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[INFO] Console - predicting pockets for proteins from dataset [angptl7.pdb] |
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[INFO] PredictPocketsRoutine - outdir: /oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_angptl7 |
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[INFO] FeatureSetup - enabledFeatures: [chem, volsite, protrusion, bfactor, atom_table] |
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[INFO] Dataset - processing dataset [angptl7.pdb] using 0 threads |
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[INFO] Dataset - |
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processing [angptl7.pdb] (1/1) |
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[INFO] Console - processing [angptl7.pdb] (1/1) |
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[INFO] Protein - loading protein [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/angptl7.pdb] |
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[INFO] PdbUtils - loading file [angptl7.pdb] |
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[INFO] Struct - groups in chain A: 346 |
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[INFO] Struct - groups in chain A: 346 |
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[INFO] Struct - 346 groups in chain A |
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[INFO] Protein - structure atoms: 2815 |
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[INFO] Protein - protein atoms: 2751 |
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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: 7365 |
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[INFO] Protein - exposed protein atoms: 1967 of 2751 |
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[INFO] InstancePredictor - Creating WekaInstancePredictor |
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[INFO] SLinkClusterer - clustering [14] elements |
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[INFO] SLinkClusterer - clusters: [id:4( 6 ), id:5( 1 ), id:7( 1 ), id:13( 6 )] |
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[INFO] SLinkClusterer - clusters together: 14 / 14 |
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[INFO] PocketPredictor - PREDICTING POCKETS.... ==================================== |
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[INFO] PocketPredictor - SAS POINTS: 7365 |
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[INFO] PocketPredictor - LIGANDABLE POINTS: 14 |
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[INFO] PocketPredictor - CLUSTERS: 4 |
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[INFO] PocketPredictor - FILTERED CLUSTERS: 2 |
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[INFO] PocketPredictor - pocket 1 - surf_atoms: 20 points: 6 score: 2.4 |
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[INFO] PocketPredictor - pocket 2 - surf_atoms: 24 points: 6 score: 1.8 |
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[INFO] OldPymolRenderer - copying [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/angptl7.pdb] to [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_angptl7/visualizations/data/angptl7.pdb] |
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[INFO] Console - predicting pockets finished in 0 hours 0 minutes 23.716 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_angptl7] |
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[INFO] Console - |
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[INFO] Console - Finished successfully in 0 hours 0 minutes 25.033 seconds. |
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