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rdkit reports "Explicit valence for atom # 0 S, 7, is greater than permitted" for six-valent sulfur?

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#9,581 6 comentarios 0 reacciones 0 asignados Ver en GitHub

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Evaluación

Dificultad
4/5
Tiempo estimado
3-5 días
Aptitud para principiantes
55/100
Tipo de issue
Error
Claridad
Bastante claro
Estado de actividad
Activo
Stack tecnológico
python
Área
backend

Línea de trabajo

Reproduce the error with the supplied ADX PDB block using Chem.MolFromPDBBlock, then trace the PDB parser's bond construction and sulfur valence validation. Compare the parsed CONECT records with the expected six-valent sulfur behavior; done means the case is handled correctly or its unsupported status is clearly established with a regression test.

Escrito por el modelo de indexación a partir del texto del issue.

Descripción

I have a PDB file for the PDBeChem (aka CCD) ligand ADX which has (as far as I can see...) a six-valent sulfur, but I get this:

from rdkit import Chem
mol = Chem.MolFromPDBBlock(ADX)
[13:51:37] Explicit valence for atom # 0 S, 7, is greater than permitted

The "CONECT" record for the S is -

CONECT 1 2 2 3 3 4 8

which looks to me as if it's 6-valent.

Python 3.11.11
rdkit 2024.03.6
MacOS High Sierra 10.13.6 (yes, I know this is old but it's running on a good machine that can't be updated further)

The code I use to convert from the CIF I download from PDBeChem works okay for thousands of other CIF files from PDBeChem, so although it could be the problem I don't think it is.

ADX is read in from a file, and is a string that contains -

HEADER    Model coordinates for ADX downloaded from PDBeChem                    
COMPND    ADX                                                                   
HETATM    1  SB  ADX A   1       1.120  -0.280  -5.646  1.00 20.00           S
HETATM    2  O1B ADX A   1       1.559  -1.323  -6.506  1.00 20.00           O
HETATM    3  O2B ADX A   1      -0.013   0.546  -5.868  1.00 20.00           O
HETATM    4  O3B ADX A   1       2.303   0.667  -5.509  1.00 20.00           O
HETATM    5  PA  ADX A   1      -0.128   0.012  -3.483  1.00 20.00           P
HETATM    6  O1A ADX A   1       0.457   1.363  -3.330  1.00 20.00           O
HETATM    7  O2A ADX A   1      -1.512   0.117  -4.299  1.00 20.00           O
HETATM    8  O3A ADX A   1       0.899  -0.930  -4.288  1.00 20.00           O
HETATM    9  O5' ADX A   1      -0.409  -0.618  -2.029  1.00 20.00           O
HETATM   10  C5' ADX A   1      -1.323   0.258  -1.367  1.00 20.00           C
HETATM   11  C4' ADX A   1      -1.634  -0.286   0.027  1.00 20.00           C
HETATM   12  O4' ADX A   1      -0.429  -0.350   0.821  1.00 20.00           O
HETATM   13  C3' ADX A   1      -2.560   0.685   0.793  1.00 20.00           C
HETATM   14  O3' ADX A   1      -3.918   0.250   0.712  1.00 20.00           O
HETATM   15  C2' ADX A   1      -2.053   0.615   2.252  1.00 20.00           C
HETATM   16  O2' ADX A   1      -3.085   0.138   3.118  1.00 20.00           O
HETATM   17  C1' ADX A   1      -0.880  -0.386   2.193  1.00 20.00           C
HETATM   18  N9  ADX A   1       0.195   0.033   3.094  1.00 20.00           N
HETATM   19  C8  ADX A   1       1.227   0.869   2.784  1.00 20.00           C
HETATM   20  N7  ADX A   1       1.998   1.026   3.820  1.00 20.00           N
HETATM   21  C5  ADX A   1       1.509   0.308   4.860  1.00 20.00           C
HETATM   22  C6  ADX A   1       1.913   0.092   6.188  1.00 20.00           C
HETATM   23  N6  ADX A   1       3.049   0.702   6.691  1.00 20.00           N
HETATM   24  N1  ADX A   1       1.175  -0.705   6.953  1.00 20.00           N
HETATM   25  C2  ADX A   1       0.089  -1.290   6.482  1.00 20.00           C
HETATM   26  N3  ADX A   1      -0.323  -1.122   5.243  1.00 20.00           N
HETATM   27  C4  ADX A   1       0.350  -0.341   4.405  1.00 20.00           C
HETATM   28 HOB3 ADX A   1       2.436   1.075  -6.376  1.00 20.00           H
HETATM   29 HOA2 ADX A   1      -1.860  -0.781  -4.377  1.00 20.00           H
HETATM   30  H5' ADX A   1      -2.245   0.325  -1.945  1.00 20.00           H
HETATM   31 H5'' ADX A   1      -0.877   1.249  -1.280  1.00 20.00           H
HETATM   32  H4' ADX A   1      -2.094  -1.271  -0.044  1.00 20.00           H
HETATM   33  H3' ADX A   1      -2.460   1.697   0.400  1.00 20.00           H
HETATM   34 HO3' ADX A   1      -4.447   0.891   1.205  1.00 20.00           H
HETATM   35  H2' ADX A   1      -1.702   1.593   2.582  1.00 20.00           H
HETATM   36 HO2' ADX A   1      -3.811   0.774   3.065  1.00 20.00           H
HETATM   37  H1' ADX A   1      -1.222  -1.388   2.454  1.00 20.00           H
HETATM   38  H8  ADX A   1       1.381   1.332   1.821  1.00 20.00           H
HETATM   39 HN61 ADX A   1       3.315   0.548   7.611  1.00 20.00           H
HETATM   40 HN62 ADX A   1       3.582   1.279   6.122  1.00 20.00           H
HETATM   41  H2  ADX A   1      -0.481  -1.931   7.137  1.00 20.00           H
CONECT    1    2    2    3    3    4    8
CONECT    4   28
CONECT    5    6    6    7    8    9
CONECT    7   29
CONECT    9   10
CONECT   10   11   30   31
CONECT   11   12   13   32
CONECT   12   17
CONECT   13   14   15   33
CONECT   14   34
CONECT   15   16   17   35
CONECT   16   36
CONECT   17   18   37
CONECT   18   19   27
CONECT   19   20   20   38
CONECT   20   21
CONECT   21   22   27   27
CONECT   22   23   24   24
CONECT   23   39   40
CONECT   24   25
CONECT   25   26   26   41
CONECT   26   27
END                                                                             
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