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[INFO] Console - predicting pockets for proteins from dataset [f10a.pdb] |
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[INFO] PredictPocketsRoutine - outdir: /oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_f10a |
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[INFO] FeatureSetup - enabledFeatures: [chem, volsite, protrusion, bfactor, atom_table] |
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[INFO] Dataset - processing dataset [f10a.pdb] using 0 threads |
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[INFO] Dataset - |
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processing [f10a.pdb] (1/1) |
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[INFO] Console - processing [f10a.pdb] (1/1) |
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[INFO] Protein - loading protein [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/proteins/f10a.pdb] |
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[INFO] PdbUtils - loading file [../proteins/f10a.pdb] |
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[INFO] Struct - groups in chain A: 488 |
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[INFO] Struct - groups in chain A: 488 |
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[INFO] Struct - 488 groups in chain A |
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[INFO] Protein - structure atoms: 3830 |
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[INFO] Protein - protein atoms: 3752 |
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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: 11433 |
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[INFO] Protein - exposed protein atoms: 2886 of 3752 |
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[INFO] InstancePredictor - Creating WekaInstancePredictor |
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[INFO] SLinkClusterer - clustering [16] elements |
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[INFO] SLinkClusterer - clusters: [id:1( 2 ), id:4( 3 ), id:8( 2 ), id:9( 1 ), id:10( 3 ), id:12( 1 ), id:13( 2 ), id:15( 2 )] |
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[INFO] SLinkClusterer - clusters together: 16 / 16 |
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[INFO] PocketPredictor - PREDICTING POCKETS.... ==================================== |
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[INFO] PocketPredictor - SAS POINTS: 11433 |
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[INFO] PocketPredictor - LIGANDABLE POINTS: 16 |
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[INFO] PocketPredictor - CLUSTERS: 8 |
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[INFO] PocketPredictor - FILTERED CLUSTERS: 2 |
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[INFO] PocketPredictor - pocket 1 - surf_atoms: 14 points: 3 score: 1.3 |
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[INFO] PocketPredictor - pocket 2 - surf_atoms: 13 points: 3 score: 1.0 |
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[INFO] OldPymolRenderer - copying [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/proteins/f10a.pdb] to [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_f10a/visualizations/data/f10a.pdb] |
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[INFO] Console - predicting pockets finished in 0 hours 0 minutes 10.511 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_f10a] |
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[INFO] Console - |
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[INFO] Console - Finished successfully in 0 hours 0 minutes 11.955 seconds. |
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