Hi Anthony,
On Fri, Jul 26, 2013 at 4:56 AM, Anthony Bradley <
[email protected]> wrote:
> Hi all, ****
>
> ** **
>
> This is my first post on the rdkit mailing list, but I’ve been using it
> for a few months now (and think it’s awesome by the way).****
>
> **
>
Welcome! and thanks!
> **
>
> I’ve found a slightly quirky behaviour.****
>
> ** **
>
> Rdkit can read in the below mol block but then the smiles it produces
> cannot be read in again.
>
I can reproduce this. Thanks for reporting it.
> ****
>
> ** **
>
> I think the problem is the lack of explicit hydrogen on the aromatic
> sulphur, leading to an inability to kekulize.****
>
> ** **
>
> I was wondering why this might occur?****
>
> **
>
I think there's actually an error in the input structure. It looks like
there should be a charge somewhere in the 5 ring.
In any case, what the RDKit is currently doing is wrong. It should either
fail on the input structure or produce a SMILES that can be read back in.
I'll file a bug for it.
-greg
> **
>
> Thanks,****
>
> ** **
>
> Anthony****
>
> ** **
>
> Sim_1 = 'C=CCn1c2ccc(S(N)(=O)=O)cc2sc1NS(=O)(=O)c1ccc(Cl)s1' # None mol ->
> what rdkit outputs****
>
> ** **
>
> Smi_2 = 'C=CCn1c2ccc(S(N)(=O)=O)cc2sc1=NS(=O)(=O)c1ccc(Cl)s1' # Not None *
> ***
>
> ** **
>
> Smi_3 = ‘C=CCn1c2ccc(S(N)(=O)=O)cc2[sH]c1NS(=O)(=O)c1ccc(Cl)s1' # Not None
> ****
>
> ** **
>
> # Smi_2 and Smi_3 both hold a different oxidation state for the sulphur.
> According to the SDF it should be Smi_3.****
>
> ** **
>
> from rdkit import Chem****
>
> ** **
>
> sdf= """probmol****
>
> RDKit 3D****
>
> ** **
>
> 26 28 0 0 0 0 0 0 0 0999 V2000****
>
> 40.2640 -47.5920 65.9800 N 0 0 0 0 0 0 0 0 0 0 0 0****
>
> 41.1750 -46.7850 66.5750 C 0 0 0 0 0 0 0 0 0 0 0 0****
>
> 41.4340 -46.7010 67.9480 C 0 0 0 0 0 0 0 0 0 0 0 0****
>
> 42.4150 -45.8090 68.3990 C 0 0 0 0 0 0 0 0 0 0 0 0****
>
> 43.1240 -45.0120 67.4860 C 0 0 0 0 0 0 0 0 0 0 0 0****
>
> 42.8540 -45.1070 66.1140 C 0 0 0 0 0 0 0 0 0 0 0 0****
>
> 41.8740 -45.9990 65.6750 C 0 0 0 0 0 0 0 0 0 0 0 0****
>
> 41.4130 -46.2370 64.0380 S 0 0 0 0 0 0 0 0 0 0 0 0****
>
> 40.2720 -47.4090 64.6280 C 0 0 0 0 0 0 0 0 0 0 0 0****
>
> 39.4590 -48.0810 63.8510 N 0 0 0 0 0 0 0 0 0 0 0 0****
>
> 39.3560 -48.5030 66.6990 C 0 0 0 0 0 0 0 0 0 0 0 0****
>
> 39.9550 -49.8630 66.8630 C 0 0 0 0 0 0 0 0 0 0 0 0****
>
> 40.2440 -50.3500 68.0660 C 0 0 0 0 0 0 0 0 0 0 0 0****
>
> 39.3310 -47.9450 62.1280 S 0 0 0 0 0 0 0 0 0 0 0 0****
>
> 40.7120 -48.0440 61.5180 O 0 0 0 0 0 0 0 0 0 0 0 0****
>
> 38.4830 -49.0830 61.6020 O 0 0 0 0 0 0 0 0 0 0 0 0****
>
> 38.5560 -46.4150 61.7050 C 0 0 0 0 0 0 0 0 0 0 0 0****
>
> 39.4690 -45.0310 61.2360 S 0 0 0 0 0 0 0 0 0 0 0 0****
>
> 37.9620 -44.2200 61.0510 C 0 0 0 0 0 0 0 0 0 0 0 0****
>
> 36.8440 -44.9740 61.3330 C 0 0 0 0 0 0 0 0 0 0 0 0****
>
> 37.8570 -42.5080 60.5230 Cl 0 0 0 0 0 0 0 0 0 0 0 0****
>
> 37.1890 -46.2470 61.7120 C 0 0 0 0 0 0 0 0 0 0 0 0****
>
> 44.3650 -43.8910 68.0560 S 0 0 0 0 0 0 0 0 0 0 0 0****
>
> 45.0700 -44.4650 69.2670 O 0 0 0 0 0 0 0 0 0 0 0 0****
>
> 45.3810 -43.6550 66.9600 O 0 0 0 0 0 0 0 0 0 0 0 0****
>
> 43.6310 -42.3950 68.5100 N 0 0 0 0 0 0 0 0 0 0 0 0****
>
> 1 2 1 0****
>
> 1 11 1 0****
>
> 2 3 2 0****
>
> 3 4 1 0****
>
> 5 23 1 0****
>
> 5 4 2 0****
>
> 6 5 1 0****
>
> 7 6 2 0****
>
> 7 2 1 0****
>
> 8 9 2 0****
>
> 8 7 1 0****
>
> 9 1 1 0****
>
> 10 9 1 0****
>
> 11 12 1 0****
>
> 12 13 2 0****
>
> 14 10 1 0****
>
> 15 14 2 0****
>
> 16 14 2 0****
>
> 17 22 2 0****
>
> 17 14 1 0****
>
> 18 17 1 0****
>
> 19 18 1 0****
>
> 19 20 2 0****
>
> 20 22 1 0****
>
> 21 19 1 0****
>
> 23 26 1 0****
>
> 23 24 2 0****
>
> 25 23 2 0****
>
> M END"""****
>
> ** **
>
> mol = Chem.MolFromMolBlock(sdf)****
>
> ** **
>
> mol is None****
>
> ** **
>
> # Gives false ****
>
> ** **
>
> # Then convert to smiles and back****
>
> smimol = Chem.MolFromSmiles(Chem.MolToSmiles(mol))****
>
> ** **
>
> smimol is None****
>
> ** **
>
> # Gives true****
>
> ** **
>
> ** **
>
>
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