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[INFO] Console - predicting pockets for proteins from dataset [dnmt3a.pdb] |
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[INFO] PredictPocketsRoutine - outdir: /oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_dnmt3a |
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[INFO] FeatureSetup - enabledFeatures: [chem, volsite, protrusion, bfactor, atom_table] |
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[INFO] Dataset - processing dataset [dnmt3a.pdb] using 0 threads |
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[INFO] Dataset - |
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processing [dnmt3a.pdb] (1/1) |
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[INFO] Console - processing [dnmt3a.pdb] (1/1) |
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[INFO] Protein - loading protein [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/proteins/dnmt3a.pdb] |
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[INFO] PdbUtils - loading file [../proteins/dnmt3a.pdb] |
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[INFO] Struct - groups in chain A: 912 |
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[INFO] Struct - groups in chain A: 912 |
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[INFO] Struct - 912 groups in chain A |
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[INFO] Protein - structure atoms: 7146 |
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[INFO] Protein - protein atoms: 6973 |
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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: 22498 |
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[INFO] Protein - exposed protein atoms: 5376 of 6973 |
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[INFO] InstancePredictor - Creating WekaInstancePredictor |
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[INFO] SLinkClusterer - clustering [93] elements |
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[INFO] SLinkClusterer - clusters: [id:0( 1 ), id:8( 15 ), id:12( 1 ), id:17( 1 ), id:18( 1 ), id:20( 2 ), id:24( 1 ), id:25( 1 ), id:26( 2 ), id:29( 1 ), id:41( 8 ), id:49( 6 ), id:52( 1 ), id:67( 1 ), id:76( 1 ), id:78( 7 ), id:79( 1 ), id:82( 24 ), id:83( 1 ), id:90( 11 ), id:91( 3 ), id:92( 3 )] |
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[INFO] SLinkClusterer - clusters together: 93 / 93 |
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[INFO] PocketPredictor - PREDICTING POCKETS.... ==================================== |
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[INFO] PocketPredictor - SAS POINTS: 22498 |
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[INFO] PocketPredictor - LIGANDABLE POINTS: 93 |
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[INFO] PocketPredictor - CLUSTERS: 22 |
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[INFO] PocketPredictor - FILTERED CLUSTERS: 8 |
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[INFO] PocketPredictor - pocket 1 - surf_atoms: 56 points: 24 score: 8.4 |
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[INFO] PocketPredictor - pocket 2 - surf_atoms: 31 points: 15 score: 5.2 |
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[INFO] PocketPredictor - pocket 3 - surf_atoms: 18 points: 11 score: 3.4 |
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[INFO] PocketPredictor - pocket 4 - surf_atoms: 26 points: 6 score: 3.1 |
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[INFO] PocketPredictor - pocket 5 - surf_atoms: 19 points: 7 score: 2.7 |
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[INFO] PocketPredictor - pocket 6 - surf_atoms: 12 points: 8 score: 2.3 |
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[INFO] PocketPredictor - pocket 7 - surf_atoms: 19 points: 3 score: 1.2 |
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[INFO] PocketPredictor - pocket 8 - surf_atoms: 18 points: 3 score: 1.1 |
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[INFO] OldPymolRenderer - copying [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/proteins/dnmt3a.pdb] to [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_dnmt3a/visualizations/data/dnmt3a.pdb] |
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[INFO] Console - predicting pockets finished in 0 hours 0 minutes 12.536 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_dnmt3a] |
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[INFO] Console - |
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[INFO] Console - Finished successfully in 0 hours 0 minutes 14.056 seconds. |
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