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[INFO] Console - predicting pockets for proteins from dataset [slc30a8.pdb] |
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[INFO] PredictPocketsRoutine - outdir: /oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_slc30a8 |
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[INFO] FeatureSetup - enabledFeatures: [chem, volsite, protrusion, bfactor, atom_table] |
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[INFO] Dataset - processing dataset [slc30a8.pdb] using 0 threads |
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[INFO] Dataset - |
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processing [slc30a8.pdb] (1/1) |
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[INFO] Console - processing [slc30a8.pdb] (1/1) |
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[INFO] Protein - loading protein [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/proteins/slc30a8.pdb] |
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[INFO] PdbUtils - loading file [../proteins/slc30a8.pdb] |
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[INFO] Struct - groups in chain A: 369 |
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[INFO] Struct - groups in chain A: 369 |
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[INFO] Struct - 369 groups in chain A |
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[INFO] Protein - structure atoms: 2861 |
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[INFO] Protein - protein atoms: 2823 |
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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: 8281 |
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[INFO] Protein - exposed protein atoms: 2201 of 2823 |
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[INFO] InstancePredictor - Creating WekaInstancePredictor |
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[INFO] SLinkClusterer - clustering [73] elements |
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[INFO] SLinkClusterer - clusters: [id:5( 2 ), id:6( 1 ), id:18( 1 ), id:27( 1 ), id:29( 3 ), id:32( 3 ), id:46( 2 ), id:47( 1 ), id:52( 4 ), id:53( 4 ), id:54( 31 ), id:66( 2 ), id:69( 13 ), id:70( 3 ), id:71( 1 ), id:72( 1 )] |
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[INFO] SLinkClusterer - clusters together: 73 / 73 |
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[INFO] PocketPredictor - PREDICTING POCKETS.... ==================================== |
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[INFO] PocketPredictor - SAS POINTS: 8281 |
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[INFO] PocketPredictor - LIGANDABLE POINTS: 73 |
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[INFO] PocketPredictor - CLUSTERS: 16 |
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[INFO] PocketPredictor - FILTERED CLUSTERS: 7 |
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[INFO] PocketPredictor - pocket 1 - surf_atoms: 52 points: 31 score: 9.4 |
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[INFO] PocketPredictor - pocket 2 - surf_atoms: 32 points: 13 score: 4.7 |
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[INFO] PocketPredictor - pocket 3 - surf_atoms: 12 points: 3 score: 1.5 |
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[INFO] PocketPredictor - pocket 4 - surf_atoms: 14 points: 4 score: 1.4 |
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[INFO] PocketPredictor - pocket 5 - surf_atoms: 10 points: 4 score: 0.9 |
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[INFO] PocketPredictor - pocket 6 - surf_atoms: 13 points: 3 score: 0.8 |
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[INFO] PocketPredictor - pocket 7 - surf_atoms: 11 points: 3 score: 0.8 |
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[INFO] OldPymolRenderer - copying [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/proteins/slc30a8.pdb] to [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_slc30a8/visualizations/data/slc30a8.pdb] |
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[INFO] Console - predicting pockets finished in 0 hours 0 minutes 11.806 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_slc30a8] |
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[INFO] Console - |
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[INFO] Console - Finished successfully in 0 hours 0 minutes 13.154 seconds. |
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