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From: Noel O'B. <bao...@gm...> - 2008-07-27 09:41:33
Attachments:
inchi.txt
inchi23dmolfile.py
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---------- Forwarded message ---------- From: Bjoern Gruening <bj...@gr...> Date: 2008/7/27 Subject: Pybel - localopt() error?! To: Noel O'Boyle <bao...@gm...> Hi Noel, as far as i know are you one of the main developer behind the great pybel bindungs for openbabel. I'm unable to find an irc channel or something like this, so i'm trying to cantact you directly. Hope that is ok. I'm playing around with the new functions draw, localopt, addh etc. And i get a strange error if i try to generate 3D structures from inchis. Attached you can find a inchi.txt with several inchis from chemid-plus. The script inchi23dmolfile.py tries to read each inchi and generate 3D structures. With one inchi i get a segmentation fault, with an other i get a small backtrace (see below). If i try these procedure in ipython i can't reproduce it. But with the script i get every time the same error. Do you have any clue what is causing by error? Any hint to debug it further, or how i can absorb these error, to proceed with the script (my initial script have a few hundred inchis)? I would be happy to provide you with more informations if you like. Thank you very much, Bjoern P.S. Is their any irc channel, or mailing list for pybel? Segmentation fault InChI=1/C10H18O6/c1-9(11)15-7-5-13-3-4-14-6-8-16-10(2)12/h3-8H2,1-2H3 InChI=1/2Cr.2Na.7O/q;;2* +1;;;;;;2*-1/rCr2O7.2Na/c3-1(4,5)9-2(6,7)8;;/q-2;2*+1 -------------- backtrace ------------------------ *** glibc detected *** python: corrupted double-linked list: 0x00000000010f3420 *** ======= Backtrace: ========= /lib/libc.so.6[0x7f2f822bc28c] /lib/libc.so.6(cfree+0x8c)[0x7f2f822bfc1c] python[0x435ed7] python[0x434944] python(PyEval_EvalFrameEx+0x85c)[0x4837fc] python(PyEval_EvalCodeEx+0x776)[0x48a376] python(PyEval_EvalCode+0x32)[0x48a492] python(PyRun_FileExFlags+0x10e)[0x4abdce] python(PyRun_SimpleFileExFlags+0x1a9)[0x4ac069] python(Py_Main+0x8fd)[0x4145ad] /lib/libc.so.6(__libc_start_main+0xf4)[0x7f2f822661c4] python[0x413b29] ======= Memory map: ======== 00400000-00522000 r-xp 00000000 08:02 574300 /usr/bin/python2.5 00721000-00753000 rw-p 00121000 08:02 574300 /usr/bin/python2.5 00753000-011c7000 rw-p 00753000 00:00 0 [heap] 401d3000-401d4000 ---p 401d3000 00:00 0 401d4000-409d4000 rw-p 401d4000 00:00 0 7f2f6c000000-7f2f6c021000 rw-p 7f2f6c000000 00:00 0 7f2f6c021000-7f2f70000000 ---p 7f2f6c021000 00:00 0 7f2f700b3000-7f2f700b8000 r-xp 00000000 08:02 781861 /usr/lib/openbabel/2.2/2.2.0/zindoformat.so 7f2f700b8000-7f2f702b8000 ---p 00005000 08:02 781861 /usr/lib/openbabel/2.2/2.2.0/zindoformat.so 7f2f702b8000-7f2f702b9000 rw-p 00005000 08:02 781861 /usr/lib/openbabel/2.2/2.2.0/zindoformat.so 7f2f702b9000-7f2f702c4000 r-xp 00000000 08:02 781720 /usr/lib/openbabel/2.2/2.2.0/fchkformat.so 7f2f702c4000-7f2f704c4000 ---p 0000b000 08:02 781720 /usr/lib/openbabel/2.2/2.2.0/fchkformat.so 7f2f704c4000-7f2f704c5000 rw-p 0000b000 08:02 781720 /usr/lib/openbabel/2.2/2.2.0/fchkformat.so 7f2f704c5000-7f2f704cf000 r-xp 00000000 08:02 781604 /usr/lib/openbabel/2.2/2.2.0/fastsearchformat.so 7f2f704cf000-7f2f706ce000 ---p 0000a000 08:02 781604 /usr/lib/openbabel/2.2/2.2.0/fastsearchformat.so 7f2f706ce000-7f2f706cf000 rw-p 00009000 08:02 781604 /usr/lib/openbabel/2.2/2.2.0/fastsearchformat.so 7f2f706cf000-7f2f706d7000 r-xp 00000000 08:02 781676 /usr/lib/openbabel/2.2/2.2.0/cacaoformat.so 7f2f706d7000-7f2f708d6000 ---p 00008000 08:02 781676 /usr/lib/openbabel/2.2/2.2.0/cacaoformat.so 7f2f708d6000-7f2f708d7000 rw-p 00007000 08:02 781676 /usr/lib/openbabel/2.2/2.2.0/cacaoformat.so 7f2f708d7000-7f2f708dd000 r-xp 00000000 08:02 781856 /usr/lib/openbabel/2.2/2.2.0/mpqcformat.so 7f2f708dd000-7f2f70add000 ---p 00006000 08:02 