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
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