You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
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.
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.
The text was updated successfully, but these errors were encountered:
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
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.
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):
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.
The text was updated successfully, but these errors were encountered: