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[INFO] Console - predicting pockets for proteins from dataset [gpr75.pdb] |
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[INFO] PredictPocketsRoutine - outdir: /oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_gpr75 |
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[INFO] FeatureSetup - enabledFeatures: [chem, volsite, protrusion, bfactor, atom_table] |
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[INFO] Dataset - processing dataset [gpr75.pdb] using 0 threads |
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[INFO] Dataset - |
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processing [gpr75.pdb] (1/1) |
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[INFO] Console - processing [gpr75.pdb] (1/1) |
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[INFO] Protein - loading protein [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/proteins/gpr75.pdb] |
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[INFO] PdbUtils - loading file [../proteins/gpr75.pdb] |
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[INFO] Struct - groups in chain A: 540 |
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[INFO] Struct - groups in chain A: 540 |
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[INFO] Struct - 540 groups in chain A |
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[INFO] Protein - structure atoms: 4169 |
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[INFO] Protein - protein atoms: 4115 |
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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: 15433 |
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[INFO] Protein - exposed protein atoms: 3484 of 4115 |
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[INFO] InstancePredictor - Creating WekaInstancePredictor |
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[INFO] SLinkClusterer - clustering [161] elements |
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[INFO] SLinkClusterer - clusters: [id:5( 1 ), id:19( 96 ), id:20( 2 ), id:46( 1 ), id:48( 1 ), id:49( 1 ), id:53( 1 ), id:55( 2 ), id:58( 3 ), id:59( 1 ), id:66( 9 ), id:79( 1 ), id:83( 1 ), id:87( 2 ), id:89( 1 ), id:95( 1 ), id:96( 3 ), id:111( 2 ), id:112( 5 ), id:115( 8 ), id:121( 6 ), id:126( 9 ), id:134( 2 ), id:149( 2 )] |
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[INFO] SLinkClusterer - clusters together: 161 / 161 |
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[INFO] PocketPredictor - PREDICTING POCKETS.... ==================================== |
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[INFO] PocketPredictor - SAS POINTS: 15433 |
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[INFO] PocketPredictor - LIGANDABLE POINTS: 161 |
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[INFO] PocketPredictor - CLUSTERS: 24 |
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[INFO] PocketPredictor - FILTERED CLUSTERS: 8 |
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[INFO] PocketPredictor - pocket 1 - surf_atoms: 88 points: 96 score: 30.8 |
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[INFO] PocketPredictor - pocket 2 - surf_atoms: 26 points: 9 score: 3.3 |
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[INFO] PocketPredictor - pocket 3 - surf_atoms: 14 points: 9 score: 2.4 |
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[INFO] PocketPredictor - pocket 4 - surf_atoms: 10 points: 8 score: 2.2 |
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[INFO] PocketPredictor - pocket 5 - surf_atoms: 13 points: 6 score: 1.8 |
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[INFO] PocketPredictor - pocket 6 - surf_atoms: 14 points: 3 score: 1.2 |
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[INFO] PocketPredictor - pocket 7 - surf_atoms: 11 points: 5 score: 1.0 |
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[INFO] PocketPredictor - pocket 8 - surf_atoms: 20 points: 3 score: 0.9 |
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[INFO] OldPymolRenderer - copying [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/proteins/gpr75.pdb] to [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_gpr75/visualizations/data/gpr75.pdb] |
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[INFO] Console - predicting pockets finished in 0 hours 0 minutes 17.014 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_gpr75] |
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[INFO] Console - |
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[INFO] Console - Finished successfully in 0 hours 0 minutes 19.672 seconds. |
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