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[INFO] Console - predicting pockets for proteins from dataset [tnfsf15.pdb] |
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[INFO] PredictPocketsRoutine - outdir: /oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_tnfsf15 |
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[INFO] FeatureSetup - enabledFeatures: [chem, volsite, protrusion, bfactor, atom_table] |
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[INFO] Dataset - processing dataset [tnfsf15.pdb] using 0 threads |
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[INFO] Dataset - |
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processing [tnfsf15.pdb] (1/1) |
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[INFO] Console - processing [tnfsf15.pdb] (1/1) |
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[INFO] Protein - loading protein [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/proteins/tnfsf15.pdb] |
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[INFO] PdbUtils - loading file [../proteins/tnfsf15.pdb] |
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[INFO] Struct - groups in chain A: 251 |
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[INFO] Struct - groups in chain A: 251 |
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[INFO] Struct - 251 groups in chain A |
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[INFO] Protein - structure atoms: 1975 |
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[INFO] Protein - protein atoms: 1942 |
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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: 6534 |
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[INFO] Protein - exposed protein atoms: 1540 of 1942 |
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[INFO] InstancePredictor - Creating WekaInstancePredictor |
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[INFO] SLinkClusterer - clustering [6] elements |
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[INFO] SLinkClusterer - clusters: [id:0( 1 ), id:2( 3 ), id:3( 1 ), id:5( 1 )] |
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[INFO] SLinkClusterer - clusters together: 6 / 6 |
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[INFO] PocketPredictor - PREDICTING POCKETS.... ==================================== |
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[INFO] PocketPredictor - SAS POINTS: 6534 |
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[INFO] PocketPredictor - LIGANDABLE POINTS: 6 |
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[INFO] PocketPredictor - CLUSTERS: 4 |
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[INFO] PocketPredictor - FILTERED CLUSTERS: 1 |
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[INFO] PocketPredictor - pocket 1 - surf_atoms: 15 points: 3 score: 1.9 |
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[INFO] OldPymolRenderer - copying [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/proteins/tnfsf15.pdb] to [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_tnfsf15/visualizations/data/tnfsf15.pdb] |
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[INFO] Console - predicting pockets finished in 0 hours 0 minutes 9.071 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_tnfsf15] |
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[INFO] Console - |
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[INFO] Console - Finished successfully in 0 hours 0 minutes 10.361 seconds. |
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