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Describe the bug
I receive pre-condition violations for every molecule I've tested when calculating BCUT descriptors. Our standardization code adds H's to each molecule first. The violations print out in my notebook multiple times per molecule and (sometimes multiple) per descriptor, resulting in thousands of outputs and eventually crashing my notebook. The descriptors that cause it are:
****
Pre-condition Violation
bad result vector size
Violation occurred on line 40 in file /project/build/temp.linux-aarch64-cpython-39/rdkit/Code/GraphMol/Descriptors/Crippen.cpp
Failed Expression: logpContribs.size() == mol.getNumAtoms() && mrContribs.size() == mol.getNumAtoms()
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Stacktrace:
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****
It also seems to be somewhat dependent on first calling AddHs and/or passing the descriptors in an iterable vs a single descriptor, although I don't know why that's the case.
To Reproduce
smiles='C#CCC(C(=O)c1ccc(C)cc1)N1CCCC1'
from rdkit import Chem
mol=Chem.MolFromSmiles(smiles)
mol=Chem.AddHs(mol)
from rdkit.Chem import Descriptors
from rdkit.ML.Descriptors import MoleculeDescriptors
calc = MoleculeDescriptors.MolecularDescriptorCalculator([x[0] for x in Descriptors._descList])
desc_names = calc.GetDescriptorNames()
calc=MoleculeDescriptors.MolecularDescriptorCalculator(['BCUT2D_MWHI'])
descriptors = calc.CalcDescriptors(mol)
Expected behavior
I'd like the warnings not to appear and not crash my notebook.
Screenshots
Configuration (please complete the following information):
RDKit version: 2023.9.5 (It happens for 2023.9.X but not 2023.3.3)
OS: [e.g. Ubuntu 20.04] Apple M2 Max running Ubuntu Lunar 23.04 ARM64 on a VM.
Python version (if relevant):
Python 3.9.17 (main, Aug 21 2023, 10:36:40)
[GCC 12.3.0] on linux
Are you using conda? No
If you are using conda, which channel did you install the rdkit from? NA
If you are not using conda: how did you install the RDKit? pip install rdkit==2023.9.5
Additional context
I believe it is NOT ARM-specific since my colleagues see the same issue on regular Linux/Ubuntu with the 2023.9.X versions.
The text was updated successfully, but these errors were encountered:
Describe the bug
I receive pre-condition violations for every molecule I've tested when calculating BCUT descriptors. Our standardization code adds H's to each molecule first. The violations print out in my notebook multiple times per molecule and (sometimes multiple) per descriptor, resulting in thousands of outputs and eventually crashing my notebook. The descriptors that cause it are:
And the violation repeatedly reads:
It also seems to be somewhat dependent on first calling AddHs and/or passing the descriptors in an iterable vs a single descriptor, although I don't know why that's the case.
To Reproduce
Expected behavior
I'd like the warnings not to appear and not crash my notebook.
Screenshots
Configuration (please complete the following information):
Python 3.9.17 (main, Aug 21 2023, 10:36:40)
[GCC 12.3.0] on linux
pip install rdkit==2023.9.5
Additional context
I believe it is NOT ARM-specific since my colleagues see the same issue on regular Linux/Ubuntu with the 2023.9.X versions.
The text was updated successfully, but these errors were encountered: