An example SMILES is
Ic1cc(cc(I)c1Oc1cc(I)c(O)cc1)CC([NH3+])C(=O)[O-] 11532858
and the code that fails is
import pybel
from openbabel import *
import sys
for mol in pybel.readfile("smi", sys.argv[1]):
atoms = [x for x in mol]
nsp3 = len(filter(lambda x: x.atomicnum == 6 and x.hyb == 3, atoms))
nsp2 = len(filter(lambda x: x.atomicnum == 6 and x.hyb == 2, atoms))
ratio = nsp3/float(nsp2+nsp3)
print mol.title, ratio
On Mon, Aug 30, 2010 at 1:04 PM, Rajarshi Guha <rajarshi.g...@gmail.com> wrote:
> Thanks for the pointer, that seemed to work. It's working now (thouhg
> I still had to manually copy the Python package from
> /usr/local/openbabel/lib/python2.5/site-packages/ to my system wide
> location).
>
> But on running a small script that goes through a SMILES file I got a
> bus error. here's the report:
>
> Process: Python [54607]
> Path:
> /System/Library/Frameworks/Python.framework/Versions/2.5/Resources/Python.app/Contents/MacOS/Python
> Identifier: Python
> Version: ??? (???)
> Code Type: X86 (Native)
> Parent Process: bash [38238]
>
> Interval Since Last Report: 1452199 sec
> Crashes Since Last Report: 39
> Per-App Interval Since Last Report: 0 sec
> Per-App Crashes Since Last Report: 1
>
> Date/Time: 2010-08-30 13:00:53.730 -0400
> OS Version: Mac OS X 10.5.8 (9L31a)
> Report Version: 6
> Anonymous UUID: A2D98871-6D26-4F54-8678-AD4490B75C0A
>
> Exception Type: EXC_BAD_ACCESS (SIGBUS)
> Exception Codes: KERN_PROTECTION_FAILURE at 0x0000000000000000
> Crashed Thread: 0
>
> Thread 0 Crashed:
> 0 smilesformat.so 0x02094f66
> OpenBabel::SMIBaseFormat::ReadMolecule(OpenBabel::OBBase*,
> OpenBabel::OBConversion*) + 1142 (smilesformat.cpp:277)
> 1 libopenbabel.4.dylib 0x00529269
> OpenBabel::OBConversion::Read(OpenBabel::OBBase*,
> std::basic_istream<char, std::char_traits<char> >*) + 217
> (obconversion.cpp:773)
> 2 libopenbabel.4.dylib 0x005295c3
> OpenBabel::OBConversion::ReadFile(OpenBabel::OBBase*,
> std::basic_string<char, std::char_traits<char>, std::allocator<char>
>>) + 403 (obconversion.cpp:979)
> 3 _openbabel.so 0x010d132b
> _wrap_OBConversion_ReadFile + 859 (openbabel-python.cpp:18106)
> 4 org.python.python 0x00121505 PyObject_Call + 50
> 5 org.python.python 0x0018f832 PyEval_EvalFrameEx + 17904
> 6 org.python.python 0x00132960 _PyExc_Fini + 1438
> 7 org.python.python 0x0018ee23 PyEval_EvalFrameEx + 15329
> 8 org.python.python 0x00191173 PyEval_EvalCodeEx + 1638
> 9 org.python.python 0x00191260 PyEval_EvalCode + 87
> 10 org.python.python 0x001a883c PyErr_Display + 1896
> 11 org.python.python 0x001a8e66 PyRun_FileExFlags + 135
> 12 org.python.python 0x001aa7d2 PyRun_SimpleFileExFlags +
> 421
> 13 org.python.python 0x001b5a57 Py_Main + 3095
> 14 org.python.pythonapp 0x00001fca 0x1000 + 4042
>
> Thread 1:
> 0 libSystem.B.dylib 0x921da6fa select$DARWIN_EXTSN + 10
> 1 libSystem.B.dylib 0x921bc155 _pthread_start + 321
> 2 libSystem.B.dylib 0x921bc012 thread_start + 34
>
> Thread 0 crashed with X86 Thread State (32-bit):
> eax: 0xbfffe1dc ebx: 0x02094b04 ecx: 0x00328c9c edx: 0x00000000
> edi: 0xbfffe1e6 esi: 0x00328c90 ebp: 0xbfffe208 esp: 0xbfff5ff0
> ss: 0x0000001f efl: 0x00010282 eip: 0x02094f66 cs: 0x00000017
> ds: 0x0000001f es: 0x0000001f fs: 0x00000000 gs: 0x00000037
> cr2: 0x00000000
>
> <snip>
>
>
> On Mon, Aug 30, 2010 at 12:49 PM, Geoffrey Hutchison
> <ge...@geoffhutchison.net> wrote:
>>> It turns out that I have v4 of the dylibs
>>
>> Do you have Open Babel installed anywhere else? You mentioned MacPorts. Did
>> you install OB at any point using MacPorts? I'd check /opt for a "v3" dylib.
>> Something is picking that up.
>>
>> Hope that helps,
>> -Geoff
>
>
>
> --
> Rajarshi Guha
> NIH Chemical Genomics Center
>
--
Rajarshi Guha
NIH Chemical Genomics Center
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