781856 /usr/lib/openbabel/2.2/2.2.0/mpqcformat.so 7f2f70add000-7f2f70ade000 rw-p 00006000 08:02 781856 /usr/lib/openbabel/2.2/2.2.0/mpqcformat.so 7f2f70ade000-7f2f70ae7000 r-xp 00000000 08:02 781606 /usr/lib/openbabel/2.2/2.2.0/thermoformat.so 7f2f70ae7000-7f2f70ce6000 ---p 00009000 08:02 781606 /usr/lib/openbabel/2.2/2.2.0/thermoformat.so 7f2f70ce6000-7f2f70ce7000 rw-p 00008000 08:02 781606 /usr/lib/openbabel/2.2/2.2.0/thermoformat.so 7f2f70ce7000-7f2f70cf5000 r-xp 00000000 08:02 781879 /usr/lib/openbabel/2.2/2.2.0/pdbformat.so 7f2f70cf5000-7f2f70ef5000 ---p 0000e000 08:02 781879 /usr/lib/openbabel/2.2/2.2.0/pdbformat.so 7f2f70ef5000-7f2f70ef6000 rw-p 0000e000 08:02 781879 /usr/lib/openbabel/2.2/2.2.0/pdbformat.so 7f2f70ef6000-7f2f70efd000 r-xp 00000000 08:02 781867 /usr/lib/openbabel/2.2/2.2.0/reportformat.so 7f2f70efd000-7f2f710fd000 ---p 00007000 08:02 781867 /usr/lib/openbabel/2.2/2.2.0/reportformat.so 7f2f710fd000-7f2f710fe000 rw-p 00007000 08:02 781867 /usr/lib/openbabel/2.2/2.2.0/reportformat.so 7f2f710fe000-7f2f71104000 r-xp 00000000 08:02 780096 /usr/lib/openbabel/2.2/2.2.0/unichemformat.so 7f2f71104000-7f2f71303000 ---p 00006000 08:02 780096 /usr/lib/openbabel/2.2/2.2.0/unichemformat.so 7f2f71303000-7f2f71304000 rw-p 00005000 08:02 780096 /usr/lib/openbabel/2.2/2.2.0/unichemformat.so 7f2f71304000-7f2f71309000 r-xp 00000000 08:02 781868 /usr/lib/openbabel/2.2/2.2.0/fhformat.so 7f2f71309000-7f2f71509000 ---p 00005000 08:02 781868 /usr/lib/openbabel/2.2/2.2.0/fhformat.so 7f2f71509000-7f2f7150a000 rw-p 00005000 08:02 781868 /usr/lib/openbabel/2.2/2.2.0/fhformat.so 7f2f7150a000-7f2f71607000 r-xp 00000000 08:02 781612 /usr/lib/openbabel/2.2/2.2.0/inchiformat.so 7f2f71607000-7f2f71806000 ---p 000fd000 08:02 781612 /usr/lib/openbabel/2.2/2.2.0/inchiformat.so 7f2f71806000-7f2f7181b000 rw-p 000fc000 08:02 781612 /usr/lib/openbabel/2.2/2.2.0/inchiformat.so 7f2f7181b000-7f2f71820000 r-xp 00000000 08:02 781885 /usr/lib/openbabel/2.2/2.2.0/molreportformat.so 7f2f71820000-7f2f71a20000 ---p 00005000 08:02 781885 /usr/lib/openbabel/2.2/2.2.0/molreportformat.so 7f2f71a20000-7f2f71a21000 rw-p 00005000 08:02 781885 /usr/lib/openbabel/2.2/2.2.0/molreportformat.so 7f2f71a21000-7f2f71a26000 r-xp 00000000 08:02 781857 /usr/lib/openbabel/2.2/2.2.0/CSRformat.so 7f2f71a26000-7f2f71c26000 ---p 00005000 08:02 781857 /usr/lib/openbabel/2.2/2.2.0/CSRformat.so 7f2f71c26000-7f2f71c27000 rw-p 00005000 08:02 781857 /usr/lib/openbabel/2.2/2.2.0/CSRformat.so 7f2f71c27000-7f2f71c30000 r-xp 00000000 08:02 781866 /usr/lib/openbabel/2.2/2.2.0/crkformat.so 7f2f71c30000-7f2f71e2f000 ---p 00009000 08:02 781866 /usr/lib/openbabel/2.2/2.2.0/crkformat.so 7f2f71e2f000-7f2f71e30000 rw-p 00008000 08:02 781866 /usr/lib/openbabel/2.2/2.2.0/crkformat.so 7f2f71e30000-7f2f71e37000 r-xp 00000000 08:02 781860 /usr/lib/openbabel/2.2/2.2.0/chem3dformat.so 7f2f71e37000-7f2f72037000 ---p 00007000 08:02 781860 /usr/lib/openbabel/2.2/2.2.0/chem3dformat.so 7f2f72037000-7f2f72038000 rw-p 00007000 08:02 781860 /usr/lib/openbabel/2.2/2.2.0/chem3dformat.so 7f2f72038000-7f2f7203e000 r-xp 00000000 08:02 780115 /usr/lib/openbabel/2.2/2.2.0/ghemicalformat.so 7f2f7203e000-7f2f7223e000 ---p 00006000 08:02 780115 /usr/lib/openbabel/2.2/2.2.0/ghemicalformat.so 7f2f7223e000-7f2f7223f000 rw-p 00006000 08:02 780115 /usr/lib/openbabel/2.2/2.2.0/ghemicalformat.so 7f2f7223f000-7f2f72245000 r-xp 00000000 08:02 781882 /usr/lib/openbabel/2.2/2.2.0/fastaformat.so 7f2f72245000-7f2f72444000 ---p 00006000 08:02 781882 /usr/lib/openbabel/2.2/2.2.0/fastaformat.so 7f2f72444000-7f2f72445000 rw-p 00005000 08:02 781882 /usr/lib/openbabel/2.2/2.2.0/fastaformat.so 7f2f72445000-7f2f7244a000 r-xp 00000000 08:02 781869 /usr/lib/openbabel/2.2/2.2.0/cssrformat.so 7f2f7244a000-7f2f7264a000 ---p 00005000 08:02 781869 /usr/lib/openbabel/2.2/2.2.0/cssrformat.so 7f2f7264a000-7f2f7264b000 rw-p 00005000 08:02 