Geoff,
Does the Python interface work for you on a Mac? (BTW, I'm almost at
the stage where I can add Pybel to the test suite, but I haven't done
so yet.)
- Noel
On 12 April 2010 20:52, Andrew Dalke <da...@dalkescientific.com> wrote:
> On Apr 12, 2010, at 9:01 PM, Noel O'Boyle wrote:
>> SetInFormat should return true for success. Does it?
>
>>>> import openbabel
>>>> obc = openbabel.OBConversion()
>>>> obc.SetInFormat("smi")
> True
>>>> mol = openbabel.OBMol()
>>>> mol
> <openbabel.OBMol; proxy of <Swig Object of type 'OpenBabel::OBMol *' at
> 0x1004e5e40> >
>>>> mol.NumAtoms()
> 0
>>>> obc.ReadString(mol, "c1ccccc1O")
> Segmentation fault
>
>
> I can work with molecules directly
>
>
>>>> import openbabel
>>>> mol = openbabel.OBMol()
>>>> mol.NewAtom(6)
> <openbabel.OBAtom; proxy of <Swig Object of type 'OpenBabel::OBAtom *' at
> 0x1004e5e10> >
>>>> mol.NumAtoms()
> 1
>>>>
>
>>>> obc = openbabel.OBConversion()
>>>> obc.SetOutFormat("smi")
> True
>>>> obc.WriteString(mol)
> Segmentation fault
>
> and for the curious, here's the most relevant part of the stack trace
>
>
> Thread 0 Crashed: Dispatch queue: com.apple.main-thread
> 0 smilesformat.so 0x0000000102206cf7
> OpenBabel::SMIBaseFormat::WriteMolecule(OpenBabel::OBBase*,
> OpenBabel::OBConversion*) + 215 (mol.h:267)
> 1 libopenbabel.4.dylib 0x000000010146c04a
> OpenBabel::OBConversion::Write(OpenBabel::OBBase*, std::ostream*) + 554
> (obconversion.cpp:811)
> 2 libopenbabel.4.dylib 0x000000010146c199
> OpenBabel::OBConversion::WriteString(OpenBabel::OBBase*, bool) + 121
> (obconversion.cpp:836)
> 3 _openbabel.so 0x000000010114b656
> _wrap_OBConversion_WriteString + 590 (basic_string.h:501)
> 4 org.python.python 0x000000010000aff3 PyObject_Call + 112
>
>
> I get the same Segmentation fault with "sdf", although with a different stack
> trace, as expected:
>
> Thread 0 Crashed: Dispatch queue: com.apple.main-thread
> 0 mdlformat.so 0x0000000102044de4
> OpenBabel::MDLFormat::WriteMolecule(OpenBabel::OBBase*,
> OpenBabel::OBConversion*) + 116 (mdlformat.cpp:604)
> 1 mdlformat.so 0x000000010204eae1
> OpenBabel::SDFormat::WriteMolecule(OpenBabel::OBBase*,
> OpenBabel::OBConversion*) + 65 (mdlformat.cpp:146)
> 2 libopenbabel.4.dylib 0x000000010146c04a
> OpenBabel::OBConversion::Write(OpenBabel::OBBase*, std::ostream*) + 554
> (obconversion.cpp:811)
> 3 libopenbabel.4.dylib 0x000000010146c199
> OpenBabel::OBConversion::WriteString(OpenBabel::OBBase*, bool) + 121
> (obconversion.cpp:836)
>
>
>
>
>
> Andrew
> da...@dalkescientific.com
>
>
>
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