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Incorrect atomic weight values for common elements (S, Cl) #7238

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markarchibald opened this issue Mar 12, 2024 · 1 comment
Open

Incorrect atomic weight values for common elements (S, Cl) #7238

markarchibald opened this issue Mar 12, 2024 · 1 comment

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@markarchibald
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Describe the bug
A number of common elements (most notably sulfur and chlorine) have incorrect atomic weight values (vs values from CIAAW).

To Reproduce
E.g. for sulfur

from rdkit import Chem
from rdkit.Chem.Descriptors import MolWt
MolWt(Chem.MolFromSmiles('[S]'))

returns 32.067

Expected behavior
The returned atomic weights should match the values published by CIAAW. Three examples are given in the table below (these are the elements in the standard 'organic' set that have significant errors). Correcting S and Cl would have the most impact.

element CIAAW standard atomic weight RDKit atomic weight
S 32.06 32.067
Cl 35.45 35.453
Se 78.971 78.96

A csv comparing all RDKit-derived atomic weights with the corresponding CIAAW values is attached, sorted by absolute difference in the values. Note that the entries with a difference >= 1 mass unit reflect selection of the wrong 'most stable' isotope, which is covered by #7237.

rdkit-atomic-weight-comparison.csv

CIAAW standard atomic weights from: https://www.ciaaw.org/atomic-weights.htm (for elements whose full standard atomic weight is expressed as a range, the recommended 'general use' values from https://www.ciaaw.org/abridged-atomic-weights.htm are used).

Configuration (please complete the following information):

  • RDKit version: 2023.9.4
  • OS: Windows 11 22H2
  • Python version (if relevant): 3.12.1
  • Are you using conda? No
  • If you are using conda, which channel did you install the rdkit from?
  • If you are not using conda: how did you install the RDKit? pip

Additional context
I've just submitted a related bug (#7237). I kept these separate as they appear to have different root issues – choosing the wrong isotope vs having an incorrect mass value stored.

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This issue was marked as stale because it has been open for 90 days with no activity.

@github-actions github-actions bot added the stale label Oct 18, 2024
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