Hi
I have managed to compile OpenBabel with the python bindings on my Mac by
following the instructions on the OpenBabel website. OpenBabel works fine form
the command line, and I can import pybel into python. However whenever I try
to use pybel I get a segmentation error For example:
>> import pybel
>> mol = pybel.readstring('smi', 'cccccc')
Gives
Process: Python [828]
Path:
/System/Library/Frameworks/Python.framework/Versions/2.6/Resources/Python.app/Contents/MacOS/Python
Identifier: Python
Version: ??? (???)
Code Type: X86-64 (Native)
Parent Process: bash [788]
PlugIn Path: /usr/local/lib/openbabel/2.3.0/smilesformat.so
PlugIn Identifier: smilesformat.so
PlugIn Version: ??? (???)
Date/Time: 2011-02-27 17:54:20.545 +0000
OS Version: Mac OS X 10.6.6 (10J567)
Report Version: 6
Interval Since Last Report: 55803 sec
Crashes Since Last Report: 9
Per-App Crashes Since Last Report: 8
Anonymous UUID: 2F0E7AD2-6BEA-4699-94B9-3084B1D5402C
Exception Type: EXC_BAD_ACCESS (SIGSEGV)
Exception Codes: KERN_INVALID_ADDRESS at 0x0000000000000090
Crashed Thread: 0 Dispatch queue: com.apple.main-thread
Thread 0 Crashed: Dispatch queue: com.apple.main-thread
0 smilesformat.so 0x0000000102a23833
OpenBabel::SMIBaseFormat::ReadMolecule(OpenBabel::OBBase*,
OpenBabel::OBConversion*) + 1011 (mol.h:355)
1 libopenbabel.4.dylib 0x00000001014e51ec
OpenBabel::OBConversion::Read(OpenBabel::OBBase*, std::istream*) + 220
(obconversion.cpp:789)
2 libopenbabel.4.dylib 0x00000001014ea49c
OpenBabel::OBConversion::ReadString(OpenBabel::OBBase*, std::string) + 508
(obconversion.cpp:937)
3 _openbabel.so 0x0000000101181d36
_wrap_OBConversion_ReadString + 262 (openbabel-python.cpp:18172)
4 org.python.python 0x000000010000aff3 PyObject_Call + 112
5 org.python.python 0x000000010008a51a PyEval_EvalFrameEx + 20328
6 org.python.python 0x00000001000892e1 PyEval_EvalFrameEx + 15663
7 org.python.python 0x000000010008acce PyEval_EvalCodeEx + 1803
8 org.python.python 0x000000010008ad61 PyEval_EvalCode + 54
9 org.python.python 0x00000001000a265a Py_CompileString + 78
10 org.python.python 0x00000001000a44dd PyRun_InteractiveOneFlags
+ 503
11 org.python.python 0x00000001000a4615 PyRun_InteractiveLoopFlags
+ 206
12 org.python.python 0x00000001000a4685 PyRun_AnyFileExFlags + 76
13 org.python.python 0x00000001000b0286 Py_Main + 2718
14 org.python.python.app 0x0000000100000e6c start + 52
Thread 0 crashed with X86 Thread State (64-bit):
rax: 0xffffffffffffffff rbx: 0xffffffffffffffff rcx: 0x0000000000000063
rdx: 0x0000000000000000
rdi: 0x0000000102a2cb0b rsi: 0x0000000000000063 rbp: 0x00007fff5fbfece0
rsp: 0x00007fff5fbf6930
r8: 0x0000000000000000 r9: 0x0000000000000002 r10: 0x00007fff89397b0f
r11: 0x00007fff80ad20d6
r12: 0x00007fff5fbf6a50 r13: 0x00000001015f6e40 r14: 0x00007fff7017f500
r15: 0x0000000000000000
rip: 0x0000000102a23833 rfl: 0x0000000000010246 cr2: 0x0000000000000090
<snip>
I have tried different smiles strings (some pulled from pubchem which render
correctly in other programs) and I have also tried reading from and sdf file:
>> molfile = pybel.readfile('sdf', 'mymols.sdf')
>> mymol = molfile.next()
<segmentation fault>
Can anyone suggest what might be happening? It would be great if I could get
Pybel to work on the Mac. I
Thanks
Hassan
Hassan Mamdani MSci MPhil MRSC
Research Scientist
ProMetic Biosciences UK
211 Cambridge Sciene Park, Milton Road
Cambridge, CB4 0ZA
Tel: +44 (0) 1223 433861
fax: +44 (0) 1223 420270
Email: hmamd...@prometicbiosciences.com<mailto:sf...@prometicbiosciences.com>
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