> For example, if I read in a mol2 into OB and wish to delete a carbon atom,
> replace it with an oxygen and re-write that into a new file (that has all the
> carbon’s extra hydrogens deleted and in general a chemically correct
> molecule). Something in those lines.
>
I think that would be something like:
OBMol mol; // read in from mol2 somewhere
OBAtom carbonAtom; // set to particular carbon atom
mol.DeleteHydrogens(carbonAtom);
carbonAtom.SetAtomicNum(8);
mol.AddHydrogens(carbonAtom);
// then write the file
Hope that helps,
-Geoff
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