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[INFO] Console - predicting pockets for proteins from dataset [ubash3a.pdb] |
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[INFO] PredictPocketsRoutine - outdir: /oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_ubash3a |
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[INFO] FeatureSetup - enabledFeatures: [chem, volsite, protrusion, bfactor, atom_table] |
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[INFO] Dataset - processing dataset [ubash3a.pdb] using 0 threads |
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[INFO] Dataset - |
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processing [ubash3a.pdb] (1/1) |
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[INFO] Console - processing [ubash3a.pdb] (1/1) |
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[INFO] Protein - loading protein [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/proteins/ubash3a.pdb] |
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[INFO] PdbUtils - loading file [../proteins/ubash3a.pdb] |
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[INFO] Struct - groups in chain A: 451 |
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[INFO] Struct - groups in chain A: 451 |
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[INFO] Struct - 451 groups in chain A |
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[INFO] Protein - structure atoms: 3548 |
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[INFO] Protein - protein atoms: 3471 |
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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: 9818 |
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[INFO] Protein - exposed protein atoms: 2625 of 3471 |
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[INFO] InstancePredictor - Creating WekaInstancePredictor |
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[INFO] SLinkClusterer - clustering [86] elements |
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[INFO] SLinkClusterer - clusters: [id:1( 2 ), id:10( 27 ), id:20( 13 ), id:25( 2 ), id:46( 1 ), id:47( 1 ), id:55( 30 ), id:77( 8 ), id:84( 1 ), id:85( 1 )] |
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[INFO] SLinkClusterer - clusters together: 86 / 86 |
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[INFO] PocketPredictor - PREDICTING POCKETS.... ==================================== |
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[INFO] PocketPredictor - SAS POINTS: 9818 |
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[INFO] PocketPredictor - LIGANDABLE POINTS: 86 |
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[INFO] PocketPredictor - CLUSTERS: 10 |
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[INFO] PocketPredictor - FILTERED CLUSTERS: 4 |
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[INFO] PocketPredictor - pocket 1 - surf_atoms: 38 points: 30 score: 10.3 |
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[INFO] PocketPredictor - pocket 2 - surf_atoms: 50 points: 27 score: 10.1 |
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[INFO] PocketPredictor - pocket 3 - surf_atoms: 20 points: 13 score: 4.3 |
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[INFO] PocketPredictor - pocket 4 - surf_atoms: 21 points: 8 score: 1.5 |
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[INFO] OldPymolRenderer - copying [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/proteins/ubash3a.pdb] to [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_ubash3a/visualizations/data/ubash3a.pdb] |
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[INFO] Console - predicting pockets finished in 0 hours 0 minutes 16.827 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_ubash3a] |
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[INFO] Console - |
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[INFO] Console - Finished successfully in 0 hours 0 minutes 19.160 seconds. |
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