Dear all,
I’m maintaining a package to perceive molecular interactions that depends on openbabel functionality using python. Historically it used openbabel 2.4.1, but recently I’ve learned that there is a version 3.x so I wanted to give it a go (newer should be better right? 😊). I made few changes according to the document here: https://open-babel.readthedocs.io/en/latest/UseTheLibrary/migration.html to comply with the breaking changes…. Long story short, in certain cases the interactions perceived by the software are not the same as with underlying openbabel 2.4.1. Namely there are missing plane-plane interactions. I can see the following message in the log that was not there with the previous version: *** Open Babel Warning in PerceiveBondOrders Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders So I suspect this may be root of the problem So my question is twofold: Is there a way how can I find out what is possibly wrong with the structure so that I can fix it? Is there any change in the way protein structure is being constructured If I do it myself? This is essentially what I do: import openbabel.openbabel as ob mol = ob.OBMol() mol.BeginModify() # residue is created like this res = mol.NewResidue() res.SetChainNum(chain_num) res.SetNum(res_id) res.SetName(res_name) res.SetInsertionCode(ins_code) # atom is created in a residue like this: atom = mol.NewAtom(atom_id) atom.SetVector(x,y,z) atomic_num = ob.GetAtomicNum(element) atom.SetAtomicNum(atomic_num) atom.SetFormalCharge(_format_formal_charge(atom_sites, i)) res.AddAtom(atom) res.SetHetAtom(atom, atom_sites["group_PDB"][i] == "HETATM") res.SetSerialNum(atom, int(atom_sites["id"][i])) # after atom reading is done this is the post-processing mol.EndModify() mol.ConnectTheDots() ob.OBAromaticTyper().AssignAromaticFlags(mol) mol.PerceiveBondOrders() My setup: Mac os: 10.15.5 Python: 3.7 Best, Lukas
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