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[INFO] Console - predicting pockets for proteins from dataset [dpp4.pdb] |
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[INFO] PredictPocketsRoutine - outdir: /oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_dpp4 |
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[INFO] FeatureSetup - enabledFeatures: [chem, volsite, protrusion, bfactor, atom_table] |
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[INFO] Dataset - processing dataset [dpp4.pdb] using 0 threads |
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[INFO] Dataset - |
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processing [dpp4.pdb] (1/1) |
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[INFO] Console - processing [dpp4.pdb] (1/1) |
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[INFO] Protein - loading protein [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/proteins/dpp4.pdb] |
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[INFO] PdbUtils - loading file [../proteins/dpp4.pdb] |
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[INFO] Struct - groups in chain A: 766 |
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[INFO] Struct - groups in chain A: 766 |
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[INFO] Struct - 766 groups in chain A |
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[INFO] Protein - structure atoms: 6238 |
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[INFO] Protein - protein atoms: 6101 |
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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: 10904 |
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[INFO] Protein - exposed protein atoms: 3759 of 6101 |
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[INFO] InstancePredictor - Creating WekaInstancePredictor |
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[INFO] SLinkClusterer - clustering [143] elements |
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[INFO] SLinkClusterer - clusters: [id:0( 1 ), id:1( 1 ), id:2( 1 ), id:3( 1 ), id:6( 1 ), id:13( 5 ), id:17( 2 ), id:22( 11 ), id:23( 1 ), id:29( 2 ), id:30( 1 ), id:36( 5 ), id:38( 3 ), id:39( 1 ), id:45( 37 ), id:50( 4 ), id:52( 4 ), id:54( 4 ), id:57( 1 ), id:60( 2 ), id:61( 2 ), id:63( 1 ), id:69( 6 ), id:91( 7 ), id:98( 28 ), id:138( 8 ), id:140( 3 )] |
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[INFO] SLinkClusterer - clusters together: 143 / 143 |
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[INFO] PocketPredictor - PREDICTING POCKETS.... ==================================== |
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[INFO] PocketPredictor - SAS POINTS: 10904 |
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[INFO] PocketPredictor - LIGANDABLE POINTS: 143 |
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[INFO] PocketPredictor - CLUSTERS: 27 |
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[INFO] PocketPredictor - FILTERED CLUSTERS: 13 |
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[INFO] PocketPredictor - pocket 1 - surf_atoms: 41 points: 37 score: 11.5 |
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[INFO] PocketPredictor - pocket 2 - surf_atoms: 47 points: 28 score: 8.8 |
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[INFO] PocketPredictor - pocket 3 - surf_atoms: 22 points: 8 score: 3.2 |
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[INFO] PocketPredictor - pocket 4 - surf_atoms: 18 points: 11 score: 3.1 |
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[INFO] PocketPredictor - pocket 5 - surf_atoms: 26 points: 7 score: 3.0 |
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[INFO] PocketPredictor - pocket 6 - surf_atoms: 16 points: 5 score: 2.2 |
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[INFO] PocketPredictor - pocket 7 - surf_atoms: 10 points: 6 score: 1.9 |
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[INFO] PocketPredictor - pocket 8 - surf_atoms: 18 points: 5 score: 1.8 |
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[INFO] PocketPredictor - pocket 9 - surf_atoms: 16 points: 4 score: 1.7 |
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[INFO] PocketPredictor - pocket10 - surf_atoms: 16 points: 4 score: 1.6 |
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[INFO] PocketPredictor - pocket11 - surf_atoms: 11 points: 4 score: 1.6 |
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[INFO] PocketPredictor - pocket12 - surf_atoms: 16 points: 3 score: 1.1 |
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[INFO] PocketPredictor - pocket13 - surf_atoms: 7 points: 3 score: 0.9 |
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[INFO] OldPymolRenderer - copying [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/proteins/dpp4.pdb] to [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_dpp4/visualizations/data/dpp4.pdb] |
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[INFO] Console - predicting pockets finished in 0 hours 0 minutes 11.892 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_dpp4] |
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[INFO] Console - |
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[INFO] Console - Finished successfully in 0 hours 0 minutes 13.572 seconds. |
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