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. Marcus ------------------------------------------------------------------------------ Precog is a next-generation analytics platform capable of advanced analytics on semi-structured data. The platform includes APIs for building apps and a phenomenal toolset for data science. Developers can use our toolset for easy data analysis & visualization. Get a free account! http://www2.precog.com/precogplatform/slashdotnewsletter _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
