Pre-condition Violation Number of atom mismatch Violation occurred on line 564 in file Code\GraphMol\ROMol.cpp Failed Expression: conf->getNumAtoms() == this->getNumAtoms() RDKIT: 2017.09.1 BOOST: 1_56

[ssalaniwal]

Hi,

When using Python Script node in Knime after the RDKit R-group Decomposition node, I am getting the following error message.

ERROR Python Script 0:54 Execute failed: Pre-condition Violation
Number of atom mismatch
Violation occurred on line 564 in file Code\GraphMol\ROMol.cpp
Failed Expression: conf->getNumAtoms() == this->getNumAtoms()
RDKIT: 2017.09.1
BOOST: 1_56

The python script only contains the following lines of code

_from rdkit import Chem
from rdkit.Chem import AllChem
import pandas as pd

mols = input_table_1['R1']
output_table_1 = input_table_1.copy()_

where R1 is generated by the RDkit R-group decomposition node.

If I feed the structures prior to R-group decomposition directly to the python script then it works just fine indicating that the Rgroup decomposition node output is likely the source of this error.

RDKIt G-Group decomp node configuration is as follows:

Knime: 4.5.0
Python: 2.7.18 installed as part of conda environment
OS: Windows 10

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• RDKit version:
• OS: [e.g. Ubuntu 20.04]
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[greglandrum]

I transferred this to the knime-rdkit repo because it sounds like it's connected with the KNIME nodes.

[greglandrum]

@ssalaniwal : you are using an ancient and unsupported version of the RDKit and (and Python itself, for that matter). It may be that the problem is due to that, but we'll see.