Compund limit for OpenBabel?

I have used OpenBabel to convert from SD format to SMILES for one of my workflows. Typically this works very smoothly, but I 've just noticed that when I have a very long list of compounds, OpenBabel fails. Looking at the debug output in the Console window suggests that the line fed to OpenBabel in incomplete - it looks as though it is truncated.


Hi Kirk,

It seems there is a limit, at least under Windows. The node calls OpenBabel for chunks of 2,000 molecules. It looks like the resulting command line is too long for Windows. Under Linux this is no problem. Unfortunately, I cannot think of a quick workaround, you could do (except using Linux). Nevertheless I will fix this bug as soon as possible. If you urgently need the fix, please drop me a PM.


Thank you for the quick reply!

At this point I'm able to work around the problem easily, so I'm in no urgent need for a fix. A little creative processing allowed the workflow to work...or flow...either one.