Hi Wallace,
I'm not much good with Perl, but for those folks who are, could you
provide a complete Perl script that reproduces the problem. The
smaller the script the better. For example, at the moment I can easily
blame everything on what everything is in @sdfdata. Also please note
that ReadFile returns a boolean that indicates whether it was
successful or not. A common cause of problems is that the user does
not check whether there was a problem before proceeding.
- Noel
On 22 November 2013 20:54, Wallace Chan <walla...@umich.edu> wrote:
> Dear All,
>
> Once again, I apologize for my utter lack of experience, but I was hoping
> y'all could help me out with a problem I've been having. Using OpenBabel in
> Perl, I have been trying to convert several 2D SDF files to 3D. The process
> appears to be stuck somewhere between the 'Do' and 'WriteFile' functions,
> shown as follows in bold:
>
> my $filename = $id . '.sdf';
> open (OUT, ">temp.sdf");
> print OUT @sdfdata;
> close OUT;
> $obConversion->ReadFile($obMol, "temp.sdf");
> $genOp->Do($obMol);
> $obConversion->WriteFile($obMol, $filename);
> print "Generated $filename.\n";
> `rm temp.sdf`;
> last;
>
> The reason I came to this conclusion was that the file, $filename, was never
> generated, while temp.sdf was. I also have the following initialized outside
> before my loop:
>
> my $obMol = Chemistry::OpenBabel::OBMol->new();
> my $obConversion = Chemistry::OpenBabel::OBConversion->new();
> my $genOp = Chemistry::OpenBabel::OBOp::FindType("gen3D");
> $obConversion->SetInAndOutFormats("sdf", "sdf");
>
> 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
>
> Thanks in advance for any advice!
>
> --
> Wallace Chan
> Zhang Lab
> Department of Biological Chemistry
> University of Michigan
> walla...@umich.edu
>
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