> Is it possible to extract coordinates (xyz) from these O, N atoms which are > attached to one/two Hs using babel (lets say from a mol2/sdf file)? Or I > need to use rdkit or custom python scripts for such tasks?
While the babel command line offers a lot of features it obviously can't offer everything (yet) That's to say that if you want only the coordinates of certain atoms, you'll need to write a script, e.g. in Python either with OB or RDKit or similar toolkit. Best regards, -Geoff
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