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Fetch by chemical name not working


#1

Hi All,

I am running Avogadro installed via the Ubuntu Software application (version 1.1.1) on Ubuntu 16.04. I have OpenBabel v2.3.2 and Qt v4.8.6 installed on this terminal as well. When I attempt to use Import > Fetch by chemical name and enter the name of a chemical (i.e methanol), no molecule appears, though the filename does change to methanol.sdf for example. No error message appears and no activity is monitored even in the terminal after running the function.

However, manually heading online to the cactus repository and getting the link to the SD file “https://cactus.nci.nih.gov/chemical/structure/methanol/sdf”, and inputting it into the Import > Fetch from URL generates the molecule rather promptly. While this is a workaround, I’d like to understand what the underlying problem for the Fetch by chemical name function is.

Please kindly assist and thank you very much for your time.


#2

This is a known bug fixed in Avogadro 1.2 and later:

Avogadro 1.1.1 is quite old and the NIH chemical resolver moved to use HTTPS


#3

Will there be an eventual update for Avogadro in the Ubuntu Software Package installer? I have difficulties installing the Avogadro 1.2 package manually.


#4

I don’t use Ubuntu, but the Debichem maintainers do have a 1.2.0 package for Debian:
https://qa.debian.org/[email protected]