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[INFO] Console - predicting pockets for proteins from dataset [scn9a.pdb] |
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[INFO] PredictPocketsRoutine - outdir: /oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_scn9a |
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[INFO] FeatureSetup - enabledFeatures: [chem, volsite, protrusion, bfactor, atom_table] |
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[INFO] Dataset - processing dataset [scn9a.pdb] using 0 threads |
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[INFO] Dataset - |
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processing [scn9a.pdb] (1/1) |
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[INFO] Console - processing [scn9a.pdb] (1/1) |
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[INFO] Protein - loading protein [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/proteins/scn9a.pdb] |
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[INFO] PdbUtils - loading file [../proteins/scn9a.pdb] |
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[INFO] Struct - groups in chain A: 1988 |
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[INFO] Struct - groups in chain A: 1988 |
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[INFO] Struct - 1988 groups in chain A |
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[INFO] Protein - structure atoms: 15915 |
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[INFO] Protein - protein atoms: 15641 |
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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: 45652 |
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[INFO] Protein - exposed protein atoms: 12302 of 15641 |
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[INFO] InstancePredictor - Creating WekaInstancePredictor |
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[INFO] SLinkClusterer - clustering [652] elements |
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[INFO] SLinkClusterer - clusters: [id:1( 1 ), id:7( 1 ), id:8( 1 ), id:27( 2 ), id:30( 7 ), id:38( 2 ), id:41( 20 ), id:58( 1 ), id:61( 1 ), id:66( 4 ), id:67( 1 ), id:72( 2 ), id:75( 6 ), id:80( 2 ), id:82( 1 ), id:84( 148 ), id:85( 1 ), id:97( 26 ), id:103( 6 ), id:123( 48 ), id:159( 7 ), id:163( 4 ), id:167( 1 ), id:168( 1 ), id:170( 3 ), id:189( 11 ), id:201( 10 ), id:217( 12 ), id:224( 9 ), id:237( 13 ), id:239( 1 ), id:242( 7 ), id:249( 3 ), id:261( 1 ), id:269( 2 ), id:270( 1 ), id:271( 3 ), id:281( 3 ), id:316( 3 ), id:318( 2 ), id:323( 6 ), id:328( 1 ), id:329( 1 ), id:331( 1 ), id:334( 1 ), id:335( 1 ), id:337( 1 ), id:338( 1 ), id:343( 7 ), id:355( 43 ), id:357( 4 ), id:377( 23 ), id:382( 2 ), id:384( 2 ), id:404( 3 ), id:430( 5 ), id:433( 6 ), id:439( 1 ), id:450( 12 ), id:456( 1 ), id:457( 1 ), id:468( 5 ), id:469( 1 ), id:470( 1 ), id:471( 1 ), id:473( 1 ), id:474( 1 ), id:477( 9 ), id:482( 2 ), id:483( 2 ), id:500( 22 ), id:522( 19 ), id:548( 23 ), id:556( 3 ), id:576( 1 ), id:577( 2 ), id:584( 1 ), id:587( 4 ), id:588( 12 ), id:624( 2 ), id:626( 4 ), id:627( 9 ), id:630( 1 ), id:639( 24 ), id:651( 1 )] |
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[INFO] SLinkClusterer - clusters together: 652 / 652 |
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[INFO] PocketPredictor - PREDICTING POCKETS.... ==================================== |
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[INFO] PocketPredictor - SAS POINTS: 45652 |
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[INFO] PocketPredictor - LIGANDABLE POINTS: 652 |
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[INFO] PocketPredictor - CLUSTERS: 85 |
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[INFO] PocketPredictor - FILTERED CLUSTERS: 41 |
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[INFO] PocketPredictor - pocket 1 - surf_atoms: 142 points: 148 score: 59.6 |
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[INFO] PocketPredictor - pocket 2 - surf_atoms: 32 points: 43 score: 22.7 |
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[INFO] PocketPredictor - pocket 3 - surf_atoms: 44 points: 48 score: 21.6 |
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[INFO] PocketPredictor - pocket 4 - surf_atoms: 39 points: 23 score: 10.1 |
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[INFO] PocketPredictor - pocket 5 - surf_atoms: 34 points: 26 score: 9.0 |
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[INFO] PocketPredictor - pocket 6 - surf_atoms: 26 points: 19 score: 8.3 |
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[INFO] PocketPredictor - pocket 7 - surf_atoms: 17 points: 22 score: 7.8 |
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[INFO] PocketPredictor - pocket 8 - surf_atoms: 51 points: 24 score: 7.4 |
