Is there any way in which I can generate the RDkit atomic partial charges and associate these with the correct atoms in an SDF file? The RDKit can obviously compute the charges for my SDF/RDkit input column, but I have no idea about how to use them in practice - I am using a node that wants an SDF or mol2 file with partial charges. Pointers?
The charge calculator gives you back a collection of partial charges that are ordered according to the input atom order.
I'm not aware of a standard for attaching partial charges to molecules in an SDF. Do you know what the node you are using expects?
 A caveat there: if your input contains Hs and you want the charges on the Hs, you need to use an rdkit from molecule node and use the advanced option to keep hydrogens.
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