Opera 2.8 - issues with the structural-standardization

kmansouri / OPERA

Free and open-source application (command line and GUI) providing QSAR models predictions as well as applicability domain and accuracy assessment for physicochemical properties, environmental fate and toxicological endpoints. ==================>Download the latest compiled version from the "releases" tab and run the executable installer.

MIT License

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Opera 2.8 - issues with the structural-standardization #28

Closed lidiaceriani0305 closed 2 years ago

lidiaceriani0305 commented 2 years ago

Hello, I just installed the new OPERA 2.8 version, and I'm encountering the same error, no matter which input file I use (mol, sdf, smi, txt) : No structures passed standardization. Check input file! This issues also occurs with the mol files provided by the US EPA CompTox Chemicals Dashboard. I currently have installed the KNIME version 4.5.2 on my PC. Could it be that this version of KNIME is creating some issues with the implemented QSAR-ready workflow? Other users have experienced similar issues with this new version of opera? Thank you for your feedback! Best, Lidia

tsufz commented 2 years ago

Hi @kmansouri, I encounter the problem in 2.9 cl opera_p as well. I gues some link is missing to KNIME. It does work without the -st switch:

kmansouri commented 2 years ago

@lidiaceriani0305 Sorry for the delay in replying to the issue. Yes, the first version of 2.8 (2.8.1) had an issue with the knime standardizer that happened during the update of the workflow to knime 4.5. This was fixed in the latest versions of 2.8 as well as in 2.9. So you can install either one of the latest versions.

kmansouri commented 2 years ago

@tsufz because of a limit in the size of the package on Github and the fact that OPERA parallel version was already a big package, the standardizer had a packaging issue for the (opera_p only). I am working on a solution. In the meanwhile you can install the regular OPERA Cl version (in the same parent folder as opera_p) and they will both share the same standardizer.