> my $filename = $id . '.sdf'; > open (OUT, ">temp.sdf"); > print OUT @sdfdata; > close OUT; > $obConversion->ReadFile($obMol, "temp.sdf”);
This just seems weird. Even if you have a bunch of data, you don’t need to save it to a file. There’s a ReadString() command too. We added these functions for scripting languages that didn’t have an analogue to C++ iostreams. > $genOp->Do($obMol); > $obConversion->WriteFile($obMol, $filename); > print "Generated $filename.\n"; > `rm temp.sdf`; > last; It’s been ages since I used Perl, so I don’t know if there are Perl debuggers. You could insert a print statement after the Do() statement to see if it completes, for example. > Here are some of the reasons why I think it doesn't work: > 1.) It isn't possible to convert 2D SDF to 3D SDF > 2.) I was successful using this converting InChI to 3D SDF, but maybe I need > to call a different class If you have questions about whether something works in your code, you can test if it works from the command-line tools. So yes, converting from 2D to 3D should work just fine. If not, that’s our bug. Can you send an example 2D SDF file? Thanks, -Geoff ------------------------------------------------------------------------------ Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now. http://pubads.g.doubleclick.net/gampad/clk?id=63431311&iu=/4140/ostg.clktrk _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
