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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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Problems with Opera CL that are not present in the GUI version #32

Open yordan-y opened 1 year ago

yordan-y commented 1 year ago

Hello,

While trying to use opera CL i encountered a couple of errors that weren't present in the GUI version:

1) i keep getting a KNIME error for the QSAR standardization. It gives me exit error code 4. I'm not sure but this might be a problem with my version of KNIME, so I am currently trying to troubleshoot this issue.

2)While running the CL version i get the following error, which is not present for the GUI version:

====================================================================== ============== Running The Models ============== Generating the general structural properties... ---------- PhysChem properties ---------- Predicting LogP values (Log10)... Weighted kNN model with 9 descriptors Predicting MP values (Deg. C)... Weighted kNN model with 15 descriptors Predicting BP values (Deg. C)... Weighted kNN model with 13 descriptors Index exceeds the number of array elements. Index must not exceed 7860.

Error in OPERA (line 2067)

MATLAB:badsubscript

kmansouri commented 1 year ago

Hi, Thank you for using OPERA and for reaching out. Are you running single or multiple structures? Does it happen every time with any file? Does it happen with the sample files provided? Can you send me the input file for troubleshooting purposes?

mnam-bruno commented 4 months ago

I have the same error message when using Opera CL on Ubuntu 22 when using the option standardize "-st" using any input SDF file.

kmansouri commented 3 months ago

Can you please provide more details?

mnam-bruno commented 3 months ago

I created a new issue (#42) with hopefully enough details to reproducted the problems I have found.

kmansouri commented 1 month ago

For the standardization issue you're facing, it's because you're not providing the absolute path for the input files. You're not providing the full path to the input in their command, so KNIME wasn’t able to locate the input file with just the name. I always recommend to use an absolute path instead of relative path which is just an assumption about the current location.

For BP model (only), when you request nearest neighbors (-n), there's a bug in the writing of the results which I'm working on. Stay tuned for a new release soon. In the meantime you can get BP predictions, just not the nearest neighbors.