781869 /usr/lib/openbabel/2.2/2.2.0/cssrformat.so 7f2f7264b000-7f2f72651000 r-xp 00000000 08:02 780107 /usr/lib/openbabel/2.2/2.2.0/hinformat.so 7f2f72651000-7f2f72850000 ---p 00006000 08:02 780107 /usr/lib/openbabel/2.2/2.2.0/hinformat.so 7f2f72850000-7f2f72851000 rw-p 00005000 08:02 780107 /usr/lib/openbabel/2.2/2.2.0/hinformat.so 7f2f72851000-7f2f72857000 r-xp 00000000 08:02 781881 /usr/lib/openbabel/2.2/2.2.0/carformat.so 7f2f72857000-7f2f72a56000 ---p 00006000 08:02 781881 /usr/lib/openbabel/2.2/2.2.0/carformat.so 7f2f72a56000-7f2f72a57000 rw-p 00005000 08:02 781881 /usr/lib/openbabel/2.2/2.2.0/carformat.so 7f2f72a57000-7f2f72a5d000 r-xp 00000000 08:02 781608 /usr/lib/openbabel/2.2/2.2.0/cacheformat.so 7f2f72a5d000-7f2f72c5c000 ---p 00006000 08:02 781608 /usr/lib/openbabel/2.2/2.2.0/cacheformat.so 7f2f72c5c000-7f2f72c5d000 rw-p 00005000 08:02 781608 /usr/lib/openbabel/2.2/2.2.0/cacheformat.so 7f2f72c5d000-7f2f72c66000 r-xp 00000000 08:02 781865 /usr/lib/openbabel/2.2/2.2.0/opendxformat.so 7f2f72c66000-7f2f72e65000 ---p 00009000 08:02 781865 /usr/lib/openbabel/2.2/2.2.0/opendxformat.so 7f2f72e65000-7f2f72e66000 rw-p 00008000 08:02 781865 /usr/lib/openbabel/2.2Aborted -- ========================================== Björn Grüning D-14612 Falkensee, Germany Tel. +49-3322-212968, Fax +49-3322-4287528 email: bj...@gr... jid: ba...@gr... |
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From: Noel O'B. <bao...@gm...> - 2008-07-27 10:49:09
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> Hi Noel, > > as far as i know are you one of the main developer behind the great > pybel bindungs for openbabel. I'm unable to find an irc channel or > something like this, so i'm trying to cantact you directly. Hope that is > ok. Google "Pybel". :-) 4th line: "If you have any problems or want to ask a question, please send an email to the openbabel-scripting mailing list." > I'm playing around with the new functions draw, localopt, addh etc. And > i get a strange error if i try to generate 3D structures from inchis. > Attached you can find a inchi.txt with several inchis from chemid-plus. > The script inchi23dmolfile.py tries to read each inchi and generate 3D > structures. With one inchi i get a segmentation fault, with an other i > get a small backtrace (see below). If i try these procedure in ipython i > can't reproduce it. But with the script i get every time the same error. > Do you have any clue what is causing by error? Any hint to debug it > further, or how i can absorb these error, to proceed with the script (my > initial script have a few hundred inchis)? The problem isn't reading the inchis but generating the 3D structures. There's some weird memory stuff going on. There's no short term solution I'm afraid. I'll file a bug and one of the other developers will look into it. > I would be happy to provide you with more informations if you like. > > Thank you very much, > Bjoern > > P.S. Is their any irc channel, or mailing list for pybel? > > Segmentation fault > InChI=1/C10H18O6/c1-9(11)15-7-5-13-3-4-14-6-8-16-10(2)12/h3-8H2,1-2H3 > > > InChI=1/2Cr.2Na.7O/q;;2* > +1;;;;;;2*-1/rCr2O7.2Na/c3-1(4,5)9-2(6,7)8;;/q-2;2*+1 > -------------- backtrace ------------------------ > *** glibc detected *** python: corrupted double-linked list: > 0x00000000010f3420 *** > ======= Backtrace: ========= > /lib/libc.so.6[0x7f2f822bc28c] > /lib/libc.so.6(cfree+0x8c)[0x7f2f822bfc1c] > python[0x435ed7] > python[0x434944] > python(PyEval_EvalFrameEx+0x85c)[0x4837fc] > python(PyEval_EvalCodeEx+0x776)[0x48a376] > python(PyEval_EvalCode+0x32)[0x48a492] > python(PyRun_FileExFlags+0x10e)[0x4abdce] > python(PyRun_SimpleFileExFlags+0x1a9)[0x4ac069] > python(Py_Main+0x8fd)[0x4145ad] > /lib/libc.so.6(__libc_start_main+0xf4)[0x7f2f822661c4] > python[0x413b29] > ======= Memory map: ======== > 00400000-00522000 r-xp 00000000 08:02 > 574300 /usr/bin/python2.5 > 00721000-00753000 rw-p 00121000 08:02 > 574300 /usr/bin/python2.5 > 00753000-011c7000 rw-p 00753000 00:00 0 > [heap] > 401d3000-401d4000 ---p 401d3000 00:00 0 > 401d4000-409d4000 rw-p 401d4000 00:00 0 > 7f2f6c000000-7f2f6c021000 rw-p 7f2f6c000000 00:00 0 > 7f2f6c021000-7f2f70000000 ---p 7f2f6c021000 00:00 0 > 7f2f700b3000-7f2f700b8000 r-xp 00000000 08:02 > 781861 /usr/lib/openbabel/2.2/2.2.0/zindoformat.so > 7f2f700b8000-7f2f702b8000 ---p 00005000 08:02 > 781861 /usr/lib/openbabel/2.2/2.2.0/zindoformat.so > 7f2f702b8000-7f2f702b9000 rw-p 00005000 08:02 > 781861 /usr/lib/openbabel/2.2/2.2.0/zindoformat.so > 7f2f702b9000-7f2f702c4000 r-xp 00000000 08:02 > 781720 /usr/lib/openbabel/2.2/2.2.0/fchkformat.so > 7f2f702c4000-7f2f704c4000 ---p 0000b000 08:02 > 781720 /usr/lib/openbabel/2.2/2.2.0/fchkformat.so > 7f2f704c4000-7f2f704c5000 rw-p 0000b000 08:02 > 781720 /usr/lib/openbabel/2.2/2.2.0/fchkformat.so > 7f2f704c5000-7f2f704cf000 r-xp 00000000 08:02 > 781604 /usr/lib/openbabel/2.2/2.2.0/fastsearchformat.so > 7f2f704cf000-7f2f706ce000 ---p 0000a000 08:02 > 781604 /usr/lib/openbabel/2.2/2.2.0/fastsearchformat.so > 7f2f706ce000-7f2f706cf000 rw-p 00009000 08:02 > 781604 /usr/lib/openbabel/2.2/2.2.0/fastsearchformat.so > 7f2f706cf000-7f2f706d7000 r-xp 00000000 08:02 > 781676 /usr/lib/openbabel/2.2/2.2.0/cacaoformat.so > 7f2f706d7000-7f2f708d6000 ---p 00008000 08:02 > 781676 /usr/lib/openbabel/2.2/2.2.0/cacaoformat.so > 7f2f708d6000-7f2f708d7000 rw-p 00007000 08:02 > 781676 /usr/lib/openbabel/2.2/2.2.0/cacaoformat.so > 7f2f708d7000-7f2f708dd000 r-xp 00000000 08:02 > 781856 /usr/lib/openbabel/2.2/2.2.0/mpqcformat.so > 7f2f708dd000-7f2f70add000 ---p 00006000 08:02 > 781856 /usr/lib/openbabel/2.2/2.2.0/mpqcformat.so > 7f2f70add000-7f2f70ade000 rw-p 00006000 08:02 > 781856 /usr/lib/openbabel/2.2/2.2.0/mpqcformat.so > 7f2f70ade000-7f2f70ae7000 r-xp 00000000 08:02 > 781606 /usr/lib/openbabel/2.2/2.2.0/thermoformat.so > 7f2f70ae7000-7f2f70ce6000 ---p 00009000 08:02 > 781606 /usr/lib/openbabel/2.2/2.2.0/thermoformat.so > 7f2f70ce6000-7f2f70ce7000 rw-p 00008000 08:02 > 781606 /usr/lib/openbabel/2.2/2.2.0/thermoformat.so > 7f2f70ce7000-7f2f70cf5000 r-xp 00000000 08:02 > 781879 /usr/lib/openbabel/2.2/2.2.0/pdbformat.so > 7f2f70cf5000-7f2f70ef5000 ---p 0000e000 08:02 > 781879 /usr/lib/openbabel/2.2/2.2.0/pdbformat.so > 7f2f70ef5000-7f2f70ef6000 rw-p 0000e000 08:02 > 781879 /usr/lib/openbabel/2.2/2.2.0/pdbformat.so > 7f2f70ef6000-7f2f70efd000 r-xp 00000000 08:02 > 781867 /usr/lib/openbabel/2.2/2.2.0/reportformat.so > 7f2f70efd000-7f2f710fd000 ---p 00007000 08:02 > 781867 /usr/lib/openbabel/2.2/2.2.0/reportformat.so > 7f2f710fd000-7f2f710fe000 rw-p 00007000 08:02 > 781867 /usr/lib/openbabel/2.2/2.2.0/reportformat.so > 7f2f710fe000-7f2f71104000 r-xp 00000000 08:02 > 780096 /usr/lib/openbabel/2.2/2.2.0/unichemformat.so > 7f2f71104000-7f2f71303000 ---p 00006000 08:02 > 780096 /usr/lib/openbabel/2.2/2.2.0/unichemformat.so > 7f2f71303000-7f2f71304000 rw-p 00005000 08:02 > 780096 /usr/lib/openbabel/2.2/2.2.0/unichemformat.so > 7f2f71304000-7f2f71309000 r-xp 00000000 08:02 > 781868 /usr/lib/openbabel/2.2/2.2.0/fhformat.so > 7f2f71309000-7f2f71509000 ---p 00005000 08:02 > 781868 /usr/lib/openbabel/2.2/2.2.0/fhformat.so > 7f2f71509000-7f2f7150a000 rw-p 00005000 08:02 > 781868 /usr/lib/openbabel/2.2/2.2.0/fhformat.so > 7f2f7150a000-7f2f71607000 r-xp 00000000 08:02 > 781612 /usr/lib/openbabel/2.2/2.2.0/inchiformat.so > 7f2f71607000-7f2f71806000 ---p 000fd000 08:02 > 781612 /usr/lib/openbabel/2.2/2.2.0/inchiformat.so > 7f2f71806000-7f2f7181b000 rw-p 000fc000 08:02 > 781612 /usr/lib/openbabel/2.2/2.2.0/inchiformat.so > 7f2f7181b000-7f2f71820000 r-xp 00000000 08:02 > 781885 /usr/lib/openbabel/2.2/2.2.0/molreportformat.so > 7f2f71820000-7f2f71a20000 ---p 00005000 08:02 > 781885 /usr/lib/openbabel/2.2/2.2.0/molreportformat.so > 7f2f71a20000-7f2f71a21000 