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[INFO] Console - predicting pockets for proteins from dataset [apol1.pdb] |
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[INFO] PredictPocketsRoutine - outdir: /oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_apol1 |
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[INFO] FeatureSetup - enabledFeatures: [chem, volsite, protrusion, bfactor, atom_table] |
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[INFO] Dataset - processing dataset [apol1.pdb] using 0 threads |
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[INFO] Dataset - |
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processing [apol1.pdb] (1/1) |
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[INFO] Console - processing [apol1.pdb] (1/1) |
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[INFO] Protein - loading protein [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/proteins/apol1.pdb] |
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[INFO] PdbUtils - loading file [proteins/apol1.pdb] |
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[INFO] Struct - groups in chain A: 398 |
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[INFO] Struct - groups in chain A: 398 |
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[INFO] Struct - 398 groups in chain A |
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[INFO] Protein - structure atoms: 3094 |
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[INFO] Protein - protein atoms: 3038 |
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[INFO] Protein - ignoring ligands |
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[INFO] FeatureSetup - enabledFeatures: [chem, volsite, protrusion, bfactor, atom_table] |
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[INFO] Protein - SAS points: 10324 |
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[INFO] Protein - exposed protein atoms: 2605 of 3038 |
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[INFO] InstancePredictor - Creating WekaInstancePredictor |
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[INFO] SLinkClusterer - clustering [142] elements |
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[INFO] SLinkClusterer - clusters: [id:49( 114 ), id:50( 4 ), id:53( 2 ), id:58( 2 ), id:59( 5 ), id:88( 10 ), id:126( 2 ), id:128( 2 ), id:134( 1 )] |
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[INFO] SLinkClusterer - clusters together: 142 / 142 |
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[INFO] PocketPredictor - PREDICTING POCKETS.... ==================================== |
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[INFO] PocketPredictor - SAS POINTS: 10324 |
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[INFO] PocketPredictor - LIGANDABLE POINTS: 142 |
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[INFO] PocketPredictor - CLUSTERS: 9 |
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[INFO] PocketPredictor - FILTERED CLUSTERS: 4 |
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[INFO] PocketPredictor - pocket 1 - surf_atoms: 123 points: 114 score: 43.1 |
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[INFO] PocketPredictor - pocket 2 - surf_atoms: 36 points: 10 score: 3.5 |
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[INFO] PocketPredictor - pocket 3 - surf_atoms: 20 points: 5 score: 1.7 |
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[INFO] PocketPredictor - pocket 4 - surf_atoms: 11 points: 4 score: 1.3 |
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[INFO] OldPymolRenderer - copying [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/proteins/apol1.pdb] to [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_apol1/visualizations/data/apol1.pdb] |
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[INFO] Console - predicting pockets finished in 0 hours 0 minutes 12.901 seconds |
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[INFO] Console - results saved to directory [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_apol1] |
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[INFO] Console - |
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[INFO] Console - Finished successfully in 0 hours 0 minutes 13.744 seconds. |
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