This appears to run properly using head (r4629) with babel but not with
obabel. Attached is my run log.
Thanks,
Jiahao Chen
MIT Chemistry
http://theochem.mit.edu
---------- Forwarded message ----------
Date: Mon, 3 Oct 2011 12:02:45
From: SourceForge.net <nore...@sourceforge.net>
To: SourceForge.net <nore...@sourceforge.net>
Subject: [OpenBabel-Devel] [ openbabel-Bugs-3417992 ] MOPAC to MOL gives
segmentation fault
Bugs item #3417992, was opened at 2011-10-03 12:02
Message generated for change (Tracker Item Submitted) made by gmagoon
You can respond by visiting:
https://sourceforge.net/tracker/?func=detail&atid=428740&aid=3417992&group_id=40728
Please note that this message will contain a full copy of the comment thread,
including the initial issue submission, for this request,
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Category: File Translation
Group: None
Status: Open
Resolution: None
Priority: 5
Private: No
Submitted By: Gregory Magoon (gmagoon)
Assigned to: Nobody/Anonymous (nobody)
Summary: MOPAC to MOL gives segmentation fault
Initial Comment:
With OpenBabel 2.2.3, I get a segmentation fault when converting the
attached MOPAC output file to a MOL file (see below). Most other MOPAC
files are processed as expected, without error. Also, I tried
processing the same file with the OpenBabel 2.2.0 GUI (on a separate
system) and the conversion to MOL file seemed to work properly.
gmagoon@pharos:~/threeDcheck_testdir$ babel -imoo
QMfiles/PFGQIDLYXOTKNT-UHFFFAOYAN.out -omol
QMfiles/PFGQIDLYXOTKNT-UHFFFAOYAN.mol2 ---errorlevel 5
==============================
*** Open Babel Audit Log in ReadChemObjectImpl
OpenBabel::Read molecule MOPAC Output format
==============================
*** Open Babel Audit Log in Clear
Ran OpenBabel::Clear Molecule
==============================
*** Open Babel Audit Log in Clear
Ran OpenBabel::Clear Molecule
==============================
*** Open Babel Audit Log in Clear
Ran OpenBabel::Clear Molecule
==============================
*** Open Babel Audit Log in Clear
Ran OpenBabel::Clear Molecule
Segmentation fault
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14:15:55 cjh@caspian:~/sandbox/babel-3417992
$ babel -imoo PFGQIDLYXOTKNT-UHFFFAOYAN.out -omol
PFGQIDLYXOTKNT-UHFFFAOYAN.mol2 ---errorlevel 5
==============================
*** Open Babel Audit Log in ReadChemObjectImpl
OpenBabel::Read molecule MOPAC Output format
==============================
*** Open Babel Audit Log in Clear
Ran OpenBabel::Clear Molecule
==============================
*** Open Babel Audit Log in Clear
Ran OpenBabel::Clear Molecule
==============================
*** Open Babel Audit Log in Clear
Ran OpenBabel::Clear Molecule
==============================
*** Open Babel Audit Log in Clear
Ran OpenBabel::Clear Molecule
==============================
*** Open Babel Audit Log in ConnectTheDots
Ran OpenBabel::ConnectTheDots
==============================
*** Open Babel Audit Log in PerceiveBondOrders
Ran OpenBabel::PerceiveBondOrders
==============================
*** Open Babel Audit Log in FindSSSR
Ran OpenBabel::FindSSSR
==============================
*** Open Babel Audit Log in FindRingAtomsAndBonds
Ran OpenBabel::FindRingAtomsAndBonds
==============================
*** Open Babel Audit Log in IsClosure
Ran OpenBabel::PerceiveClosureBonds
==============================
*** Open Babel Audit Log in AssignAromaticFlags
Ran OpenBabel::AssignAromaticFlags
==============================
*** Open Babel Audit Log in AssignImplicitValence
Ran OpenBabel::AssignImplicitValence
