Hello Thank you very much, this is very helpful.
For a quick description of DSSP please see: https://en.m.wikipedia.org/wiki/DSSP_(hydrogen_bond_estimation_algorithm) All the best AA On Sun, 1 Mar 2020, 09:27 Noel O'Boyle, <baoille...@gmail.com> wrote: > atom.GetResidue() has the PDB information. > > for atom in ob.OBMolAtomIter(mol.OBMol): > residue = atom.GetResidue() > print("%d %s %s" % (residue.GetIdx(), residue.GetName(), > residue.GetAtomID(atom))) > > Regarding addh(), I'm not sure what DSSP is. > > On Sun, 16 Feb 2020 at 15:40, Athanasios Anastasiou < > athanastas...@gmail.com> wrote: > >> Hello >> >> I am trying to obtain some information from a PDB file, using openbabel, >> but I find myself going in a roundabout way getting it....and this is not a >> good sign, so I was wondering if I could get some help around the following >> (?): >> >> 1. Having read a PDB and obtained a reference to a pybel.Atom / OBAtom, >> which attribute corresponds to the "Element Symbol" of the ATOM record? >> Alternatively, what would be a generic way of inferring it from the "type"? >> Is it always "[A-Z][a-z]*[0-9]+"? >> >> 2. Alternatively to 1, how can I select all atoms that belong to a main >> chain of a molecule? >> >> 3. How close is the "addh()" function to the way the DSSP works? Once >> "addh()" is called, hydrogens are added and their bond lengths are worked >> out. Each "H" is marked as a "donor_h" and adjacent atoms are marked with >> donor / acceptor attributes. However, that "H" appears to be attached only >> on one side (to its donor) and the acceptor is flagged but not "attached". >> Would I be too wrong if I run a "nearest neighbour that is also acceptor" >> query and "attach" it myself? And if I was to do this wouldn't I now know >> where the hydrogen bonds are and from the respective distances to all known >> atoms, be able to work out its energy (?). (Just as DSSP does). >> >> 4. There are H Bonds that are also flagged away from (what I think is) >> the main chain of a molecule. In one example, there are two H that are >> flagged as the hbond_donor_h's which are attached to a "Nam" (?) that is >> marked as "donor". This in turn is attached to a C and that C is also >> attached to an O. That O is marked as an "acceptor". What happens in that >> case? Would I simply ignore that or attempt to still go ahead and infer a >> bond? >> >> All the best >> thanOS >> >> >> _______________________________________________ >> OpenBabel-discuss mailing list >> OpenBabel-discuss@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss >> >
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