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[INFO] Console - predicting pockets for proteins from dataset [card6.pdb] |
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[INFO] PredictPocketsRoutine - outdir: /oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_card6 |
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[INFO] FeatureSetup - enabledFeatures: [chem, volsite, protrusion, bfactor, atom_table] |
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[INFO] Dataset - processing dataset [card6.pdb] using 0 threads |
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[INFO] Dataset - |
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processing [card6.pdb] (1/1) |
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[INFO] Console - processing [card6.pdb] (1/1) |
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[INFO] Protein - loading protein [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/proteins/card6.pdb] |
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[INFO] PdbUtils - loading file [../proteins/card6.pdb] |
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[INFO] Struct - groups in chain A: 1037 |
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[INFO] Struct - groups in chain A: 1037 |
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[INFO] Struct - 1037 groups in chain A |
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[INFO] Protein - structure atoms: 8178 |
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[INFO] Protein - protein atoms: 8046 |
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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: 33308 |
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[INFO] Protein - exposed protein atoms: 6763 of 8046 |
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[INFO] InstancePredictor - Creating WekaInstancePredictor |
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[INFO] SLinkClusterer - clustering [104] elements |
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[INFO] SLinkClusterer - clusters: [id:3( 1 ), id:4( 2 ), id:16( 1 ), id:23( 10 ), id:27( 2 ), id:40( 12 ), id:44( 2 ), id:45( 1 ), id:60( 1 ), id:62( 4 ), id:63( 1 ), id:65( 3 ), id:76( 4 ), id:77( 2 ), id:84( 19 ), id:87( 2 ), id:95( 34 ), id:102( 2 ), id:103( 1 )] |
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[INFO] SLinkClusterer - clusters together: 104 / 104 |
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[INFO] PocketPredictor - PREDICTING POCKETS.... ==================================== |
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[INFO] PocketPredictor - SAS POINTS: 33308 |
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[INFO] PocketPredictor - LIGANDABLE POINTS: 104 |
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[INFO] PocketPredictor - CLUSTERS: 19 |
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[INFO] PocketPredictor - FILTERED CLUSTERS: 7 |
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[INFO] PocketPredictor - pocket 1 - surf_atoms: 37 points: 34 score: 13.4 |
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[INFO] PocketPredictor - pocket 2 - surf_atoms: 27 points: 19 score: 5.9 |
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[INFO] PocketPredictor - pocket 3 - surf_atoms: 25 points: 12 score: 4.9 |
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[INFO] PocketPredictor - pocket 4 - surf_atoms: 31 points: 10 score: 3.8 |
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[INFO] PocketPredictor - pocket 5 - surf_atoms: 18 points: 4 score: 1.8 |
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[INFO] PocketPredictor - pocket 6 - surf_atoms: 14 points: 4 score: 1.7 |
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[INFO] PocketPredictor - pocket 7 - surf_atoms: 3 points: 3 score: 1.0 |
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[INFO] OldPymolRenderer - copying [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/proteins/card6.pdb] to [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_card6/visualizations/data/card6.pdb] |
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[INFO] Console - predicting pockets finished in 0 hours 0 minutes 14.310 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_card6] |
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[INFO] Console - |
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[INFO] Console - Finished successfully in 0 hours 0 minutes 15.874 seconds. |
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