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#104 Set handling of charges
How are charges handled? If there are two molecules with the same atoms and bonds but one has a charge at an atom and the other not, are these different molecules for Scaffold Hunter? It would be nice to choose the behavior like one can choose it for chirality information (checkbox during import).
As far as i understand the chemical background we are currently consider different charges to be distinct. The charges are incuded in the SMILES representing the molecules for indenticy identification and are used in the molecules depiction (see screenshots below)
Thus, your proposal is to allow to disable the charges during import. In the case we simply remove the charge information, the molecule becomes invalid, or am i wrong? In some cases one can add hydrogens or tomething like that, but afaik this is not always possible. If it is possible it would still lead to distinct molecular structures.
=> can you please elaborate, how we should proceed when we remove a charge information from a molecule.
depiction screenshot
We can't just omit the charge in the SMILES. In easier cases it would be possible to remove or add protons (H+), as you suggested. For rdkit I found a function that neutralizes charges here. For CDK there is a discussion here. But both solutions seem to me not comprehensive.
Do Scaffold Hunter correct structures like setting a charge where one is needed?
I think if there is a charge which is not due to de-/protonation then the structures are different ,e.g., different number of bounds/bond types. The use case I thought of was merging protomers in a dataset. Meaning only the cases where the charge is caused by de-/protonation (easier cases) should be handled by Scaffold Hunter.