Partial charges

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?

alastair

Hi,

The charge calculator gives you back a collection of partial charges that are ordered according to the input atom order.[1]

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?

-greg

[1] 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.