On Tue, Jul 6, 2010 at 3:52 PM, Noel O'Boyle <baoille...@gmail.com> wrote:
> Hi Tim,
>
> I recently updated to latest trunk and I'm getting a segfault which
> seems to be due to some problem in ring.cpp (but I could be wrong).
> The segfault is triggered by GetParent() Line 606 in ring.cpp which
> does not return a valid molecule. I'd appreciate if you could look
> into it.
>
> Here's the code to reproduce it:
>
> OBConversion conv;
> OB_REQUIRE( conv.SetInFormat("sdf") );
>
> OBMol mol;
> OB_REQUIRE( conv.ReadFile(&mol, GetFilename("tmp.sdf")) );
>
> OBBuilder builder;
> builder.Build(mol);
>
> mol.AddHydrogens();
mol.UnsetFlag(OB_SSSR_MOL);
mol.UnsetFlag(OB_LSSR_MOL);
mol.UnsetFlag(OB_RINGFLAGS_MOL);
mol.UnsetFlag(OB_AROMATIC_MOL);
mol.UnsetFlag(OB_KEKULE_MOL);
mol.UnsetFlag(OB_CLOSURE_MOL);
mol.UnsetFlag(OB_AROM_CORRECTED_MOL);
mol.UnsetFlag(OB_RINGTYPES_MOL);
This fixes the problem. :-) I still have to find out which one it is
though. One of these lines should probably go in Builder or
AddHydrogens...
> OBForceField* pff = OBForceField::FindType("mmff94");
> OB_REQUIRE(pff->Setup(mol)); // Segfault
>
> This passes with r3799 (prior to all of the LSSR changes, etc.), but
> segfaults with the HEAD. If the builder lines are commented out,
> there's no segfault.
>
> The test case is attached.
>
> - Noel
>
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