rw-p 00005000 08:02 > 781885 /usr/lib/openbabel/2.2/2.2.0/molreportformat.so > 7f2f71a21000-7f2f71a26000 r-xp 00000000 08:02 > 781857 /usr/lib/openbabel/2.2/2.2.0/CSRformat.so > 7f2f71a26000-7f2f71c26000 ---p 00005000 08:02 > 781857 /usr/lib/openbabel/2.2/2.2.0/CSRformat.so > 7f2f71c26000-7f2f71c27000 rw-p 00005000 08:02 > 781857 /usr/lib/openbabel/2.2/2.2.0/CSRformat.so > 7f2f71c27000-7f2f71c30000 r-xp 00000000 08:02 > 781866 /usr/lib/openbabel/2.2/2.2.0/crkformat.so > 7f2f71c30000-7f2f71e2f000 ---p 00009000 08:02 > 781866 /usr/lib/openbabel/2.2/2.2.0/crkformat.so > 7f2f71e2f000-7f2f71e30000 rw-p 00008000 08:02 > 781866 /usr/lib/openbabel/2.2/2.2.0/crkformat.so > 7f2f71e30000-7f2f71e37000 r-xp 00000000 08:02 > 781860 /usr/lib/openbabel/2.2/2.2.0/chem3dformat.so > 7f2f71e37000-7f2f72037000 ---p 00007000 08:02 > 781860 /usr/lib/openbabel/2.2/2.2.0/chem3dformat.so > 7f2f72037000-7f2f72038000 rw-p 00007000 08:02 > 781860 /usr/lib/openbabel/2.2/2.2.0/chem3dformat.so > 7f2f72038000-7f2f7203e000 r-xp 00000000 08:02 > 780115 /usr/lib/openbabel/2.2/2.2.0/ghemicalformat.so > 7f2f7203e000-7f2f7223e000 ---p 00006000 08:02 > 780115 /usr/lib/openbabel/2.2/2.2.0/ghemicalformat.so > 7f2f7223e000-7f2f7223f000 rw-p 00006000 08:02 > 780115 /usr/lib/openbabel/2.2/2.2.0/ghemicalformat.so > 7f2f7223f000-7f2f72245000 r-xp 00000000 08:02 > 781882 /usr/lib/openbabel/2.2/2.2.0/fastaformat.so > 7f2f72245000-7f2f72444000 ---p 00006000 08:02 > 781882 /usr/lib/openbabel/2.2/2.2.0/fastaformat.so > 7f2f72444000-7f2f72445000 rw-p 00005000 08:02 > 781882 /usr/lib/openbabel/2.2/2.2.0/fastaformat.so > 7f2f72445000-7f2f7244a000 r-xp 00000000 08:02 > 781869 /usr/lib/openbabel/2.2/2.2.0/cssrformat.so > 7f2f7244a000-7f2f7264a000 ---p 00005000 08:02 > 781869 /usr/lib/openbabel/2.2/2.2.0/cssrformat.so > 7f2f7264a000-7f2f7264b000 rw-p 00005000 08:02 > 781869 /usr/lib/openbabel/2.2/2.2.0/cssrformat.so > 7f2f7264b000-7f2f72651000 r-xp 00000000 08:02 > 780107 /usr/lib/openbabel/2.2/2.2.0/hinformat.so > 7f2f72651000-7f2f72850000 ---p 00006000 08:02 > 780107 /usr/lib/openbabel/2.2/2.2.0/hinformat.so > 7f2f72850000-7f2f72851000 rw-p 00005000 08:02 > 780107 /usr/lib/openbabel/2.2/2.2.0/hinformat.so > 7f2f72851000-7f2f72857000 r-xp 00000000 08:02 > 781881 /usr/lib/openbabel/2.2/2.2.0/carformat.so > 7f2f72857000-7f2f72a56000 ---p 00006000 08:02 > 781881 /usr/lib/openbabel/2.2/2.2.0/carformat.so > 7f2f72a56000-7f2f72a57000 rw-p 00005000 08:02 > 781881 /usr/lib/openbabel/2.2/2.2.0/carformat.so > 7f2f72a57000-7f2f72a5d000 r-xp 00000000 08:02 > 781608 /usr/lib/openbabel/2.2/2.2.0/cacheformat.so > 7f2f72a5d000-7f2f72c5c000 ---p 00006000 08:02 > 781608 /usr/lib/openbabel/2.2/2.2.0/cacheformat.so > 7f2f72c5c000-7f2f72c5d000 rw-p 00005000 08:02 > 781608 /usr/lib/openbabel/2.2/2.2.0/cacheformat.so > 7f2f72c5d000-7f2f72c66000 r-xp 00000000 08:02 > 781865 /usr/lib/openbabel/2.2/2.2.0/opendxformat.so > 7f2f72c66000-7f2f72e65000 ---p 00009000 08:02 > 781865 /usr/lib/openbabel/2.2/2.2.0/opendxformat.so > 7f2f72e65000-7f2f72e66000 rw-p 00008000 08:02 > 781865 /usr/lib/openbabel/2.2Aborted > > -- > ========================================== > Björn Grüning > D-14612 Falkensee, Germany > Tel. +49-3322-212968, Fax +49-3322-4287528 > email: bj...@gr... > jid: ba...@gr... > |
|
From: Noel O'B. <bao...@gm...> - 2008-10-04 15:44:10
|
Tim has solved this problem. The main problem was that pybel wasn't
checking whether the force field was able to initialise properly. To
workaround in pybel.py, you will need to replace the line:
ff.Setup(self.OBMol)
with
success = ff.Setup(self.OBMol)
if not success:
return
Noel
2008/7/27 Noel O'Boyle <bao...@gm...>:
>> Hi Noel,
>>
>> as far as i know are you one of the main developer behind the great
>> pybel bindungs for openbabel. I'm unable to find an irc channel or
>> something like this, so i'm trying to cantact you directly. Hope that is
>> ok.
