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[INFO] Console - predicting pockets for proteins from dataset [adcy5.pdb] |
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[INFO] PredictPocketsRoutine - outdir: /oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_adcy5 |
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[INFO] FeatureSetup - enabledFeatures: [chem, volsite, protrusion, bfactor, atom_table] |
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[INFO] Dataset - processing dataset [adcy5.pdb] using 0 threads |
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[INFO] Dataset - |
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processing [adcy5.pdb] (1/1) |
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[INFO] Console - processing [adcy5.pdb] (1/1) |
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[INFO] Protein - loading protein [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/proteins/adcy5.pdb] |
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[INFO] PdbUtils - loading file [proteins/adcy5.pdb] |
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[INFO] Struct - groups in chain A: 1261 |
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[INFO] Struct - groups in chain A: 1261 |
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[INFO] Struct - 1261 groups in chain A |
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[INFO] Protein - structure atoms: 9748 |
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[INFO] Protein - protein atoms: 9553 |
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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: 24834 |
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[INFO] Protein - exposed protein atoms: 7060 of 9553 |
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[INFO] InstancePredictor - Creating WekaInstancePredictor |
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[INFO] SLinkClusterer - clustering [262] elements |
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[INFO] SLinkClusterer - clusters: [id:1( 2 ), id:2( 1 ), id:23( 1 ), id:24( 1 ), id:41( 41 ), id:50( 2 ), id:56( 8 ), id:63( 31 ), id:75( 1 ), id:121( 16 ), id:129( 15 ), id:130( 1 ), id:133( 9 ), id:151( 4 ), id:158( 17 ), id:171( 1 ), id:173( 2 ), id:174( 2 ), id:177( 3 ), id:178( 1 ), id:180( 1 ), id:182( 3 ), id:189( 1 ), id:191( 3 ), id:219( 31 ), id:221( 1 ), id:225( 6 ), id:226( 1 ), id:227( 1 ), id:230( 1 ), id:235( 29 ), id:236( 1 ), id:249( 20 ), id:255( 3 ), id:261( 1 )] |
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[INFO] SLinkClusterer - clusters together: 262 / 262 |
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[INFO] PocketPredictor - PREDICTING POCKETS.... ==================================== |
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[INFO] PocketPredictor - SAS POINTS: 24834 |
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[INFO] PocketPredictor - LIGANDABLE POINTS: 262 |
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[INFO] PocketPredictor - CLUSTERS: 35 |
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[INFO] PocketPredictor - FILTERED CLUSTERS: 16 |
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[INFO] PocketPredictor - pocket 1 - surf_atoms: 51 points: 41 score: 16.0 |
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[INFO] PocketPredictor - pocket 2 - surf_atoms: 64 points: 31 score: 10.5 |
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[INFO] PocketPredictor - pocket 3 - surf_atoms: 37 points: 29 score: 10.4 |
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[INFO] PocketPredictor - pocket 4 - surf_atoms: 43 points: 31 score: 10.2 |
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[INFO] PocketPredictor - pocket 5 - surf_atoms: 29 points: 20 score: 7.8 |
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[INFO] PocketPredictor - pocket 6 - surf_atoms: 44 points: 17 score: 6.9 |
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[INFO] PocketPredictor - pocket 7 - surf_atoms: 16 points: 15 score: 6.7 |
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[INFO] PocketPredictor - pocket 8 - surf_atoms: 33 points: 16 score: 5.2 |
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[INFO] PocketPredictor - pocket 9 - surf_atoms: 23 points: 9 score: 3.2 |
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[INFO] PocketPredictor - pocket10 - surf_atoms: 22 points: 8 score: 2.6 |
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[INFO] PocketPredictor - pocket11 - surf_atoms: 21 points: 6 score: 1.8 |
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[INFO] PocketPredictor - pocket12 - surf_atoms: 15 points: 3 score: 1.5 |
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[INFO] PocketPredictor - pocket13 - surf_atoms: 17 points: 3 score: 1.2 |
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[INFO] PocketPredictor - pocket14 - surf_atoms: 11 points: 4 score: 1.1 |
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[INFO] PocketPredictor - pocket15 - surf_atoms: 13 points: 3 score: 1.0 |
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[INFO] PocketPredictor - pocket16 - surf_atoms: 9 points: 3 score: 1.0 |
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[INFO] OldPymolRenderer - copying [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/proteins/adcy5.pdb] to [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_adcy5/visualizations/data/adcy5.pdb] |
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[INFO] Console - predicting pockets finished in 0 hours 0 minutes 15.612 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_adcy5] |
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[INFO] Console - |
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[INFO] Console - Finished successfully in 0 hours 0 minutes 16.447 seconds. |
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