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[INFO] Console - predicting pockets for proteins from dataset [mfge8.pdb] |
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[INFO] PredictPocketsRoutine - outdir: /oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_mfge8 |
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[INFO] FeatureSetup - enabledFeatures: [chem, volsite, protrusion, bfactor, atom_table] |
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[INFO] Dataset - processing dataset [mfge8.pdb] using 0 threads |
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[INFO] Dataset - |
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processing [mfge8.pdb] (1/1) |
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[INFO] Console - processing [mfge8.pdb] (1/1) |
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[INFO] Protein - loading protein [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/mfge8.pdb] |
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[INFO] PdbUtils - loading file [mfge8.pdb] |
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[INFO] Struct - groups in chain A: 387 |
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[INFO] Struct - groups in chain A: 387 |
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[INFO] Struct - 387 groups in chain A |
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[INFO] Protein - structure atoms: 3038 |
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[INFO] Protein - protein atoms: 2977 |
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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: 6766 |
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[INFO] Protein - exposed protein atoms: 1959 of 2977 |
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[INFO] InstancePredictor - Creating WekaInstancePredictor |
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[INFO] SLinkClusterer - clustering [13] elements |
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[INFO] SLinkClusterer - clusters: [id:2( 4 ), id:5( 2 ), id:7( 3 ), id:8( 1 ), id:10( 1 ), id:11( 1 ), id:12( 1 )] |
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[INFO] SLinkClusterer - clusters together: 13 / 13 |
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[INFO] PocketPredictor - PREDICTING POCKETS.... ==================================== |
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[INFO] PocketPredictor - SAS POINTS: 6766 |
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[INFO] PocketPredictor - LIGANDABLE POINTS: 13 |
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[INFO] PocketPredictor - CLUSTERS: 7 |
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[INFO] PocketPredictor - FILTERED CLUSTERS: 2 |
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[INFO] PocketPredictor - pocket 1 - surf_atoms: 14 points: 3 score: 2.0 |
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[INFO] PocketPredictor - pocket 2 - surf_atoms: 17 points: 4 score: 1.2 |
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[INFO] OldPymolRenderer - copying [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/mfge8.pdb] to [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_mfge8/visualizations/data/mfge8.pdb] |
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[INFO] Console - predicting pockets finished in 0 hours 0 minutes 16.656 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_mfge8] |
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[INFO] Console - |
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[INFO] Console - Finished successfully in 0 hours 0 minutes 17.991 seconds. |
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