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tlemenestrel
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Smiles2Dock

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Smiles2Dock
File size: 6,612 Bytes 
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[INFO] Console - predicting pockets for proteins from dataset [scn10a.pdb]
[INFO] PredictPocketsRoutine - outdir: /oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_scn10a
[INFO] FeatureSetup - enabledFeatures: [chem, volsite, protrusion, bfactor, atom_table]
[INFO] Dataset - processing dataset [scn10a.pdb] using 0 threads
[INFO] Dataset - 
------------------------------------------------------------------------------------------------------------------------
processing [scn10a.pdb] (1/1)
------------------------------------------------------------------------------------------------------------------------

[INFO] Console - processing [scn10a.pdb] (1/1)
[INFO] Protein - loading protein [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/proteins/scn10a.pdb]
[INFO] PdbUtils - loading file [../proteins/scn10a.pdb]
[INFO] Struct - groups in chain A: 1956
[INFO] Struct - groups in chain A: 1956
[INFO] Struct - 1956 groups in chain A
[INFO] Protein - structure atoms: 15534
[INFO] Protein - protein   atoms: 15276
[INFO] Protein - ignoring ligands
[INFO] FeatureSetup - enabledFeatures: [chem, volsite, protrusion, bfactor, atom_table]
[INFO] Protein - SAS points: 44369
[INFO] Protein - exposed protein atoms: 12132 of 15276
[INFO] InstancePredictor - Creating WekaInstancePredictor
[INFO] SLinkClusterer - clustering [680] elements
[INFO] SLinkClusterer - clusters: [id:8( 1 ), id:9( 1 ), id:25( 27 ), id:32( 2 ), id:41( 3 ), id:42( 6 ), id:52( 10 ), id:67( 1 ), id:81( 1 ), id:83( 1 ), id:86( 2 ), id:88( 2 ), id:89( 1 ), id:91( 1 ), id:92( 2 ), id:117( 2 ), id:135( 36 ), id:140( 2 ), id:172( 1 ), id:173( 1 ), id:174( 1 ), id:180( 1 ), id:181( 1 ), id:184( 4 ), id:192( 1 ), id:197( 1 ), id:209( 2 ), id:215( 26 ), id:256( 8 ), id:270( 12 ), id:277( 6 ), id:280( 7 ), id:286( 2 ), id:287( 1 ), id:293( 1 ), id:304( 2 ), id:308( 87 ), id:323( 13 ), id:333( 1 ), id:344( 4 ), id:348( 2 ), id:352( 6 ), id:353( 3 ), id:354( 1 ), id:357( 3 ), id:358( 1 ), id:359( 1 ), id:368( 3 ), id:378( 7 ), id:419( 31 ), id:421( 1 ), id:422( 1 ), id:440( 30 ), id:441( 1 ), id:489( 4 ), id:490( 10 ), id:491( 70 ), id:513( 14 ), id:515( 1 ), id:519( 2 ), id:524( 1 ), id:526( 37 ), id:537( 1 ), id:552( 22 ), id:576( 12 ), id:577( 1 ), id:580( 4 ), id:602( 1 ), id:604( 1 ), id:608( 16 ), id:620( 40 ), id:621( 1 ), id:625( 8 ), id:634( 4 ), id:635( 1 ), id:641( 7 ), id:644( 11 ), id:661( 7 ), id:671( 2 ), id:674( 21 ), id:676( 2 ), id:678( 3 ), id:679( 1 )]
[INFO] SLinkClusterer - clusters together: 680 / 680
[INFO] PocketPredictor - PREDICTING POCKETS.... ====================================
[INFO] PocketPredictor - SAS POINTS: 44369
[INFO] PocketPredictor - LIGANDABLE POINTS: 680
[INFO] PocketPredictor - CLUSTERS: 83
[INFO] PocketPredictor - FILTERED CLUSTERS: 38
[INFO] PocketPredictor - pocket 1 -  surf_atoms:  49   points:  70   score:   34.0
[INFO] PocketPredictor - pocket 2 -  surf_atoms:  88   points:  87   score:   27.4
[INFO] PocketPredictor - pocket 3 -  surf_atoms:  31   points:  40   score:   21.3
[INFO] PocketPredictor - pocket 4 -  surf_atoms:  36   points:  36   score:   17.2
