Alright, I had a deeper look into Win32::OLE and came across the following
$tool->LetProperty('Molecule',$data);
$tool->setProperty('Molecule, $data);
So it turns out that the LetProperty method loads the $data instance into the Molecule attribute of the $tool instance. I'll be looking more closely at this to understand why this worked over the previous syntactic sugars that i was using.
I hope this node helps someone else in the future
MadraghRua
yet another biologist hacking perl....
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