Hi all, I am tracking down a memory issue triggered by OpFillUC::Do, but which happens deep down in the bowels of openbabel. Since I'm new to this project, I don't have a good view of its overall architecture and I'm having a hard time finding what happens and how to correct it, so I'm asking here for help!
Now, let's get to it. I am chasing down a memory issue that sometimes shows up
when using "babel --fillUC" as an OS warning ("incorrect checksum for freed
object - object was probably modified after being freed"). As such, I ran
openbabel under valgrind, which shows a series of invalid reads when using
"babel --fillUC" which aren't encountered when doing the same conversion
without --fillUC. The first of these messages is:
> Invalid read of size 8
> at 0xD759A: OpenBabel::OBSmartsPattern::GetCharge(int) (in
> /opt/openbabel-2.3.1/lib/libopenbabel.4.0.1.dylib)
> by 0xE1C20: OpenBabel::OBChemTsfm::Init(std::string&, std::string&) (in
> /opt/openbabel-2.3.1/lib/libopenbabel.4.0.1.dylib)
> by 0xE0D1C: OpenBabel::OBPhModel::ParseLine(char const*) (in
> /opt/openbabel-2.3.1/lib/libopenbabel.4.0.1.dylib)
> by 0x4A79E: OpenBabel::OBGlobalDataBase::Init() (in
> /opt/openbabel-2.3.1/lib/libopenbabel.4.0.1.dylib)
> by 0xE1EBC:
> OpenBabel::OBPhModel::AssignSeedPartialCharge(OpenBabel::OBMol&) (in
> /opt/openbabel-2.3.1/lib/libopenbabel.4.0.1.dylib)
> by 0x1E767: OpenBabel::OBAtom::GetPartialCharge() (in
> /opt/openbabel-2.3.1/lib/libopenbabel.4.0.1.dylib)
> by 0x21AB3: OpenBabel::OBAtom::Duplicate(OpenBabel::OBAtom*) (in
> /opt/openbabel-2.3.1/lib/libopenbabel.4.0.1.dylib)
> by 0x1190CE6: OpenBabel::OpFillUC::Do(OpenBabel::OBBase*, char const*,
> std::map<std::string, std::string, std::less<std::string>,
> std::allocator<std::pair<std::string const, std::string> > > const*,
> OpenBabel::OBConversion*) (in
> /opt/openbabel-2.3.1/lib/openbabel/2.3.1/plugin_ops.so)
> by 0x10139D: OpenBabel::OBOp::DoOps(OpenBabel::OBBase*,
> std::map<std::string, std::string, std::less<std::string>,
> std::allocator<std::pair<std::string const, std::string> > > const*,
> OpenBabel::OBConversion*) (in
> /opt/openbabel-2.3.1/lib/libopenbabel.4.0.1.dylib)
> by 0xFF583: OpenBabel::OBMol::DoTransformations(std::map<std::string,
> std::string, std::less<std::string>, std::allocator<std::pair<std::string
> const, std::string> > > const*, OpenBabel::OBConversion*) (in
> /opt/openbabel-2.3.1/lib/libopenbabel.4.0.1.dylib)
> by 0x1081DC:
> OpenBabel::OBMoleculeFormat::ReadChemObjectImpl(OpenBabel::OBConversion*,
> OpenBabel::OBFormat*) (in /opt/openbabel-2.3.1/lib/libopenbabel.4.0.1.dylib)
> by 0x6BD8A3:
> OpenBabel::OBMoleculeFormat::ReadChemObject(OpenBabel::OBConversion*) (in
> /opt/openbabel-2.3.1/lib/openbabel/2.3.1/abinitformat.so)
So, it happens when OpFillUC::Do calls OBAtom::Duplicate, which in turn tries
to do a lot of things that look, well, clever. The code in question is from
src/ops/fillUC.cpp:
OBAtom *newAtom = pmol->NewAtom();
newAtom->Duplicate(atom->first);
newAtom->SetVector( pUC->FractionalToCartesian(atom->second[i]));
where atom->first is an OBAtom* (the original atom) and atom->second[i] is a
vector3 (the coordinates). I'm seeing the same kind of code in
src/generic.cpp's OBUnitCell::FillUnitCell:
newAtom = mol->NewAtom();
newAtom->Duplicate(*i);
newAtom->SetVector(FractionalToCartesian(updatedCoordinate));
So, that leaves me wondering:
1. Why is atom duplication doing a "deep copy" (trying to infer properties it
doesn't know), and not a "shallow copy"? Is there a way to perform the latter
instead? (I look at OBAtom's methods, but couldn't find anything)
2. Even if it does try to figure out atomic partial charges, why does it lead
to a memory mishandling?
I hope someone can help me with that issue. If you want to play around with it,
just run "babel --fillUC AFO.cif AFO.pdb" on the attached AFO.cif file.
Many thanks in advance,
FX
AFO.cif
Description: Binary data
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