I encountered almost exactly the same problem with running
RD Kit using Python. So it looks like it is a swig / python
issue. (I did not write earlier because I was not sure about
the cause. Actually I have been eagerly waiting for an answer!)
So, it looks like one cannot write python functions to operate
on a molecule or an atom in the conventional way. Fred's
workaround of having the function return the molecule
(or the atom) may well be the correct way of doing it.
Ling
>________________________________
> From: Noel O'Boyle <[email protected]>
>To: Fred Ludlow <[email protected]>
>Cc: "[email protected]"
><[email protected]>
>Sent: Monday, July 8, 2013 2:04 PM
>Subject: Re: [Open Babel] Segfault when merging molecules through python API
>
>
>I've reproduced this behaviour. As you say it's fairly subtle. In fact
>I can't tell whether it's a bug at our end or a feature of swig in
>general.
>
>It appears that obmol += newmol replaces the underlying OBMol with a
>new one. You can see this by printing out the obmol (the address
>changes) in a non-segfaulting version:
> mol = pybel.readstring("smi", "C").OBMol
> newmol = pybel.readstring("smi", "C").OBMol
> print mol
> mol += newmol
> print mol
> print pybel.Molecule(mol).write("smi")
>
><openbabel.OBMol; proxy of <Swig Object of type 'OpenBabel::OBMol *'
>at 0x022F5290> >
><openbabel.OBMol; proxy of <Swig Object of type 'OpenBabel::OBMol *'
>at 0x028CDF08> >
>C.C
>
>If you do the addition in a function, then the mol variable remains
>pointing to an OBMol which has been destroyed or something.
>
>If you can find any clues to this in the SWIG docs, I'm happy to try
>to fix it but I've just taken a look and don't see anything obvious. I
>don't see anything fishy about our C++ code either:
> OBMol &OBMol::operator+=(const OBMol &source)
>
>?
>
>- Noel
>
>On 3 July 2013 11:31, Fred Ludlow <[email protected]> wrote:
>> Hi,
>>
>> I've come across a subtle bug (or misunderstanding on my part..?) when
>> merging molecules from python... I've attached a minimal example that
>> segfaults (tested on Red Hat Enterprise Linux, python 2.7, openbabel
>> 2.3.1). Essentially, it seems that if I do something like
>>
>> mol1 += mol2
>>
>> inside a function, mol1 (or more likely the C++ object underneath) is
>> no longer valid and doing things like converting it to an output
>> string fails with a segfault. I'm guessing swig or python has decided
>> there aren't any more references to it and has triggered deletion of
>> the C++ object?
>> e.g something like:
>>
>> def addNewFragment(obmol):
>> frag = newFrag() # Create some OBMol instance
>> obmol += frag
>>
>> mymol = getMol() # Some function to return OBMol instance
>> addNewFragment(mymol)
>> # At this point the mymol object is broken, and calls to many of its
>> methods fail with a segfault
>>
>>
>> Storing another reference to it (e.g. by returning the molecule from
>> the function and assigning it to something ) fixes the problem, e.g:
>>
>> def addNewFragmentAndReturn(obmol):
>> frag = newFrag()
>> obmol += frag
>> return obmol
>>
>> mymol =getMol()
>> foo = addNewFragmentAndReturn(mymol)
>> # mymol is still valid... (creating the "foo" reference seems to have
>> kept it alive...)
>>
>>
>> I think this is a bug - Can anyone else reproduce this (demo script
>> attached) or is it me not understanding how to use the library :)
>>
>> Fred
>>
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