Before 3.0, aromaticity perception was performed as if the position of the hydrogens were unknown, and the hydrogens were inferred afterwards. This makes sense for structures from the PDB, but not for anything else (e.g. SMILES) where there were occasional errors and it was much slower than necessary. Now, the perception is the other way around; it makes sense for everything except for structures where the bond order is unknown, like for PDB structures.
It would be nice to return the PDB structure perception to the same level as before - I 'just' need to adapt the old procedure to the job. But in the short term, for this particular problem, you may find it best to use OB 2.4.1. Regards, - Noel On Tue, 14 Jul 2020 at 13:49, Lukas Pravda <lpra...@ebi.ac.uk> wrote: > 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: > > 1. Is there a way how can I find out what is possibly wrong with the > structure so that I can fix it? > 2. 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 > _______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss >
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