==============================
*** Open Babel Audit Log in Kekulize
Ran OpenBabel::Kekulize
==============================
*** Open Babel Audit Log in AssignSpinMultiplicity
Ran OpenBabel::AssignSpinMultiplicity
==============================
*** Open Babel Audit Log in AssignImplicitValence
Ran OpenBabel::AssignImplicitValence
==============================
*** Open Babel Audit Log in AssignHyb
Ran OpenBabel::AssignHybridization
==============================
*** Open Babel Audit Log in Kekulize
Ran OpenBabel::Kekulize
==============================
*** Open Babel Audit Log in FindLSSR
Ran OpenBabel::FindLSSR
==============================
*** Open Babel Audit Log in FindRingAtomsAndBonds
Ran OpenBabel::FindRingAtomsAndBonds
==============================
*** Open Babel Audit Log in IsClosure
Ran OpenBabel::PerceiveClosureBonds
==============================
*** Open Babel Audit Log in WriteChemObjectImpl
OpenBabel::Write molecule MDL MOL format
==============================
*** Open Babel Audit Log in StereoFrom3D
Ran OpenBabel::StereoFrom3D
==============================
*** Open Babel Audit Log in FindSSSR
Ran OpenBabel::FindSSSR
==============================
*** Open Babel Audit Log in AssignAromaticFlags
Ran OpenBabel::AssignAromaticFlags
==============================
*** Open Babel Audit Log in AssignImplicitValence
Ran OpenBabel::AssignImplicitValence
==============================
*** Open Babel Audit Log in AssignHyb
Ran OpenBabel::AssignHybridization
==============================
*** Open Babel Audit Log in AssignHyb
Ran OpenBabel::AssignHybridization
==============================
*** Open Babel Audit Log in TetrahedralFrom3D
Ran OpenBabel::TetrahedralFrom3D
==============================
*** Open Babel Audit Log in CisTransFrom3D
Ran OpenBabel::CisTransFrom3D
==============================
*** Open Babel Audit Log in PerceiveStereo
Ran OpenBabel::PerceiveStereo
1 molecule converted
30 audit log messages
14:15:56 cjh@caspian:~/sandbox/babel-3417992
$ obabel -imoo PFGQIDLYXOTKNT-UHFFFAOYAN.out -omol
PFGQIDLYXOTKNT-UHFFFAOYAN.mol2 ---errorlevel 5
==============================
*** Open Babel Audit Log in ReadChemObjectImpl
OpenBabel::Read molecule MOPAC Output format
==============================
*** Open Babel Audit Log in Clear
Ran OpenBabel::Clear Molecule
==============================
*** Open Babel Audit Log in Clear
Ran OpenBabel::Clear Molecule
==============================
*** Open Babel Audit Log in Clear
Ran OpenBabel::Clear Molecule
==============================
*** Open Babel Audit Log in Clear
Ran OpenBabel::Clear Molecule
==============================
*** Open Babel Audit Log in ConnectTheDots
Ran OpenBabel::ConnectTheDots
==============================
*** Open Babel Audit Log in PerceiveBondOrders
Ran OpenBabel::PerceiveBondOrders
==============================
*** Open Babel Audit Log in FindSSSR
Ran OpenBabel::FindSSSR
==============================
*** Open Babel Audit Log in FindRingAtomsAndBonds
Ran OpenBabel::FindRingAtomsAndBonds
==============================
*** Open Babel Audit Log in IsClosure
Ran OpenBabel::PerceiveClosureBonds
==============================
*** Open Babel Audit Log in AssignAromaticFlags
Ran OpenBabel::AssignAromaticFlags
==============================
*** Open Babel Audit Log in AssignImplicitValence
Ran OpenBabel::AssignImplicitValence
==============================
*** Open Babel Audit Log in Kekulize
Ran OpenBabel::Kekulize
