Re: [Open Babel] Conversion of 2D SDF to 3D SDF in Perl

[Geoffrey H. <geo...@gm...>]

>                 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