.49218246 -1.65023820
H 3.48134020 2.58359136 0.12250721
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Re: Including molecular charge when converting xyz to SMILES

Geoff Hutchison
> Is there a way to tell babel what the charge of the molecule in the xyz file is?  

From the command-line? No. Even if there was, it’s not going to suddenly assign formal charges to your de-protonated functional groups.

(Yes, as humans we can find the most likely places to put the negative charges, but there’s nothing in the codebase that can do that.)

-Geoff
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