==============================
*** Open Babel Audit Log in AssignSpinMultiplicity
Ran OpenBabel::AssignSpinMultiplicity
==============================
*** Open Babel Audit Log in AssignImplicitValence
Ran OpenBabel::AssignImplicitValence
==============================
*** Open Babel Audit Log in AssignHyb
Ran OpenBabel::AssignHybridization
==============================
*** Open Babel Audit Log in Kekulize
Ran OpenBabel::Kekulize
==============================
*** Open Babel Audit Log in FindLSSR
Ran OpenBabel::FindLSSR
==============================
*** Open Babel Audit Log in FindRingAtomsAndBonds
Ran OpenBabel::FindRingAtomsAndBonds
==============================
*** Open Babel Audit Log in IsClosure
Ran OpenBabel::PerceiveClosureBonds
==============================
*** Open Babel Audit Log in WriteChemObjectImpl
OpenBabel::Write molecule MDL MOL format
==============================
*** Open Babel Audit Log in StereoFrom3D
Ran OpenBabel::StereoFrom3D
==============================
*** Open Babel Audit Log in FindSSSR
Ran OpenBabel::FindSSSR
==============================
*** Open Babel Audit Log in AssignAromaticFlags
Ran OpenBabel::AssignAromaticFlags
==============================
*** Open Babel Audit Log in AssignImplicitValence
Ran OpenBabel::AssignImplicitValence
==============================
*** Open Babel Audit Log in AssignHyb
Ran OpenBabel::AssignHybridization
==============================
*** Open Babel Audit Log in AssignHyb
Ran OpenBabel::AssignHybridization
==============================
*** Open Babel Audit Log in TetrahedralFrom3D
Ran OpenBabel::TetrahedralFrom3D
==============================
*** Open Babel Audit Log in CisTransFrom3D
Ran OpenBabel::CisTransFrom3D
==============================
*** Open Babel Audit Log in PerceiveStereo
Ran OpenBabel::PerceiveStereo
PFGQIDLYXOTKNT-UHFFFAOYAN.out
OpenBabel10101114153D
12 12 0 0 1 0 0 0 0 0999 V2000
-1.0043 0.9014 -0.3032 C 0 0 2 0 0 0 0 0 0 0 0 0
0.0278 1.1492 0.6861 O 0 0 0 0 0 0 0 0 0 0 0 0
-1.5858 1.8152 -0.5595 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.8759 -0.2149 -0.0004 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.6044 -1.1237 0.2463 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.2563 -1.9363 0.4670 H 0 0 0 0 0 0 0 0 0 0 0 0
1.0716 0.8321 -0.2706 C 0 0 2 0 0 0 0 0 0 0 0 0
0.0405 0.6098 -1.2670 O 0 0 0 0 0 0 0 0 0 0 0 0
1.7208 1.7047 -0.5073 H 0 0 0 0 0 0 0 0 0 0 0 0
1.8568 -0.3396 0.0581 C 0 0 0 0 0 0 0 0 0 0 0 0
2.5148 -1.2948 0.3262 C 0 0 0 0 0 0 0 0 0 0 0 0
3.1037 -2.1491 0.5660 H 0 0 0 0 0 0 0 0 0 0 0 0
1 3 1 6 0 0 0
1 4 1 0 0 0 0
1 2 1 0 0 0 0
4 5 3 0 0 0 0
5 6 1 0 0 0 0
7 9 1 6 0 0 0
7 10 1 0 0 0 0
7 2 1 0 0 0 0
8 1 1 0 0 0 0
8 7 1 0 0 0 0
10 11 3 0 0 0 0
11 12 1 0 0 0 0
M END
$$$$
==============================
*** Open Babel Audit Log in ReadChemObjectImpl
OpenBabel::Read molecule MOPAC Output format
==============================
*** Open Babel Audit Log in Clear
Ran OpenBabel::Clear Molecule
1 molecule converted
14:15:57 cjh@caspian:~/sandbox/babel-3417992
$
------------------------------------------------------------------------------
All the data continuously generated in your IT infrastructure contains a
definitive record of customers, application performance, security
threats, fraudulent activity and more. Splunk takes this data and makes
sense of it. Business sense. IT sense. Common sense.
http://p.sf.net/sfu/splunk-d2dcopy1
_______________________________________________
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