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[INFO] Console - predicting pockets for proteins from dataset [slc6a19.pdb] |
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[INFO] PredictPocketsRoutine - outdir: /oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_slc6a19 |
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[INFO] FeatureSetup - enabledFeatures: [chem, volsite, protrusion, bfactor, atom_table] |
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[INFO] Dataset - processing dataset [slc6a19.pdb] using 0 threads |
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[INFO] Dataset - |
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processing [slc6a19.pdb] (1/1) |
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[INFO] Console - processing [slc6a19.pdb] (1/1) |
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[INFO] Protein - loading protein [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/slc6a19.pdb] |
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[INFO] PdbUtils - loading file [slc6a19.pdb] |
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[INFO] Struct - groups in chain A: 634 |
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[INFO] Struct - groups in chain A: 634 |
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[INFO] Struct - 634 groups in chain A |
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[INFO] Protein - structure atoms: 5017 |
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[INFO] Protein - protein atoms: 4935 |
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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: 8548 |
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[INFO] Protein - exposed protein atoms: 2919 of 4935 |
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[INFO] InstancePredictor - Creating WekaInstancePredictor |
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[INFO] SLinkClusterer - clustering [188] elements |
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[INFO] SLinkClusterer - clusters: [id:27( 2 ), id:36( 2 ), id:46( 3 ), id:47( 1 ), id:48( 1 ), id:49( 1 ), id:55( 1 ), id:56( 1 ), id:58( 2 ), id:63( 3 ), id:76( 10 ), id:88( 1 ), id:89( 1 ), id:90( 2 ), id:95( 2 ), id:109( 19 ), id:113( 3 ), id:114( 3 ), id:118( 5 ), id:120( 3 ), id:127( 13 ), id:128( 4 ), id:129( 1 ), id:155( 3 ), id:166( 20 ), id:167( 5 ), id:170( 8 ), id:173( 2 ), id:177( 47 ), id:181( 10 ), id:182( 9 )] |
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[INFO] SLinkClusterer - clusters together: 188 / 188 |
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[INFO] PocketPredictor - PREDICTING POCKETS.... ==================================== |
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[INFO] PocketPredictor - SAS POINTS: 8548 |
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[INFO] PocketPredictor - LIGANDABLE POINTS: 188 |
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[INFO] PocketPredictor - CLUSTERS: 31 |
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[INFO] PocketPredictor - FILTERED CLUSTERS: 17 |
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[INFO] PocketPredictor - pocket 1 - surf_atoms: 54 points: 47 score: 14.9 |
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[INFO] PocketPredictor - pocket 2 - surf_atoms: 37 points: 20 score: 7.0 |
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[INFO] PocketPredictor - pocket 3 - surf_atoms: 35 points: 19 score: 6.0 |
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[INFO] PocketPredictor - pocket 4 - surf_atoms: 23 points: 13 score: 5.1 |
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[INFO] PocketPredictor - pocket 5 - surf_atoms: 12 points: 9 score: 5.1 |
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[INFO] PocketPredictor - pocket 6 - surf_atoms: 30 points: 10 score: 4.4 |
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[INFO] PocketPredictor - pocket 7 - surf_atoms: 16 points: 8 score: 3.6 |
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[INFO] PocketPredictor - pocket 8 - surf_atoms: 13 points: 10 score: 2.4 |
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[INFO] PocketPredictor - pocket 9 - surf_atoms: 10 points: 5 score: 2.1 |
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[INFO] PocketPredictor - pocket10 - surf_atoms: 16 points: 4 score: 1.7 |
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[INFO] PocketPredictor - pocket11 - surf_atoms: 11 points: 3 score: 1.3 |
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[INFO] PocketPredictor - pocket12 - surf_atoms: 13 points: 3 score: 1.3 |
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[INFO] PocketPredictor - pocket13 - surf_atoms: 12 points: 5 score: 1.1 |
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[INFO] PocketPredictor - pocket14 - surf_atoms: 3 points: 3 score: 1.1 |
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[INFO] PocketPredictor - pocket15 - surf_atoms: 13 points: 3 score: 0.8 |
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[INFO] PocketPredictor - pocket16 - surf_atoms: 4 points: 3 score: 0.6 |
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[INFO] PocketPredictor - pocket17 - surf_atoms: 8 points: 3 score: 0.5 |
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[INFO] OldPymolRenderer - copying [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/slc6a19.pdb] to [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_slc6a19/visualizations/data/slc6a19.pdb] |
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[INFO] Console - predicting pockets finished in 0 hours 0 minutes 18.133 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_slc6a19] |
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[INFO] Console - |
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[INFO] Console - Finished successfully in 0 hours 0 minutes 19.351 seconds. |
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