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[INFO] Console - predicting pockets for proteins from dataset [ifih1.pdb] |
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[INFO] PredictPocketsRoutine - outdir: /oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_ifih1 |
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[INFO] FeatureSetup - enabledFeatures: [chem, volsite, protrusion, bfactor, atom_table] |
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[INFO] Dataset - processing dataset [ifih1.pdb] using 0 threads |
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[INFO] Dataset - |
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processing [ifih1.pdb] (1/1) |
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[INFO] Console - processing [ifih1.pdb] (1/1) |
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[INFO] Protein - loading protein [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/proteins/ifih1.pdb] |
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[INFO] PdbUtils - loading file [../proteins/ifih1.pdb] |
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[INFO] Struct - groups in chain A: 921 |
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[INFO] Struct - groups in chain A: 921 |
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[INFO] Struct - 921 groups in chain A |
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[INFO] Protein - structure atoms: 7353 |
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[INFO] Protein - protein atoms: 7244 |
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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: 18250 |
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[INFO] Protein - exposed protein atoms: 5205 of 7244 |
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[INFO] InstancePredictor - Creating WekaInstancePredictor |
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[INFO] SLinkClusterer - clustering [123] elements |
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[INFO] SLinkClusterer - clusters: [id:1( 2 ), id:25( 31 ), id:32( 4 ), id:33( 3 ), id:47( 1 ), id:52( 1 ), id:58( 2 ), id:73( 1 ), id:81( 25 ), id:86( 1 ), id:87( 2 ), id:89( 2 ), id:90( 1 ), id:95( 12 ), id:98( 4 ), id:100( 5 ), id:109( 15 ), id:111( 2 ), id:112( 1 ), id:117( 4 ), id:118( 1 ), id:120( 1 ), id:121( 1 ), id:122( 1 )] |
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[INFO] SLinkClusterer - clusters together: 123 / 123 |
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[INFO] PocketPredictor - PREDICTING POCKETS.... ==================================== |
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[INFO] PocketPredictor - SAS POINTS: 18250 |
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[INFO] PocketPredictor - LIGANDABLE POINTS: 123 |
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[INFO] PocketPredictor - CLUSTERS: 24 |
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[INFO] PocketPredictor - FILTERED CLUSTERS: 9 |
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[INFO] PocketPredictor - pocket 1 - surf_atoms: 34 points: 31 score: 11.0 |
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[INFO] PocketPredictor - pocket 2 - surf_atoms: 37 points: 25 score: 8.6 |
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[INFO] PocketPredictor - pocket 3 - surf_atoms: 31 points: 15 score: 5.8 |
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[INFO] PocketPredictor - pocket 4 - surf_atoms: 26 points: 12 score: 4.3 |
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[INFO] PocketPredictor - pocket 5 - surf_atoms: 34 points: 5 score: 2.6 |
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[INFO] PocketPredictor - pocket 6 - surf_atoms: 16 points: 4 score: 1.8 |
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[INFO] PocketPredictor - pocket 7 - surf_atoms: 18 points: 4 score: 1.5 |
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[INFO] PocketPredictor - pocket 8 - surf_atoms: 9 points: 4 score: 1.4 |
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[INFO] PocketPredictor - pocket 9 - surf_atoms: 8 points: 3 score: 0.6 |
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[INFO] OldPymolRenderer - copying [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/proteins/ifih1.pdb] to [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_ifih1/visualizations/data/ifih1.pdb] |
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[INFO] Console - predicting pockets finished in 0 hours 0 minutes 12.392 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_ifih1] |
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[INFO] Console - |
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[INFO] Console - Finished successfully in 0 hours 0 minutes 13.975 seconds. |
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