Dear Experts,
I was trying to read in the attached SD file (downloaded from HMDB)
and trying to calculate the exact mass of each entry:
structures.sdf
<https://drive.google.com/file/d/0B3AmIbK_SzZhdGY3NVgyMDJiQjA/view?usp=drive_web>
from rdkit import Chem
from rdkit.Chem import Descriptors
suppl = Chem.SDMolSupplier(input_file)
low_mass=50
high_mass=1000
ms = []
for mol in suppl :
if mol is None: continue
try:
if mol and
round(Descriptors.ExactMolWt(mol),4)>=low_mass and
round(Descriptors.ExactMolWt(mol),4)<=high_mass:
ms.append(mol)
except:
pass
By running the script, I got a barrage of errors as:
[13:15:14] ERROR: Could not sanitize molecule ending on line 1993855
[13:15:14] ERROR: Explicit valence for atom # 9 O, 3, is greater than
permitted
[13:15:14] Explicit valence for atom # 9 O, 3, is greater than permitted
[13:15:14] ERROR: Could not sanitize molecule ending on line 1994014
[13:15:14] ERROR: Explicit valence for atom # 9 O, 3, is greater than
permitted
[13:15:14] Explicit valence for atom # 9 O, 3, is greater than permitted
[13:15:14] ERROR: Could not sanitize molecule ending on line 1996036
[13:15:14] ERROR: Explicit valence for atom # 9 O, 3, is greater than
permitted
[13:15:16] Explicit valence for atom # 46 N, 4, is greater than permitted
[13:15:16] ERROR: Could not sanitize molecule ending on line 2302532
[13:15:16] ERROR: Explicit valence for atom # 46 N, 4, is greater than
permitte
[13:15:16] Explicit valence for atom # 16 N, 4, is greater than permitted
[13:15:16] ERROR: Could not sanitize molecule ending on line 2302918
[13:15:16] ERROR: Explicit valence for atom # 16 N, 4, is greater than
permitte
[13:15:17] Explicit valence for atom # 11 N, 4, is greater than permitted
[13:15:17] ERROR: Could not sanitize molecule ending on line 2556541
[13:15:17] ERROR: Explicit valence for atom # 11 N, 4, is greater than
permitte
[13:15:18] S group SUP ignored on line 2836416
[13:15:18] Explicit valence for atom # 1 Cl, 4, is greater than permitted
[13:15:18] ERROR: Could not sanitize molecule ending on line 2841449
[13:15:18] ERROR: Explicit valence for atom # 1 Cl, 4, is greater than
permitte
[13:15:19] Warning: conflicting stereochemistry at atom 10 ignored.
[13:15:19] Warning: conflicting stereochemistry at atom 10 ignored.
[13:15:19] Warning: conflicting stereochemistry at atom 17 ignored.
[13:15:19] Warning: conflicting stereochemistry at atom 17 ignored.
[13:15:19] Explicit valence for atom # 3 B, 4, is greater than permitted
[13:15:19] ERROR: Could not sanitize molecule ending on line 3107498
[13:15:19] ERROR: Explicit valence for atom # 3 B, 4, is greater than
permitted
[13:15:19] Warning: conflicting stereochemistry at atom 6 ignored.
[13:15:19] Warning: conflicting stereochemistry at atom 6 ignored.
[13:15:20] Unhandled CTAB feature: S group SRU on line: 3205922.
Molecule skip
[13:15:20] Explicit valence for atom # 0 Mg, 4, is greater than permitted
[13:15:20] ERROR: Could not sanitize molecule ending on line 3222378
[13:15:20] ERROR: Explicit valence for atom # 0 Mg, 4, is greater than
permitte
[13:15:20] Explicit valence for atom # 2 N, 4, is greater than permitted
[13:15:20] ERROR: Could not sanitize molecule ending on line 3265386
[13:15:20] ERROR: Explicit valence for atom # 2 N, 4, is greater than
permitted
[13:15:20] Explicit valence for atom # 31 N, 4, is greater than permitted
[13:15:20] ERROR: Could not sanitize molecule ending on line 3305754
[13:15:20] ERROR: Explicit valence for atom # 31 N, 4, is greater than
permitte
[13:15:21] Explicit valence for atom # 45 N, 4, is greater than permitted
[13:15:21] ERROR: Could not sanitize molecule ending on line 3437055
[13:15:21] ERROR: Explicit valence for atom # 45 N, 4, is greater than
permitte
[13:15:56] Explicit valence for atom # 3 C, 5, is greater than permitted
[13:15:56] ERROR: Could not sanitize molecule ending on line 8391489
[13:15:56] ERROR: Explicit valence for atom # 3 C, 5, is greater than
permitted
What causes these errors? there a way to suppress or solve the errors?
or way to stop priting them up in the command prompt.
--
Thanks,
Milinda Samaraweera,
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