I have a problem using the 'RDKit calculate charge' node.
What I have : A file containing 2 columns : Canonical Smiles + Inchi Key
What I want : Convert SMILES into SDF file with gasteiger charges.
What I do : I use the 'molconvert' node to convert SMILES into SDF then the 'RDKit calculate charge' node to calculate the charges.
What is the problem : For some of the molecules I have the following error :
"ERROR RDKit Calculate Charges 4:16 Failed to convert cell SDF Parsing Error (MolSanitizeException) for MoleculeX"
"WARN RDKit Calculate Charges 4:16 Empty cell in ('SDF', 'Row436544'). All result cells will be empty."
But I have not any empty cell when I look at the file.
Is there any solution to this or this is a problem that can not be avoid ?
Thank you for your answer
The error/warning messages you are describing are typically due to molecules that have atoms with unrealistic valences, but it's tough to tell from the information provided so far.
I'm not 100% sure what format you would like to have in the output SDF, but the attached workflow shows a relatively simple way to, starting from SMILES, generate an SDF that includes a "charges" data field for each molecule.
I hope this helps,
Thank you for your answer, the workflow you sent me work perfectly for what i want to do.
have a good day