Just as a follow up, I'm getting a similar error with the following ligand
molecule:
ValueError: Sanitization error: Explicit valence for atom # 21 F, 2, is greater
than permitted
### Molecule SDF ###
C15836516_1
-OEChem-06041915443D
35 38 0 0 0 0 0 0 0999 V2000
-0.0860 -13.4464 10.3875 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.8595 -13.0611 11.4209 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.0456 -12.6304 9.1357 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.0545 -14.6571 12.8727 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.7592 -11.8504 11.3525 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.8775 -11.3676 9.0585 C 0 0 0 0 0 0 0 0 0 0 0 0
0.7867 -14.6771 10.4820 C 0 0 1 0 0 0 0 0 0 0 0 0
1.1317 -14.9419 11.9651 C 0 0 2 0 0 0 0 0 0 0 0 0
-2.1463 -11.4368 9.9188 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.1581 -15.3850 14.1896 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.1565 -12.4343 9.3137 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.8105 -10.0486 9.9553 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.9545 -13.7595 12.6050 N 0 0 0 0 0 0 0 0 0 0 0 0
0.6894 -12.9502 8.2016 O 0 0 0 0 0 0 0 0 0 0 0 0
-1.3086 -17.7691 9.7487 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.9878 -18.0241 8.4154 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.7307 -16.6855 10.4101 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.0889 -17.1956 7.7436 C 0 0 0 0 0 0 0 0 0 0 0 0
0.1681 -15.8570 9.7384 C 0 0 0 0 0 0 0 0 0 0 0 0
0.4891 -16.1120 8.4051 C 0 0 0 0 0 0 0 0 0 0 0 0
1.4492 -15.2393 7.6653 C 0 0 0 0 0 0 0 0 0 0 0 0
0.8478 -14.2161 6.9909 F 0 0 0 0 0 0 0 0 0 0 0 0
2.3744 -14.6416 8.4716 F 0 0 0 0 0 0 0 0 0 0 0 0
2.1655 -15.9259 6.7293 F 0 0 0 0 0 0 0 0 0 0 0 0
1.7821 -16.2803 12.1461 C 0 0 0 0 0 0 0 0 0 0 0 0
0.8835 -17.2086 12.6564 N 0 0 0 0 0 0 0 0 0 0 0 0
2.9611 -16.4505 11.8532 O 0 0 0 0 0 0 0 0 0 0 0 0
-0.0649 -16.8862 12.8376 H 0 0 0 0 0 0 0 0 0 0 0 0
1.1544 -19.5173 11.9361 C 0 0 0 0 0 0 0 0 0 0 0 0
1.3463 -18.9614 14.2795 C 0 0 0 0 0 0 0 0 0 0 0 0
1.3969 -20.8582 12.2343 C 0 0 0 0 0 0 0 0 0 0 0 0
1.5888 -20.3024 14.5777 C 0 0 0 0 0 0 0 0 0 0 0 0
1.1292 -18.5689 12.9587 C 0 0 0 0 0 0 0 0 0 0 0 0
1.6141 -21.2507 13.5550 C 0 0 0 0 0 0 0 0 0 0 0 0
1.8458 -22.5385 13.8418 F 0 0 0 0 0 0 0 0 0 0 0 0
15 16 1 0 0 0 0
15 17 2 0 0 0 0
16 18 2 0 0 0 0
17 19 1 0 0 0 0
18 20 1 0 0 0 0
29 31 2 0 0 0 0
29 33 1 0 0 0 0
30 32 1 0 0 0 0
30 33 2 0 0 0 0
31 34 1 0 0 0 0
32 34 2 0 0 0 0
19 20 2 0 0 0 0
7 19 1 0 0 0 0
20 21 1 0 0 0 0
26 33 1 0 0 0 0
34 35 1 0 0 0 0
1 2 2 0 0 0 0
1 3 1 0 0 0 0
1 7 1 0 0 0 0
2 5 1 0 0 0 0
2 13 1 0 0 0 0
3 6 1 0 0 0 0
3 14 2 0 0 0 0
4 8 1 0 0 0 0
4 10 1 0 0 0 0
4 13 2 0 0 0 0
8 25 1 0 0 0 0
25 26 1 0 0 0 0
25 27 2 0 0 0 0
5 9 1 0 0 0 0
6 9 1 0 0 0 0
7 8 1 0 0 0 0
9 11 1 0 0 0 0
9 12 1 0 0 0 0
21 22 1 0 0 0 0
21 23 1 0 0 0 0
21 24 1 0 0 0 0
26 28 1 0 0 0 0
M END
> <minimizedAffinity>
-3.90246
$$$$
From: Mateo Vacacela <mvacac...@cdrd.ca>
Sent: June 6, 2019 9:27 AM
To: rdkit-discuss@lists.sourceforge.net
Subject: [Rdkit-discuss] Sanitization Error: Explicit valence greater than
permitted for normal protein
Hello,
I'm getting the following error when trying to sanitize a protein from a
published pdb file (1E66):
ValueError: Sanitization error: Explicit valence for atom # 1254 C, 5, is
greater than permitted
Here is the script I'm running to recreate the error. I've replicated it based
off of a script from the deepchem library:
######## Script Starts ########
import tempfile
import os
from rdkit import Chem
from rdkit.Chem import rdmolops
protein_pdb = 'receptor.pdb'
with open(protein_pdb) as protein_file:
protein_pdb_lines = protein_file.readlines()
tempdir = tempfile.mkdtemp()
protein_pdb_file = os.path.join(tempdir, "protein.pdb")
with open(protein_pdb_file, "w") as protein_f:
protein_f.writelines(protein_pdb_lines)
molecule_file = protein_pdb_file
my_mol = Chem.MolFromPDBFile(str(molecule_file), sanitize=False, removeHs=False)
mol = Chem.SanitizeMol(my_mol) # Error occurs here
######## Script Ends #########
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