Open Babel Linux vs Windows difference? Specifically: pubchem read only is missing on Linux

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1

Am retrieving data via API from PubChem (as XML data) and use Open Babel to extract the structure directly via “pc - pubchem format (read only)”. This is on Windows.
On Linux, this isn’t possible, since it is not available.
Bug or feature?

Knime V4.2.3 on both platform. No updates available at this point.

2

Hi,

Thank you for your question. Could you share a simple workflow containing what you want to do? Then I could reproduce it and try to solve it.

Thanks,
Jeany

3

well, all you need to do is create a molecule (fetch it from anywhere/draw, whatever) and add the open babel node. you don’t even need a pubchem/xml type of data to simply open the node and check the list of available read formats. do this on linux and compare to windows.
(don’t have a w/f at hand here on this pc atm otherwise I’d post)

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openbabel_lin_vs_win.knwf (14.0 KB)
here is a workflow, hope that helps (exported from Linux; on windows you will have to scroll in the list to find “pc - pubchem”, it will probably not be pre-selected.

5

Thank you for pointing out that bug. I was able to reproduce it on my Ubuntu machine and forwarded the issue to our developers.

Best,
Jeany

1 Like
6

Thanks.
Probably not used a lot, otherwise someone would have complained earlier :smile:

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