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[INFO] Console - predicting pockets for proteins from dataset [dpp9.pdb] |
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[INFO] PredictPocketsRoutine - outdir: /oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_dpp9 |
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[INFO] FeatureSetup - enabledFeatures: [chem, volsite, protrusion, bfactor, atom_table] |
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[INFO] Dataset - processing dataset [dpp9.pdb] using 0 threads |
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[INFO] Dataset - |
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processing [dpp9.pdb] (1/1) |
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[INFO] Console - processing [dpp9.pdb] (1/1) |
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[INFO] Protein - loading protein [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/proteins/dpp9.pdb] |
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[INFO] PdbUtils - loading file [../proteins/dpp9.pdb] |
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[INFO] Struct - groups in chain A: 863 |
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[INFO] Struct - groups in chain A: 863 |
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[INFO] Struct - 863 groups in chain A |
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[INFO] Protein - structure atoms: 6944 |
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[INFO] Protein - protein atoms: 6805 |
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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: 11568 |
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[INFO] Protein - exposed protein atoms: 4221 of 6805 |
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[INFO] InstancePredictor - Creating WekaInstancePredictor |
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[INFO] SLinkClusterer - clustering [198] elements |
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[INFO] SLinkClusterer - clusters: [id:4( 7 ), id:5( 1 ), id:11( 2 ), id:22( 2 ), id:37( 41 ), id:54( 1 ), id:56( 7 ), id:67( 1 ), id:68( 1 ), id:73( 1 ), id:76( 1 ), id:80( 7 ), id:85( 4 ), id:121( 31 ), id:123( 17 ), id:132( 21 ), id:147( 1 ), id:148( 3 ), id:156( 1 ), id:176( 34 ), id:177( 1 ), id:178( 1 ), id:186( 9 ), id:187( 1 ), id:188( 1 ), id:195( 1 )] |
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[INFO] SLinkClusterer - clusters together: 198 / 198 |
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[INFO] PocketPredictor - PREDICTING POCKETS.... ==================================== |
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[INFO] PocketPredictor - SAS POINTS: 11568 |
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[INFO] PocketPredictor - LIGANDABLE POINTS: 198 |
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[INFO] PocketPredictor - CLUSTERS: 26 |
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[INFO] PocketPredictor - FILTERED CLUSTERS: 11 |
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[INFO] PocketPredictor - pocket 1 - surf_atoms: 69 points: 41 score: 13.7 |
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[INFO] PocketPredictor - pocket 2 - surf_atoms: 32 points: 34 score: 13.1 |
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[INFO] PocketPredictor - pocket 3 - surf_atoms: 51 points: 31 score: 9.7 |
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[INFO] PocketPredictor - pocket 4 - surf_atoms: 34 points: 21 score: 8.6 |
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[INFO] PocketPredictor - pocket 5 - surf_atoms: 22 points: 17 score: 4.4 |
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[INFO] PocketPredictor - pocket 6 - surf_atoms: 18 points: 9 score: 2.7 |
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[INFO] PocketPredictor - pocket 7 - surf_atoms: 21 points: 7 score: 2.2 |
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[INFO] PocketPredictor - pocket 8 - surf_atoms: 13 points: 7 score: 2.2 |
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[INFO] PocketPredictor - pocket 9 - surf_atoms: 17 points: 7 score: 2.1 |
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[INFO] PocketPredictor - pocket10 - surf_atoms: 23 points: 4 score: 1.4 |
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[INFO] PocketPredictor - pocket11 - surf_atoms: 8 points: 3 score: 0.8 |
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[INFO] OldPymolRenderer - copying [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/proteins/dpp9.pdb] to [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_dpp9/visualizations/data/dpp9.pdb] |
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[INFO] Console - predicting pockets finished in 0 hours 0 minutes 11.498 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_dpp9] |
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[INFO] Console - |
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[INFO] Console - Finished successfully in 0 hours 0 minutes 13.029 seconds. |
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