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).
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 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?
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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