Datasets:
File size: 3,405 Bytes
3c49a60 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 | [INFO] Console - predicting pockets for proteins from dataset [ifih1.pdb]
[INFO] PredictPocketsRoutine - outdir: /oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_ifih1
[INFO] FeatureSetup - enabledFeatures: [chem, volsite, protrusion, bfactor, atom_table]
[INFO] Dataset - processing dataset [ifih1.pdb] using 0 threads
[INFO] Dataset -
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processing [ifih1.pdb] (1/1)
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[INFO] Console - processing [ifih1.pdb] (1/1)
[INFO] Protein - loading protein [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/proteins/ifih1.pdb]
[INFO] PdbUtils - loading file [../proteins/ifih1.pdb]
[INFO] Struct - groups in chain A: 921
[INFO] Struct - groups in chain A: 921
[INFO] Struct - 921 groups in chain A
[INFO] Protein - structure atoms: 7353
[INFO] Protein - protein atoms: 7244
[INFO] Protein - ignoring ligands
[INFO] FeatureSetup - enabledFeatures: [chem, volsite, protrusion, bfactor, atom_table]
[INFO] Protein - SAS points: 18250
[INFO] Protein - exposed protein atoms: 5205 of 7244
[INFO] InstancePredictor - Creating WekaInstancePredictor
[INFO] SLinkClusterer - clustering [123] elements
[INFO] SLinkClusterer - clusters: [id:1( 2 ), id:25( 31 ), id:32( 4 ), id:33( 3 ), id:47( 1 ), id:52( 1 ), id:58( 2 ), id:73( 1 ), id:81( 25 ), id:86( 1 ), id:87( 2 ), id:89( 2 ), id:90( 1 ), id:95( 12 ), id:98( 4 ), id:100( 5 ), id:109( 15 ), id:111( 2 ), id:112( 1 ), id:117( 4 ), id:118( 1 ), id:120( 1 ), id:121( 1 ), id:122( 1 )]
[INFO] SLinkClusterer - clusters together: 123 / 123
[INFO] PocketPredictor - PREDICTING POCKETS.... ====================================
[INFO] PocketPredictor - SAS POINTS: 18250
[INFO] PocketPredictor - LIGANDABLE POINTS: 123
[INFO] PocketPredictor - CLUSTERS: 24
[INFO] PocketPredictor - FILTERED CLUSTERS: 9
[INFO] PocketPredictor - pocket 1 - surf_atoms: 34 points: 31 score: 11.0
[INFO] PocketPredictor - pocket 2 - surf_atoms: 37 points: 25 score: 8.6
[INFO] PocketPredictor - pocket 3 - surf_atoms: 31 points: 15 score: 5.8
[INFO] PocketPredictor - pocket 4 - surf_atoms: 26 points: 12 score: 4.3
[INFO] PocketPredictor - pocket 5 - surf_atoms: 34 points: 5 score: 2.6
[INFO] PocketPredictor - pocket 6 - surf_atoms: 16 points: 4 score: 1.8
[INFO] PocketPredictor - pocket 7 - surf_atoms: 18 points: 4 score: 1.5
[INFO] PocketPredictor - pocket 8 - surf_atoms: 9 points: 4 score: 1.4
[INFO] PocketPredictor - pocket 9 - surf_atoms: 8 points: 3 score: 0.6
[INFO] OldPymolRenderer - copying [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/proteins/ifih1.pdb] to [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_ifih1/visualizations/data/ifih1.pdb]
[INFO] Console - predicting pockets finished in 0 hours 0 minutes 12.392 seconds
[INFO] Console - results saved to directory [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_ifih1]
[INFO] Console -
[INFO] Console - Finished successfully in 0 hours 0 minutes 13.975 seconds.
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