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Smiles2Dock

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Smiles2Dock
File size: 3,147 Bytes
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[INFO] Console - predicting pockets for proteins from dataset [slc30a8.pdb]
[INFO] PredictPocketsRoutine - outdir: /oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_slc30a8
[INFO] FeatureSetup - enabledFeatures: [chem, volsite, protrusion, bfactor, atom_table]
[INFO] Dataset - processing dataset [slc30a8.pdb] using 0 threads
[INFO] Dataset - 
------------------------------------------------------------------------------------------------------------------------
processing [slc30a8.pdb] (1/1)
------------------------------------------------------------------------------------------------------------------------

[INFO] Console - processing [slc30a8.pdb] (1/1)
[INFO] Protein - loading protein [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/proteins/slc30a8.pdb]
[INFO] PdbUtils - loading file [../proteins/slc30a8.pdb]
[INFO] Struct - groups in chain A: 369
[INFO] Struct - groups in chain A: 369
[INFO] Struct - 369 groups in chain A
[INFO] Protein - structure atoms: 2861
[INFO] Protein - protein   atoms: 2823
[INFO] Protein - ignoring ligands
[INFO] FeatureSetup - enabledFeatures: [chem, volsite, protrusion, bfactor, atom_table]
[INFO] Protein - SAS points: 8281
[INFO] Protein - exposed protein atoms: 2201 of 2823
[INFO] InstancePredictor - Creating WekaInstancePredictor
[INFO] SLinkClusterer - clustering [73] elements
[INFO] SLinkClusterer - clusters: [id:5( 2 ), id:6( 1 ), id:18( 1 ), id:27( 1 ), id:29( 3 ), id:32( 3 ), id:46( 2 ), id:47( 1 ), id:52( 4 ), id:53( 4 ), id:54( 31 ), id:66( 2 ), id:69( 13 ), id:70( 3 ), id:71( 1 ), id:72( 1 )]
[INFO] SLinkClusterer - clusters together: 73 / 73
[INFO] PocketPredictor - PREDICTING POCKETS.... ====================================
[INFO] PocketPredictor - SAS POINTS: 8281
[INFO] PocketPredictor - LIGANDABLE POINTS: 73
[INFO] PocketPredictor - CLUSTERS: 16
[INFO] PocketPredictor - FILTERED CLUSTERS: 7
[INFO] PocketPredictor - pocket 1 -  surf_atoms:  52   points:  31   score:    9.4
[INFO] PocketPredictor - pocket 2 -  surf_atoms:  32   points:  13   score:    4.7
[INFO] PocketPredictor - pocket 3 -  surf_atoms:  12   points:   3   score:    1.5
[INFO] PocketPredictor - pocket 4 -  surf_atoms:  14   points:   4   score:    1.4
[INFO] PocketPredictor - pocket 5 -  surf_atoms:  10   points:   4   score:    0.9
[INFO] PocketPredictor - pocket 6 -  surf_atoms:  13   points:   3   score:    0.8
[INFO] PocketPredictor - pocket 7 -  surf_atoms:  11   points:   3   score:    0.8
[INFO] OldPymolRenderer - copying [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/proteins/slc30a8.pdb] to [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_slc30a8/visualizations/data/slc30a8.pdb]
[INFO] Console - predicting pockets finished in 0 hours 0 minutes 11.806 seconds
[INFO] Console - results saved to directory [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_slc30a8]
[INFO] Console - 
[INFO] Console - Finished successfully in 0 hours 0 minutes 13.154 seconds.