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This was most likely a compiler bug with MinGW gcc 3.4.2. After updating to the current MinGW gcc 3.4.5. and recompiling, everything works fine. And it comes with it's own gettimeofday() also, no need to tinker with the Makefiles anymore. :)
2007-10-11 12:16:57 UTC in Open Babel
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Update: I have removed the call to AddHydrogens() as suggested and now it works. So if there is really a bug, it's most likely in AddHydrogens().
2007-10-09 06:16:21 UTC in Open Babel
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>I think your code has a (common) programming error.
>In ob_hillformula the pointer tmpFormula does not have any memory assigned
>to it. So depending on where it pointed, the function could work, or it
Objection your honor!
man strdup (3):
The strdup() function allocates sufficient memory for a copy of the string str, does the copy, and returns a pointer to it. The pointer may...
2007-10-09 06:09:31 UTC in Open Babel
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OpenBabel 2.1.1 library, self-compiled with MinGW on Win32 (XP).
I found that GetMolWt() and GetFormula() never return when e.g. fed with the appended Molecule in MDL V2000 format.
It worked (and still works) with 2.0.x and for a lot of other input molecules, so this might be a bug.
Here is the code calling the library functions:
extern "C" char *
ob_hillformula (char *molfile)
{.
2007-09-18 06:00:57 UTC in Open Babel
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This was deleted because the error was in my program, not in OB.
2007-05-24 13:47:48 UTC in Open Babel
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File Added: SNomatch.mol.
2007-05-22 13:48:25 UTC in Open Babel
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File Added: SMatch.mol.
2007-05-22 13:48:01 UTC in Open Babel
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If I do a type 2 fingerpeint screening for substructure candidates with SQuery.mol, SMatch.mol is found but SNomatch.mol not. Is this a bug or a feature?.
2007-05-22 13:47:31 UTC in Open Babel
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This may be no bug at all and I'm no chemist, but this
was reported to me by a chemist, so it might have some
credibility.
Amide C-N bonds are usually not considered to be
rotatable because of their high rotational energy
barrier (e.g.
http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/jm020017n)
Page 2617, but the NumRotors() method does.
There might be other affected bonds...
2006-04-03 12:13:01 UTC in Open Babel
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Logged In: YES
user_id=1391954
Here is the requested backtrace from gdb: gdb.txt
regards,
Ernst-Georg.
2006-03-16 08:43:13 UTC in Open Babel