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[INFO] PocketPredictor - pocket 9 - surf_atoms: 24 points: 13 score: 7.3 |
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[INFO] PocketPredictor - pocket10 - surf_atoms: 28 points: 23 score: 6.7 |
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[INFO] PocketPredictor - pocket11 - surf_atoms: 41 points: 20 score: 6.6 |
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[INFO] PocketPredictor - pocket12 - surf_atoms: 30 points: 12 score: 5.8 |
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[INFO] PocketPredictor - pocket13 - surf_atoms: 21 points: 9 score: 4.5 |
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[INFO] PocketPredictor - pocket14 - surf_atoms: 30 points: 11 score: 4.3 |
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[INFO] PocketPredictor - pocket15 - surf_atoms: 36 points: 9 score: 4.3 |
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[INFO] PocketPredictor - pocket16 - surf_atoms: 28 points: 10 score: 4.2 |
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[INFO] PocketPredictor - pocket17 - surf_atoms: 19 points: 12 score: 4.1 |
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[INFO] PocketPredictor - pocket18 - surf_atoms: 19 points: 12 score: 3.9 |
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[INFO] PocketPredictor - pocket19 - surf_atoms: 33 points: 9 score: 3.7 |
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[INFO] PocketPredictor - pocket20 - surf_atoms: 17 points: 7 score: 3.3 |
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[INFO] PocketPredictor - pocket21 - surf_atoms: 18 points: 7 score: 3.1 |
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[INFO] PocketPredictor - pocket22 - surf_atoms: 22 points: 5 score: 2.8 |
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[INFO] PocketPredictor - pocket23 - surf_atoms: 17 points: 7 score: 2.6 |
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[INFO] PocketPredictor - pocket24 - surf_atoms: 14 points: 7 score: 2.4 |
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[INFO] PocketPredictor - pocket25 - surf_atoms: 23 points: 6 score: 2.3 |
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[INFO] PocketPredictor - pocket26 - surf_atoms: 16 points: 6 score: 2.3 |
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[INFO] PocketPredictor - pocket27 - surf_atoms: 20 points: 4 score: 2.2 |
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[INFO] PocketPredictor - pocket28 - surf_atoms: 22 points: 3 score: 2.1 |
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[INFO] PocketPredictor - pocket29 - surf_atoms: 15 points: 6 score: 2.0 |
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[INFO] PocketPredictor - pocket30 - surf_atoms: 14 points: 4 score: 1.9 |
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[INFO] PocketPredictor - pocket31 - surf_atoms: 12 points: 4 score: 1.8 |
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[INFO] PocketPredictor - pocket32 - surf_atoms: 11 points: 5 score: 1.6 |
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[INFO] PocketPredictor - pocket33 - surf_atoms: 8 points: 4 score: 1.6 |
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[INFO] PocketPredictor - pocket34 - surf_atoms: 10 points: 6 score: 1.5 |
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[INFO] PocketPredictor - pocket35 - surf_atoms: 7 points: 3 score: 1.4 |
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[INFO] PocketPredictor - pocket36 - surf_atoms: 17 points: 4 score: 1.2 |
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[INFO] PocketPredictor - pocket37 - surf_atoms: 11 points: 3 score: 1.1 |
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[INFO] PocketPredictor - pocket38 - surf_atoms: 11 points: 3 score: 1.1 |
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[INFO] PocketPredictor - pocket39 - surf_atoms: 4 points: 3 score: 0.9 |
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[INFO] PocketPredictor - pocket40 - surf_atoms: 6 points: 3 score: 0.8 |
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[INFO] PocketPredictor - pocket41 - surf_atoms: 6 points: 3 score: 0.8 |
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[INFO] OldPymolRenderer - copying [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/proteins/scn9a.pdb] to [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_scn9a/visualizations/data/scn9a.pdb] |
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[INFO] Console - predicting pockets finished in 0 hours 0 minutes 18.249 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_scn9a] |
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[INFO] Console - |
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[INFO] Console - Finished successfully in 0 hours 0 minutes 19.632 seconds. |
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