Re: [Open Babel] pybel.write() produces truncated pdbqt? (R. K. Belew)

[R. K. B. <rb...@uc...>]

thanks very much David and Torsten.  i can also make
this work on (ubuntu 14.04) linux.

that's the good news.  the bad news (for my purposes) is that
the output PDBQT file is considerably perturbed from the original:
user/remark lines dropped, torsion tree traversal order, and
esp. atom numbering.

and given my aversion to all things C++, i'm afraid i'm not
motivated to dig in and find the OSX version of this bug.
he said guiltily(:

thanks again for helping me puzzle this through in any case.

	Rik

On 8/5/15 1:53 AM, Torsten Sachse wrote:
> Hi all,
>
> I can confirm that writing the pdbqt file works without problems on several
> Linux distributions (including some CentOS, RedHat and Debian Systems and
> derivates). Hence, unfortunately, I cannot try to find the location of
> the bug
> as I don't have a MacOS-system available.
>
> It should not be too hard to add some simple debug output to the place
> where the
> output file is written to check where exactly the error happens.
> Although it's
> important to flush the output as shown below [1]. Maybe a programme like
> Valgrind could help to find the issue if it's memory related? You could
> also try
> to turn of optimization during the compilation. If it's a matter of
> trying to
> access memory that is already allocated by a different programme, the
> issue is
> more likely to occur with high optimization (at least that's what I
> experienced
> on Linux). It'd still need to be fixed though.
>
> Hope this helps,
> Torsten
>
> [1]: Example debug output (in case you don't know):
> std::cerr << "Debug: 1" << std::endl << std::flush;
>
> On Tue, 4 Aug 2015, David Hall wrote:
>
>> It seems I can reproduce the segfault on OS X Yosemite, but not on
>> Ubuntu 14.04.
>>
>> -David
>>
>>
>>> On Aug 4, 2015, at 8:02 PM, R. K. Belew <rb...@uc...> wrote:
>>>
>>> update, if anyone is interested:  it seems quite clear the
>>> bug is in the PDBQT output filter:
>>>
>>>>> obabel file1.pdbqt -O file2.pdbqt
>>>>> Segmentation fault: 11
>>>>> obabel file1.pdbqt -O file2.pdb
>>>>> 1 molecule converted
>>>
>>> and has nothing particular to do with pybel;  pybel is
>>> silently eating this fault and generating only partial
>>> output before it dies.
>>>
>>>     Rik
>>>
>>>
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>>>
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>>
>>
> .
>