Hi,
I am currently upgrading our code from openbabel 2.4.2 to openbabel 3.0 (using the python bindings). I am having trouble with the EndModify command. What the code is doing: 1. Load a pdb file and a mol2 file of an amino acid (aa_mol) into seperate obMols 2. Set both ObMol to BeginModify() 3. Calculate a rotation vector and remove overlapping atoms via DeleteAtom() from aa_mol and pdb obmol 4. Then create a new obatom in the pdb file and copy all information and remake the bonds new_atom.SetId(id) new_atom.SetVector(frag_atom.GetVector()) new_atom.SetAtomicNum(frag_atom.GetAtomicNum()) new_atom.SetType(frag_atom.GetType()) new_atom.SetSpinMultiplicity(frag_atom.GetSpinMultiplicity()) new_atom.SetFormalCharge(frag_atom.GetFormalCharge()) #new_atom.SetImplicitValence(frag_atom.GetImplicitValence()) #old 2.4.2 replaced with line below new_atom.SetImplicitHCount(frag_atom.GetImplicitHCount()) new_atom.SetPartialCharge(frag_atom.GetPartialCharge()) for obbond in openbabel.OBMolBondIter(fragment): begin_atom = obbond.GetBeginAtom() end_atom = obbond.GetEndAtom() mol.AddBond(obbond.GetBeginAtomIdx() + prevAtoms, obbond.GetEndAtomIdx() + prevAtoms, obbond.GetBondOrder(), obbond.GetFlags()) 5. Renumber the atoms so that the newly inserted atoms are at the desired location 6. Make a bond between the fragment and the CA atom in the pdb file 7. Set name of residue. 8. Set Dihedral angle. Now this code was working perfectly fine in ob2.4.2, but now in 3.0 it does not anymore. I get a Segmentation fault when setting the Dihedral angle. If I move the mol.EndModify() before the SetTorsion command the segmentation fault disappears but all the atoms become unlinked (Residue UNL). If I write out a PDB file just before the EndModify command everything looks alright (correct CONECT statements, positions, order etc.). Any ideas where the problem is? Thank you for your help, Simon Simon Dürr i...@simonduerr.eu<mailto:i...@simonduerr.eu> https://simonduerr.eu<https://simonduerr.eu/>
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