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[INFO] Console - predicting pockets for proteins from dataset [umod.pdb] |
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[INFO] PredictPocketsRoutine - outdir: /oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_umod |
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[INFO] FeatureSetup - enabledFeatures: [chem, volsite, protrusion, bfactor, atom_table] |
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[INFO] Dataset - processing dataset [umod.pdb] using 0 threads |
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[INFO] Dataset - |
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processing [umod.pdb] (1/1) |
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[INFO] Console - processing [umod.pdb] (1/1) |
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[INFO] Protein - loading protein [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/proteins/umod.pdb] |
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[INFO] PdbUtils - loading file [../proteins/umod.pdb] |
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[INFO] Struct - groups in chain A: 640 |
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[INFO] Struct - groups in chain A: 640 |
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[INFO] Struct - 640 groups in chain A |
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[INFO] Protein - structure atoms: 4858 |
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[INFO] Protein - protein atoms: 4764 |
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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: 12917 |
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[INFO] Protein - exposed protein atoms: 3486 of 4764 |
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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:1( 2 ), id:2( 1 ), id:3( 1 ), id:4( 1 ), id:9( 1 ), id:12( 7 ), id:13( 1 )] |
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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: 12917 |
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[INFO] PocketPredictor - LIGANDABLE POINTS: 14 |
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[INFO] PocketPredictor - CLUSTERS: 7 |
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[INFO] PocketPredictor - FILTERED CLUSTERS: 1 |
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[INFO] PocketPredictor - pocket 1 - surf_atoms: 19 points: 7 score: 2.3 |
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[INFO] OldPymolRenderer - copying [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/proteins/umod.pdb] to [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_umod/visualizations/data/umod.pdb] |
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[INFO] Console - predicting pockets finished in 0 hours 0 minutes 12.066 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_umod] |
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[INFO] Console - |
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[INFO] Console - Finished successfully in 0 hours 0 minutes 13.468 seconds. |
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