[Open Babel] Deleting atoms given their indices-> unexpected result

[Michael B. <mb...@ya...>]

Dear all,

Given an OBmol molecule I would like to delete part of its atoms, 
that I previously identified by a smarts pattern match.
Problem is that the wrong atoms end up being deleted.
When i check which atoms have been identified by smarts.Match()
using atom->GetIdx() the returned numbers and the serial numbers
of the atoms in the mol2 file that correspond to the smarts pattern agree.
But when i then use DeleteAtom(mol.GetAtom(index)) and look at the 
remainder of the molecule after the atoms have been deleted it turns out 
that a number of atoms were deleted that had indices different from
those I originally used to identify the atoms i want to remove.

I am confused about the indices. Maybe the problem
is also that after each OBmol.DeleteAtom(atom) the
indices are reassigned in part (are they?). To test that
I used DestroyAtom instead, which gave me a Segmentation fault
once i tried to remove and then reassign hydrogens to clean
up the chopped molecule.

In the docu on OBmol.GetAtom() it says:
"Atom indexing will change. Use iterator methods instead"
i am not sure how to do that in this context, or if it would help ...

a rough "symbolic" outline of what i tried is below.
(the code assumes that there is only one unique
match per molecule which is always true in my case)

I'd appreciate any help, TIA!
Michael

=== code:

OBmol mymol;
conv.Read(&mymol); // define mymol by reading a mol2 file.
OBAtom *atom;

smarts.Init(<smarts patttern provided as string>);

if (smarts.Match(mymol)) {

  maplist = smarts.GetUMapList();

  for (matches = maplist.begin(); matches != maplist.end(); matches++) {

    for(int nat=0;nat<smarts.NumAtoms();nat++) {
          atom = mymol.GetAtom((*matches)[nat]); // at this point both (*matches)[nat] and atom.GetIdx() agree
                                                                       // and the numbers are as expected 
          mymol.DeleteAtom(atom);
    }
  }
}

mymol.DeleteHydrogens();
mymol.AddHydrogens(false,true,7.4);
conv.Write(&mymol);         // upon visual inspection of the output molecule
                                       // i see that in part wrong atoms have been deleted...