Babel: Choice Mac Os X

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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


Path: /System/Library/Frameworks/Python.framework/Versions/2.6/Resources/Python.app/Contents/MacOS/Python
Version: ??? (???)
Parent Process: bash [788]
PlugIn Path: /usr/local/lib/openbabel/2.3.0/smilesformat.so
PlugIn Version: ??? (???)
Date/Time: 2011-02-27 17:54:20.545 +0000
Report Version: 6
Interval Since Last Report: 55803 sec
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

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')


Can anyone suggest what might be happening? It would be great if I could get Pybel to work on the Mac. I
Thanks

Hassan Mamdani MSci MPhil MRSC

Widsmob hdr 2 8. 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: [hidden email]

P Please consider the environment before printing this e-mail.

Babel: choice mac os x 10.13

Avant d'imprimer ce courriel, pensez à l'environnement.

Notice: This email is confidential and intended for the exclusive use of the addressee. If you are not the intended addressee, please notify us immediately by e-mail, delete the original without keeping a copy and do not disclose its content or use the information for any purpose.

Avis :Ce courriel est confidentiel et à l'usage exclusif du destinataire. Si vous avez reçu ce courriel par erreur, veuillez nous en informer immédiatement par courriel, effacer l'original sans en conserver de copie et ne pas en dévoiler le contenu ni utiliser l'information pour quelque fin que ce soit.


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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


Babel: Choice Mac Os X 10.13

Path: /System/Library/Frameworks/Python.framework/Versions/2.6/Resources/Python.app/Contents/MacOS/Python
Version: ??? (???)
Parent Process: bash [788]
PlugIn Path: /usr/local/lib/openbabel/2.3.0/smilesformat.so
PlugIn Version: ??? (???)
Date/Time: 2011-02-27 17:54:20.545 +0000
Report Version: 6
Interval Since Last Report: 55803 sec
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

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')

Babel: Choice Mac Os X 10.8



Can anyone suggest what might be happening? It would be great if I could get Pybel to work on the Mac. I
Thanks

Hassan Mamdani MSci MPhil MRSC

Research Scientist

ProMetic Biosciences UK

211 Cambridge Sciene Park, Milton Road

Babel: Choice Mac Os X 10.10

Owlet 1 1 0 download free. Cambridge, CB4 0ZA

Tel: +44 (0) 1223 433861

fax: +44 (0) 1223 420270

Email: [hidden email]

P Please consider the environment before printing this e-mail.

Avant d'imprimer ce courriel, pensez à l'environnement.

Notice: This email is confidential and intended for the exclusive use of the addressee. If you are not the intended addressee, please notify us immediately by e-mail, delete the original without keeping a copy and do not disclose its content or use the information for any purpose.

Avis :Ce courriel est confidentiel et à l'usage exclusif du destinataire. Si vous avez reçu ce courriel par erreur, veuillez nous en informer immédiatement par courriel, effacer l'original sans en conserver de copie et ne pas en dévoiler le contenu ni utiliser l'information pour quelque fin que ce soit.


Babel: Choice Mac Os X 10.7

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Mac

Avant d'imprimer ce courriel, pensez à l'environnement.

Notice: This email is confidential and intended for the exclusive use of the addressee. If you are not the intended addressee, please notify us immediately by e-mail, delete the original without keeping a copy and do not disclose its content or use the information for any purpose.

Avis :Ce courriel est confidentiel et à l'usage exclusif du destinataire. Si vous avez reçu ce courriel par erreur, veuillez nous en informer immédiatement par courriel, effacer l'original sans en conserver de copie et ne pas en dévoiler le contenu ni utiliser l'information pour quelque fin que ce soit.


------------------------------------------------------------------------------
free. software download: Index, Search & Analyze Logs and other IT data in
Real-Time with Splunk. Collect, index and harness all the fast moving IT data
generated by your applications, servers and devices whether physical, virtual
or in the cloud. Deliver compliance at lower cost and gain new business
insights. http://p.sf.net/sfu/splunk-dev2dev
_______________________________________________
OpenBabel-discuss mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
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


Babel: Choice Mac Os X 10.13

Path: /System/Library/Frameworks/Python.framework/Versions/2.6/Resources/Python.app/Contents/MacOS/Python
Version: ??? (???)
Parent Process: bash [788]
PlugIn Path: /usr/local/lib/openbabel/2.3.0/smilesformat.so
PlugIn Version: ??? (???)
Date/Time: 2011-02-27 17:54:20.545 +0000
Report Version: 6
Interval Since Last Report: 55803 sec
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

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')

Babel: Choice Mac Os X 10.8



Can anyone suggest what might be happening? It would be great if I could get Pybel to work on the Mac. I
Thanks

Hassan Mamdani MSci MPhil MRSC

Research Scientist

ProMetic Biosciences UK

211 Cambridge Sciene Park, Milton Road

Babel: Choice Mac Os X 10.10

Owlet 1 1 0 download free. Cambridge, CB4 0ZA

Tel: +44 (0) 1223 433861

fax: +44 (0) 1223 420270

Email: [hidden email]

P Please consider the environment before printing this e-mail.

Avant d'imprimer ce courriel, pensez à l'environnement.

Notice: This email is confidential and intended for the exclusive use of the addressee. If you are not the intended addressee, please notify us immediately by e-mail, delete the original without keeping a copy and do not disclose its content or use the information for any purpose.

Avis :Ce courriel est confidentiel et à l'usage exclusif du destinataire. Si vous avez reçu ce courriel par erreur, veuillez nous en informer immédiatement par courriel, effacer l'original sans en conserver de copie et ne pas en dévoiler le contenu ni utiliser l'information pour quelque fin que ce soit.


Babel: Choice Mac Os X 10.7

------------------------------------------------------------------------------
free. software download: Index, Search & Analyze Logs and other IT data in
Real-Time with Splunk. Collect, index and harness all the fast moving IT data
generated by your applications, servers and devices whether physical, virtual
or in the cloud. Deliver compliance at lower cost and gain new business
insights. http://p.sf.net/sfu/splunk-dev2dev
_______________________________________________
OpenBabel-discuss mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss




broken image