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

[Geoffrey H. <ge...@ge...>]

>    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);

At the moment, index numbers are the direct index into a vector --  
they're not unique ids for an atom. So once you delete an atom, the  
vector is adjusted and the previous index numbers are invalid.

I don't have time to check this, but you want something like:

std::list <OBAtom*> deletedAtomList;
...
for (int nat = 0; nat < smarts.NumAtoms(); ++nat) {
    atom = mymol.GetAtom((*matches)[nat]);
    deletedAtomList.push_back(atom);
}

// Now, once you have deletedAtomList, iterate through *that* and  
delete the atoms

Hope that helps,
-Geoff