[INFO] PocketPredictor - pocket 5 -  surf_atoms:  46   points:  31   score:   14.3
[INFO] PocketPredictor - pocket 6 -  surf_atoms:  32   points:  37   score:   12.1
[INFO] PocketPredictor - pocket 7 -  surf_atoms:  41   points:  30   score:   10.3
[INFO] PocketPredictor - pocket 8 -  surf_atoms:  42   points:  26   score:    9.7
[INFO] PocketPredictor - pocket 9 -  surf_atoms:  37   points:  21   score:    8.5
[INFO] PocketPredictor - pocket10 -  surf_atoms:  43   points:  27   score:    7.9
[INFO] PocketPredictor - pocket11 -  surf_atoms:  27   points:  22   score:    6.8
[INFO] PocketPredictor - pocket12 -  surf_atoms:  29   points:  12   score:    5.3
[INFO] PocketPredictor - pocket13 -  surf_atoms:  19   points:  10   score:    4.8
[INFO] PocketPredictor - pocket14 -  surf_atoms:  20   points:  16   score:    4.7
[INFO] PocketPredictor - pocket15 -  surf_atoms:  43   points:  13   score:    4.1
[INFO] PocketPredictor - pocket16 -  surf_atoms:  38   points:  14   score:    4.1
[INFO] PocketPredictor - pocket17 -  surf_atoms:  25   points:  12   score:    4.1
[INFO] PocketPredictor - pocket18 -  surf_atoms:  40   points:  11   score:    3.8
[INFO] PocketPredictor - pocket19 -  surf_atoms:  17   points:   8   score:    3.7
[INFO] PocketPredictor - pocket20 -  surf_atoms:  21   points:  10   score:    3.4
[INFO] PocketPredictor - pocket21 -  surf_atoms:  17   points:   7   score:    3.1
[INFO] PocketPredictor - pocket22 -  surf_atoms:  22   points:   7   score:    3.0
[INFO] PocketPredictor - pocket23 -  surf_atoms:  25   points:   7   score:    2.9
[INFO] PocketPredictor - pocket24 -  surf_atoms:  15   points:   6   score:    2.6
[INFO] PocketPredictor - pocket25 -  surf_atoms:  20   points:   8   score:    2.6
[INFO] PocketPredictor - pocket26 -  surf_atoms:  21   points:   7   score:    2.3
[INFO] PocketPredictor - pocket27 -  surf_atoms:  19   points:   6   score:    2.3
[INFO] PocketPredictor - pocket28 -  surf_atoms:  21   points:   4   score:    2.2
[INFO] PocketPredictor - pocket29 -  surf_atoms:  12   points:   6   score:    1.6
[INFO] PocketPredictor - pocket30 -  surf_atoms:  10   points:   4   score:    1.6
[INFO] PocketPredictor - pocket31 -  surf_atoms:  10   points:   4   score:    1.6
[INFO] PocketPredictor - pocket32 -  surf_atoms:  13   points:   3   score:    1.6
[INFO] PocketPredictor - pocket33 -  surf_atoms:  11   points:   3   score:    1.4
[INFO] PocketPredictor - pocket34 -  surf_atoms:  12   points:   4   score:    1.3
[INFO] PocketPredictor - pocket35 -  surf_atoms:  13   points:   3   score:    0.9
[INFO] PocketPredictor - pocket36 -  surf_atoms:   9   points:   3   score:    0.9
[INFO] PocketPredictor - pocket37 -  surf_atoms:  12   points:   3   score:    0.8
[INFO] PocketPredictor - pocket38 -  surf_atoms:   7   points:   4   score:    0.7
[INFO] OldPymolRenderer - copying [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/proteins/scn10a.pdb] to [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_scn10a/visualizations/data/scn10a.pdb]
[INFO] Console - predicting pockets finished in 0 hours 0 minutes 28.114 seconds
[INFO] Console - results saved to directory [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_scn10a]
[INFO] Console - 
[INFO] Console - Finished successfully in 0 hours 0 minutes 29.622 seconds.