>
> Google "Pybel". :-) 4th line:
> "If you have any problems or want to ask a question, please send an
> email to the openbabel-scripting mailing list."
>
>> I'm playing around with the new functions draw, localopt, addh etc. And
>> i get a strange error if i try to generate 3D structures from inchis.
>> Attached you can find a inchi.txt with several inchis from chemid-plus.
>> The script inchi23dmolfile.py tries to read each inchi and generate 3D
>> structures. With one inchi i get a segmentation fault, with an other i
>> get a small backtrace (see below). If i try these procedure in ipython i
>> can't reproduce it. But with the script i get every time the same error.
>> Do you have any clue what is causing by error? Any hint to debug it
>> further, or how i can absorb these error, to proceed with the script (my
>> initial script have a few hundred inchis)?
>
> The problem isn't reading the inchis but generating the 3D structures.
> There's some weird memory stuff going on. There's no short term
> solution I'm afraid. I'll file a bug and one of the other developers
> will look into it.
>> I would be happy to provide you with more informations if you like.
>>
>> Thank you very much,
>> Bjoern
>>
>> P.S. Is their any irc channel, or mailing list for pybel?
>>
>> Segmentation fault
>> InChI=1/C10H18O6/c1-9(11)15-7-5-13-3-4-14-6-8-16-10(2)12/h3-8H2,1-2H3
>>
>>
>> InChI=1/2Cr.2Na.7O/q;;2*
>> +1;;;;;;2*-1/rCr2O7.2Na/c3-1(4,5)9-2(6,7)8;;/q-2;2*+1
>> -------------- backtrace ------------------------
>> *** glibc detected *** python: corrupted double-linked list:
>> 0x00000000010f3420 ***
>> ======= Backtrace: =========
>> /lib/libc.so.6[0x7f2f822bc28c]
>> /lib/libc.so.6(cfree+0x8c)[0x7f2f822bfc1c]
>> python[0x435ed7]
>> python[0x434944]
>> python(PyEval_EvalFrameEx+0x85c)[0x4837fc]
>> python(PyEval_EvalCodeEx+0x776)[0x48a376]
>> python(PyEval_EvalCode+0x32)[0x48a492]
>> python(PyRun_FileExFlags+0x10e)[0x4abdce]
>> python(PyRun_SimpleFileExFlags+0x1a9)[0x4ac069]
>> python(Py_Main+0x8fd)[0x4145ad]
>> /lib/libc.so.6(__libc_start_main+0xf4)[0x7f2f822661c4]
>> python[0x413b29]
>> ======= Memory map: ========
>> 00400000-00522000 r-xp 00000000 08:02
>> 574300 /usr/bin/python2.5
>> 00721000-00753000 rw-p 00121000 08:02
>> 574300 /usr/bin/python2.5
>> 00753000-011c7000 rw-p 00753000 00:00 0
>> [heap]
>> 401d3000-401d4000 ---p 401d3000 00:00 0
>> 401d4000-409d4000 rw-p 401d4000 00:00 0
>> 7f2f6c000000-7f2f6c021000 rw-p 7f2f6c000000 00:00 0
>> 7f2f6c021000-7f2f70000000 ---p 7f2f6c021000 00:00 0
>> 7f2f700b3000-7f2f700b8000 r-xp 00000000 08:02
>> 781861 /usr/lib/openbabel/2.2/2.2.0/zindoformat.so
>> 7f2f700b8000-7f2f702b8000 ---p 00005000 08:02
>> 781861 /usr/lib/openbabel/2.2/2.2.0/zindoformat.so
>> 7f2f702b8000-7f2f702b9000 rw-p 00005000 08:02
>> 781861 /usr/lib/openbabel/2.2/2.2.0/zindoformat.so
>> 7f2f702b9000-7f2f702c4000 r-xp 00000000 08:02
>> 781720 /usr/lib/openbabel/2.2/2.2.0/fchkformat.so
>> 7f2f702c4000-7f2f704c4000 ---p 0000b000 08:02
>> 781720 /usr/lib/openbabel/2.2/2.2.0/fchkformat.so
>> 7f2f704c4000-7f2f704c5000 rw-p 0000b000 08:02
>> 781720 /usr/lib/openbabel/2.2/2.2.0/fchkformat.so
>> 7f2f704c5000-7f2f704cf000 r-xp 00000000 08:02
