Re: [OpenBabel-scripting] Pybel - localopt() error?!

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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...
>