Bugs item #2956135, was opened at 2010-02-21 18:36
Message generated for change (Tracker Item Submitted) made by mr_grieves
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Category: None
Group: None
Status: Open
Resolution: None
Priority: 1
Private: No
Submitted By: Mr_Grieves (mr_grieves)
Assigned to: Nobody/Anonymous (nobody)
Summary: Crash in Kekulize
Initial Comment:
The attached gamout file crashes when OB tries to read it. The file
contains three separate molecules interacting by VDW forces.
Backtrace:
Program received signal SIGSEGV, Segmentation fault.
0xb7b85fb6 in OpenBabel::OBBond::GetBeginAtom (this=0x0) at
/usr/src/openbabel/include/openbabel/bond.h:210
210 OBAtom *GetBeginAtom() { return(_bgn); }
(gdb) bt
#0 0xb7b85fb6 in OpenBabel::OBBond::GetBeginAtom (this=0x0) at
/usr/src/openbabel/include/openbabel/bond.h:210
#1 0xb7c0d6b2 in OpenBabel::OBMol::expand_kekulize (this=0xbffff484,
bond_idx=11, atomState=..., bondState=...)
at /usr/src/openbabel/src/kekulize.cpp:431
#2 0xb7c0d744 in OpenBabel::OBMol::expand_kekulize (this=0xbffff484,
bond_idx=10, atomState=..., bondState=...)
at /usr/src/openbabel/src/kekulize.cpp:438
#3 0xb7c0d744 in OpenBabel::OBMol::expand_kekulize (this=0xbffff484,
bond_idx=9, atomState=..., bondState=...)
at /usr/src/openbabel/src/kekulize.cpp:438
#4 0xb7c0d744 in OpenBabel::OBMol::expand_kekulize (this=0xbffff484,
bond_idx=8, atomState=..., bondState=...)
at /usr/src/openbabel/src/kekulize.cpp:438
#5 0xb7c0d744 in OpenBabel::OBMol::expand_kekulize (this=0xbffff484,
bond_idx=7, atomState=..., bondState=...)
at /usr/src/openbabel/src/kekulize.cpp:438
#6 0xb7c0d744 in OpenBabel::OBMol::expand_kekulize (this=0xbffff484,
bond_idx=6, atomState=..., bondState=...)
at /usr/src/openbabel/src/kekulize.cpp:438
#7 0xb7c0d744 in OpenBabel::OBMol::expand_kekulize (this=0xbffff484,
bond_idx=5, atomState=..., bondState=...)
at /usr/src/openbabel/src/kekulize.cpp:438
#8 0xb7c0d744 in OpenBabel::OBMol::expand_kekulize (this=0xbffff484,
bond_idx=4, atomState=..., bondState=...)
at /usr/src/openbabel/src/kekulize.cpp:438
#9 0xb7c0d744 in OpenBabel::OBMol::expand_kekulize (this=0xbffff484,
bond_idx=3, atomState=..., bondState=...)
at /usr/src/openbabel/src/kekulize.cpp:438
#10 0xb7c0d744 in OpenBabel::OBMol::expand_kekulize (this=0xbffff484,
bond_idx=2, atomState=..., bondState=...)
at /usr/src/openbabel/src/kekulize.cpp:438
#11 0xb7c0d744 in OpenBabel::OBMol::expand_kekulize (this=0xbffff484,
bond_idx=1, atomState=..., bondState=...)
at /usr/src/openbabel/src/kekulize.cpp:438
#12 0xb7c0d744 in OpenBabel::OBMol::expand_kekulize (this=0xbffff484,
bond_idx=0, atomState=..., bondState=...)
at /usr/src/openbabel/src/kekulize.cpp:438
#13 0xb7c0d361 in OpenBabel::OBMol::start_kekulize (this=0xbffff484,
cycle=..., electron=...) at /usr/src/openbabel/src/kekulize.cpp:356
#14 0xb7c0ce74 in OpenBabel::OBMol::NewPerceiveKekuleBonds
(this=0xbffff484) at /usr/src/openbabel/src/kekulize.cpp:276
#15 0xb7b934c5 in OpenBabel::OBBond::IsKSingle (this=0x8083f28) at
/usr/src/openbabel/src/bond.cpp:449
#16 0xb7c59070 in OpenBabel::OBMol::Kekulize (this=0xbffff484) at
/usr/src/openbabel/src/mol.cpp:2793
#17 0xb7c5defd in OpenBabel::OBMol::PerceiveBondOrders
(this=0xbffff484) at /usr/src/openbabel/src/mol.cpp:3624
#18 0xb7303cc9 in OpenBabel::GAMESSOutputFormat::ReadMolecule
(this=0xb7312a38, pOb=0xbffff484, pConv=0xbffff3c0)
at /usr/src/openbabel/src/formats/gamessformat.cpp:751
#19 0xb7c70134 in OpenBabel::OBConversion::Read (this=0xbffff3c0,
pOb=0xbffff484, pin=0xbffff194)
at /usr/src/openbabel/src/obconversion.cpp:746
#20 0x0804b2e5 in main (argc=2, argv=0xbffff644) at
/usr/src/openbabel/tools/obenergy.cpp:125
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