>> 781604 /usr/lib/openbabel/2.2/2.2.0/fastsearchformat.so
>> 7f2f704cf000-7f2f706ce000 ---p 0000a000 08:02
>> 781604 /usr/lib/openbabel/2.2/2.2.0/fastsearchformat.so
>> 7f2f706ce000-7f2f706cf000 rw-p 00009000 08:02
>> 781604 /usr/lib/openbabel/2.2/2.2.0/fastsearchformat.so
>> 7f2f706cf000-7f2f706d7000 r-xp 00000000 08:02
>> 781676 /usr/lib/openbabel/2.2/2.2.0/cacaoformat.so
>> 7f2f706d7000-7f2f708d6000 ---p 00008000 08:02
>> 781676 /usr/lib/openbabel/2.2/2.2.0/cacaoformat.so
>> 7f2f708d6000-7f2f708d7000 rw-p 00007000 08:02
>> 781676 /usr/lib/openbabel/2.2/2.2.0/cacaoformat.so
>> 7f2f708d7000-7f2f708dd000 r-xp 00000000 08:02
>> 781856 /usr/lib/openbabel/2.2/2.2.0/mpqcformat.so
>> 7f2f708dd000-7f2f70add000 ---p 00006000 08:02
>> 781856 /usr/lib/openbabel/2.2/2.2.0/mpqcformat.so
>> 7f2f70add000-7f2f70ade000 rw-p 00006000 08:02
>> 781856 /usr/lib/openbabel/2.2/2.2.0/mpqcformat.so
>> 7f2f70ade000-7f2f70ae7000 r-xp 00000000 08:02
>> 781606 /usr/lib/openbabel/2.2/2.2.0/thermoformat.so
>> 7f2f70ae7000-7f2f70ce6000 ---p 00009000 08:02
>> 781606 /usr/lib/openbabel/2.2/2.2.0/thermoformat.so
>> 7f2f70ce6000-7f2f70ce7000 rw-p 00008000 08:02
>> 781606 /usr/lib/openbabel/2.2/2.2.0/thermoformat.so
>> 7f2f70ce7000-7f2f70cf5000 r-xp 00000000 08:02
>> 781879 /usr/lib/openbabel/2.2/2.2.0/pdbformat.so
>> 7f2f70cf5000-7f2f70ef5000 ---p 0000e000 08:02
>> 781879 /usr/lib/openbabel/2.2/2.2.0/pdbformat.so
>> 7f2f70ef5000-7f2f70ef6000 rw-p 0000e000 08:02
>> 781879 /usr/lib/openbabel/2.2/2.2.0/pdbformat.so
>> 7f2f70ef6000-7f2f70efd000 r-xp 00000000 08:02
>> 781867 /usr/lib/openbabel/2.2/2.2.0/reportformat.so
>> 7f2f70efd000-7f2f710fd000 ---p 00007000 08:02
>> 781867 /usr/lib/openbabel/2.2/2.2.0/reportformat.so
>> 7f2f710fd000-7f2f710fe000 rw-p 00007000 08:02
>> 781867 /usr/lib/openbabel/2.2/2.2.0/reportformat.so
>> 7f2f710fe000-7f2f71104000 r-xp 00000000 08:02
>> 780096 /usr/lib/openbabel/2.2/2.2.0/unichemformat.so
>> 7f2f71104000-7f2f71303000 ---p 00006000 08:02
>> 780096 /usr/lib/openbabel/2.2/2.2.0/unichemformat.so
>> 7f2f71303000-7f2f71304000 rw-p 00005000 08:02
>> 780096 /usr/lib/openbabel/2.2/2.2.0/unichemformat.so
>> 7f2f71304000-7f2f71309000 r-xp 00000000 08:02
>> 781868 /usr/lib/openbabel/2.2/2.2.0/fhformat.so
>> 7f2f71309000-7f2f71509000 ---p 00005000 08:02
>> 781868 /usr/lib/openbabel/2.2/2.2.0/fhformat.so
>> 7f2f71509000-7f2f7150a000 rw-p 00005000 08:02
>> 781868 /usr/lib/openbabel/2.2/2.2.0/fhformat.so
>> 7f2f7150a000-7f2f71607000 r-xp 00000000 08:02
>> 781612 /usr/lib/openbabel/2.2/2.2.0/inchiformat.so
>> 7f2f71607000-7f2f71806000 ---p 000fd000 08:02
>> 781612 /usr/lib/openbabel/2.2/2.2.0/inchiformat.so
>> 7f2f71806000-7f2f7181b000 rw-p 000fc000 08:02
>> 781612 /usr/lib/openbabel/2.2/2.2.0/inchiformat.so
>> 7f2f7181b000-7f2f71820000 r-xp 00000000 08:02
>> 781885 /usr/lib/openbabel/2.2/2.2.0/molreportformat.so
>> 7f2f71820000-7f2f71a20000 ---p 00005000 08:02
>> 781885 /usr/lib/openbabel/2.2/2.2.0/molreportformat.so
>> 7f2f71a20000-7f2f71a21000 rw-p 00005000 08:02
>> 781885 /usr/lib/openbabel/2.2/2.2.0/molreportformat.so
>> 7f2f71a21000-7f2f71a26000 r-xp 00000000 08:02
>> 781857 /usr/lib/openbabel/2.2/2.2.0/CSRformat.so
