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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