On Thu, Apr 11, 2013 at 3:26 PM, Marcus D. Hanwell <marcus.hanw...@kitware.com> wrote: > On Tue, Apr 9, 2013 at 7:06 AM, Noel O'Boyle <baoille...@gmail.com> wrote: >> On 9 April 2013 00:20, David van der Spoel <sp...@xray.bmc.uu.se> wrote: >>> On 2013-04-09 03:28, Marcus D. Hanwell wrote: >>>> Hi, >>>> >>>> We are using obabel to perform geometry optimizations etc on the >>>> command line, and we are hitting a bug that seems to only present >>>> itself on the Mac. If the input and output formats are the same then >>>> the operation fails, for example, >>>> >>>> obabel -icml -ocml --minimize --log --ff UFF >>>> >>>> That is using standard in/out, but it also seems to happen when using >>>> files. This works as expected on Linux and Windows, are we diverging >>>> from expected use too much or is this a bug. This is the same in 2.3.2 >>>> and master, using 10.6.8 and GCC 4.2.1. >>>> >>> Interesting, it seems to be something with writing cml. I'm using trunk >>> but I get: >>> [artemisia:~/tmp] % obabel -isdf ethanol.sdf -ocml ethanol.cml >>> ============================== >>> *** Open Babel Error in OpenAndSetFormat >>> Cannot open ethanol.cml >>> >>> and then all the output is dumped on the terminal instead (it does do >>> the minimization as requested). So it seems something goes wrong opening >>> a cml file for writing. >>> >> -O ethanol.cml > > obabel -icml -ocml --minimize produces the same result, using -O > out.cml also doesn't help, but -O out.xyz etc works as expected. > > As David pointed out, it seems to be specific to CML. I can do the > same operation with xyz being the input and output format with no > noticeable issue. This also only seems to affect Mac as far as I can > tell. > For now we are working around this by switching to another file format, as far as I can tell this only affects CML on the Mac. If there is interest I can enter a bug report (still SourceForce?)
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