>> 7f2f71a26000-7f2f71c26000 ---p 00005000 08:02
>> 781857 /usr/lib/openbabel/2.2/2.2.0/CSRformat.so
>> 7f2f71c26000-7f2f71c27000 rw-p 00005000 08:02
>> 781857 /usr/lib/openbabel/2.2/2.2.0/CSRformat.so
>> 7f2f71c27000-7f2f71c30000 r-xp 00000000 08:02
>> 781866 /usr/lib/openbabel/2.2/2.2.0/crkformat.so
>> 7f2f71c30000-7f2f71e2f000 ---p 00009000 08:02
>> 781866 /usr/lib/openbabel/2.2/2.2.0/crkformat.so
>> 7f2f71e2f000-7f2f71e30000 rw-p 00008000 08:02
>> 781866 /usr/lib/openbabel/2.2/2.2.0/crkformat.so
>> 7f2f71e30000-7f2f71e37000 r-xp 00000000 08:02
>> 781860 /usr/lib/openbabel/2.2/2.2.0/chem3dformat.so
>> 7f2f71e37000-7f2f72037000 ---p 00007000 08:02
>> 781860 /usr/lib/openbabel/2.2/2.2.0/chem3dformat.so
>> 7f2f72037000-7f2f72038000 rw-p 00007000 08:02
>> 781860 /usr/lib/openbabel/2.2/2.2.0/chem3dformat.so
>> 7f2f72038000-7f2f7203e000 r-xp 00000000 08:02
>> 780115 /usr/lib/openbabel/2.2/2.2.0/ghemicalformat.so
>> 7f2f7203e000-7f2f7223e000 ---p 00006000 08:02
>> 780115 /usr/lib/openbabel/2.2/2.2.0/ghemicalformat.so
>> 7f2f7223e000-7f2f7223f000 rw-p 00006000 08:02
>> 780115 /usr/lib/openbabel/2.2/2.2.0/ghemicalformat.so
>> 7f2f7223f000-7f2f72245000 r-xp 00000000 08:02
>> 781882 /usr/lib/openbabel/2.2/2.2.0/fastaformat.so
>> 7f2f72245000-7f2f72444000 ---p 00006000 08:02
>> 781882 /usr/lib/openbabel/2.2/2.2.0/fastaformat.so
>> 7f2f72444000-7f2f72445000 rw-p 00005000 08:02
>> 781882 /usr/lib/openbabel/2.2/2.2.0/fastaformat.so
>> 7f2f72445000-7f2f7244a000 r-xp 00000000 08:02
>> 781869 /usr/lib/openbabel/2.2/2.2.0/cssrformat.so
>> 7f2f7244a000-7f2f7264a000 ---p 00005000 08:02
>> 781869 /usr/lib/openbabel/2.2/2.2.0/cssrformat.so
>> 7f2f7264a000-7f2f7264b000 rw-p 00005000 08:02
>> 781869 /usr/lib/openbabel/2.2/2.2.0/cssrformat.so
>> 7f2f7264b000-7f2f72651000 r-xp 00000000 08:02
>> 780107 /usr/lib/openbabel/2.2/2.2.0/hinformat.so
>> 7f2f72651000-7f2f72850000 ---p 00006000 08:02
>> 780107 /usr/lib/openbabel/2.2/2.2.0/hinformat.so
>> 7f2f72850000-7f2f72851000 rw-p 00005000 08:02
>> 780107 /usr/lib/openbabel/2.2/2.2.0/hinformat.so
>> 7f2f72851000-7f2f72857000 r-xp 00000000 08:02
>> 781881 /usr/lib/openbabel/2.2/2.2.0/carformat.so
>> 7f2f72857000-7f2f72a56000 ---p 00006000 08:02
>> 781881 /usr/lib/openbabel/2.2/2.2.0/carformat.so
>> 7f2f72a56000-7f2f72a57000 rw-p 00005000 08:02
>> 781881 /usr/lib/openbabel/2.2/2.2.0/carformat.so
>> 7f2f72a57000-7f2f72a5d000 r-xp 00000000 08:02
>> 781608 /usr/lib/openbabel/2.2/2.2.0/cacheformat.so
>> 7f2f72a5d000-7f2f72c5c000 ---p 00006000 08:02
>> 781608 /usr/lib/openbabel/2.2/2.2.0/cacheformat.so
>> 7f2f72c5c000-7f2f72c5d000 rw-p 00005000 08:02
>> 781608 /usr/lib/openbabel/2.2/2.2.0/cacheformat.so
>> 7f2f72c5d000-7f2f72c66000 r-xp 00000000 08:02
>> 781865 /usr/lib/openbabel/2.2/2.2.0/opendxformat.so
>> 7f2f72c66000-7f2f72e65000 ---p 00009000 08:02
>> 781865 /usr/lib/openbabel/2.2/2.2.0/opendxformat.so
>> 7f2f72e65000-7f2f72e66000 rw-p 00008000 08:02
>> 781865 /usr/lib/openbabel/2.2Aborted
>>
>> --
>> ==========================================
>> Björn Grüning
>> D-14612 Falkensee, Germany
>> Tel. +49-3322-212968, Fax +49-3322-4287528
>> email: bj...@gr...
>> jid: ba...@gr...
>>
>
|
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