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[INFO] Console - predicting pockets for proteins from dataset [ankh.pdb] |
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[INFO] PredictPocketsRoutine - outdir: /oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_ankh |
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[INFO] FeatureSetup - enabledFeatures: [chem, volsite, protrusion, bfactor, atom_table] |
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[INFO] Dataset - processing dataset [ankh.pdb] using 0 threads |
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[INFO] Dataset - |
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processing [ankh.pdb] (1/1) |
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[INFO] Console - processing [ankh.pdb] (1/1) |
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[INFO] Protein - loading protein [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/proteins/ankh.pdb] |
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[INFO] PdbUtils - loading file [../proteins/ankh.pdb] |
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[INFO] Struct - groups in chain A: 492 |
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[INFO] Struct - groups in chain A: 492 |
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[INFO] Struct - 492 groups in chain A |
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[INFO] Protein - structure atoms: 3816 |
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[INFO] Protein - protein atoms: 3754 |
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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: 8101 |
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[INFO] Protein - exposed protein atoms: 2480 of 3754 |
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[INFO] InstancePredictor - Creating WekaInstancePredictor |
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[INFO] SLinkClusterer - clustering [167] elements |
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[INFO] SLinkClusterer - clusters: [id:4( 1 ), id:13( 2 ), id:44( 1 ), id:48( 25 ), id:50( 1 ), id:53( 13 ), id:67( 39 ), id:74( 1 ), id:81( 1 ), id:87( 1 ), id:90( 1 ), id:129( 8 ), id:133( 4 ), id:134( 1 ), id:136( 1 ), id:137( 2 ), id:145( 3 ), id:151( 4 ), id:154( 3 ), id:162( 44 ), id:166( 11 )] |
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[INFO] SLinkClusterer - clusters together: 167 / 167 |
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[INFO] PocketPredictor - PREDICTING POCKETS.... ==================================== |
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[INFO] PocketPredictor - SAS POINTS: 8101 |
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[INFO] PocketPredictor - LIGANDABLE POINTS: 167 |
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[INFO] PocketPredictor - CLUSTERS: 21 |
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[INFO] PocketPredictor - FILTERED CLUSTERS: 10 |
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[INFO] PocketPredictor - pocket 1 - surf_atoms: 41 points: 44 score: 16.1 |
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[INFO] PocketPredictor - pocket 2 - surf_atoms: 47 points: 39 score: 15.5 |
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[INFO] PocketPredictor - pocket 3 - surf_atoms: 32 points: 25 score: 8.4 |
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[INFO] PocketPredictor - pocket 4 - surf_atoms: 24 points: 13 score: 7.0 |
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[INFO] PocketPredictor - pocket 5 - surf_atoms: 20 points: 8 score: 4.1 |
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[INFO] PocketPredictor - pocket 6 - surf_atoms: 25 points: 11 score: 3.7 |
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[INFO] PocketPredictor - pocket 7 - surf_atoms: 19 points: 4 score: 2.6 |
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[INFO] PocketPredictor - pocket 8 - surf_atoms: 17 points: 3 score: 1.4 |
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[INFO] PocketPredictor - pocket 9 - surf_atoms: 9 points: 4 score: 1.3 |
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[INFO] PocketPredictor - pocket10 - surf_atoms: 8 points: 3 score: 1.0 |
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[INFO] OldPymolRenderer - copying [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/proteins/ankh.pdb] to [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_ankh/visualizations/data/ankh.pdb] |
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[INFO] Console - predicting pockets finished in 0 hours 0 minutes 10.626 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_ankh] |
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[INFO] Console - |
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[INFO] Console - Finished successfully in 0 hours 0 minutes 12.089 seconds. |
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