Thanks for the great/funny comments on my last post! It's really helping improve my day. :)
My test set atoms are definitely bondless, and that's also what made some of my output look weird: it was missing some of the output (including the newlines!) which only printed if an "if" statement was true... and when there's no bonds, the "if" is false. Now I need to track down why my atoms weren't being assigned bonds... is it a problem with the code generating the bonds, or are the atoms themselves getting lost? I'll keep you posted. ;) (Yeah, like you have a clue what I'm blathering about anyway.)
The only problem is... I had been working in my advisor's office to help stay awake... but he's had to leave early. :( Hopefully I'll figure out this bug before the end of the day, even with having to battle sleepiness.
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