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[INFO] Console - predicting pockets for proteins from dataset [rnf186.pdb] |
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[INFO] PredictPocketsRoutine - outdir: /oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_rnf186 |
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[INFO] FeatureSetup - enabledFeatures: [chem, volsite, protrusion, bfactor, atom_table] |
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[INFO] Dataset - processing dataset [rnf186.pdb] using 0 threads |
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[INFO] Dataset - |
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processing [rnf186.pdb] (1/1) |
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[INFO] Console - processing [rnf186.pdb] (1/1) |
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[INFO] Protein - loading protein [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/proteins/rnf186.pdb] |
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[INFO] PdbUtils - loading file [../proteins/rnf186.pdb] |
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[INFO] Struct - groups in chain A: 227 |
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[INFO] Struct - groups in chain A: 227 |
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[INFO] Struct - 227 groups in chain A |
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[INFO] Protein - structure atoms: 1682 |
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[INFO] Protein - protein atoms: 1657 |
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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: 7132 |
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[INFO] Protein - exposed protein atoms: 1479 of 1657 |
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[INFO] InstancePredictor - Creating WekaInstancePredictor |
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[INFO] PocketPredictor - PREDICTING POCKETS.... ==================================== |
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[INFO] PocketPredictor - SAS POINTS: 7132 |
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[INFO] PocketPredictor - LIGANDABLE POINTS: 1 |
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[INFO] PocketPredictor - CLUSTERS: 1 |
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[INFO] PocketPredictor - FILTERED CLUSTERS: 0 |
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[INFO] OldPymolRenderer - copying [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/proteins/rnf186.pdb] to [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_rnf186/visualizations/data/rnf186.pdb] |
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[INFO] Console - predicting pockets finished in 0 hours 0 minutes 10.453 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_rnf186] |
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[INFO] Console - |
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[INFO] Console - Finished successfully in 0 hours 0 minutes 11.914 seconds. |
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