I've done some extra testing, when I wanted to write the simplest script to recreate that problem. It seams it was my fault, and Setup does work (although the weird error). I found out by the way that += operator on OBmol class doesn't work resulting empty value. How would you recommend to append ligand to pocket structure in perl instead of: $mol = $mol_pocket; $mol += $mol_ligand; where every variable is initialized OBmol object and both prefixed ones are read from files.
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