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rdk / p2rank

P2Rank: Protein-ligand binding site prediction tool based on machine learning. Stand-alone command line program / Java library for predicting ligand binding pockets from protein structure.

Home Page:https://rdk.github.io/p2rank/

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failFast for conservation

skodapetr opened this issue · comments

commented

I used the command:

.\p2rank-develop\prank.bat traineval -t .\datasets\chen11.ds -e .\datasets\joined(mlig).ds -threads 4 -rf_trees 128 delete_models 0 -loop 1 -seed 42 -delete_vectors 0 -feature_importances 1 -failFast 1 -l conserv_cloud -extra_features 'conserv_cloud' -load_conservation 1 -load_conservation_paths 1  -conservation_dir .\..\conservation

in LOG file I see

[ERROR] ConservationScore - Score file doesn't exist [.\datasets\.\..\conservation\a.029.003.001_1rx0aA.hssp.hom.gz]

I would expect p2rank to fail with -failFast 1 option in case of error, as now it seems like all is ok but in fact no conservation is loaded as the path is wrong.

Tested with f4c1e63.

commented

Fixed on develop branch and will be released in v2.3

-fail_fast 1 mode was not always respected when running the program with multiple threads.