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[INFO] Console - predicting pockets for proteins from dataset [inhbe.pdb] |
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[INFO] PredictPocketsRoutine - outdir: /oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_inhbe |
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[INFO] FeatureSetup - enabledFeatures: [chem, volsite, protrusion, bfactor, atom_table] |
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[INFO] Dataset - processing dataset [inhbe.pdb] using 0 threads |
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[INFO] Dataset - |
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processing [inhbe.pdb] (1/1) |
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[INFO] Console - processing [inhbe.pdb] (1/1) |
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[INFO] Protein - loading protein [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/proteins/inhbe.pdb] |
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[INFO] PdbUtils - loading file [../proteins/inhbe.pdb] |
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[INFO] Struct - groups in chain A: 350 |
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[INFO] Struct - groups in chain A: 350 |
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[INFO] Struct - 350 groups in chain A |
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[INFO] Protein - structure atoms: 2713 |
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[INFO] Protein - protein atoms: 2637 |
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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: 7397 |
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[INFO] Protein - exposed protein atoms: 2076 of 2637 |
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[INFO] InstancePredictor - Creating WekaInstancePredictor |
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[INFO] SLinkClusterer - clustering [49] elements |
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[INFO] SLinkClusterer - clusters: [id:0( 1 ), id:11( 1 ), id:12( 1 ), id:15( 1 ), id:18( 4 ), id:19( 2 ), id:22( 9 ), id:30( 18 ), id:31( 2 ), id:40( 2 ), id:46( 3 ), id:48( 5 )] |
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[INFO] SLinkClusterer - clusters together: 49 / 49 |
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[INFO] PocketPredictor - PREDICTING POCKETS.... ==================================== |
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[INFO] PocketPredictor - SAS POINTS: 7397 |
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[INFO] PocketPredictor - LIGANDABLE POINTS: 49 |
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[INFO] PocketPredictor - CLUSTERS: 12 |
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[INFO] PocketPredictor - FILTERED CLUSTERS: 5 |
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[INFO] PocketPredictor - pocket 1 - surf_atoms: 43 points: 18 score: 5.7 |
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[INFO] PocketPredictor - pocket 2 - surf_atoms: 23 points: 9 score: 2.8 |
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[INFO] PocketPredictor - pocket 3 - surf_atoms: 18 points: 5 score: 2.5 |
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[INFO] PocketPredictor - pocket 4 - surf_atoms: 13 points: 4 score: 1.4 |
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[INFO] PocketPredictor - pocket 5 - surf_atoms: 8 points: 3 score: 1.0 |
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[INFO] OldPymolRenderer - copying [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/proteins/inhbe.pdb] to [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_inhbe/visualizations/data/inhbe.pdb] |
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[INFO] Console - predicting pockets finished in 0 hours 0 minutes 10.715 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_inhbe] |
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[INFO] Console - |
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[INFO] Console - Finished successfully in 0 hours 0 minutes 12.221 seconds. |
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