-
Notifications
You must be signed in to change notification settings - Fork 0
Expand file tree
/
Copy pathtest_output.txt
More file actions
138 lines (121 loc) · 17.4 KB
/
test_output.txt
File metadata and controls
138 lines (121 loc) · 17.4 KB
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
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
================================================================================
PILOT STUDY: Gyrase Selectivity Assay
================================================================================
[Step 1] Setting up directories...
Γ£ô Directories created in: pilot_study
[Step 2] Preparing proteins...
Γ£ô WT: pilot_study\data\receptors\3NUU_WT.pdbqt
Γ£ô MUT: pilot_study\data\receptors\3NUU_MUT.pdbqt
[Step 3] Preparing ligands...
Γ£ô ciprofloxacin: pilot_study\data\ligands\ciprofloxacin.pdbqt
Γ£ô levofloxacin: pilot_study\data\ligands\levofloxacin.pdbqt
Γ£ô moxifloxacin: pilot_study\data\ligands\moxifloxacin.pdbqt
Γ£ô nalidixic_acid: pilot_study\data\ligands\nalidixic_acid.pdbqt
Γ£ô novobiocin: pilot_study\data\ligands\novobiocin.pdbqt
[Step 4] Running docking simulations...
(This will dock 5 drugs × 2 targets = 10 simulations)
🧪 Docking ciprofloxacin into WT (Wild-Type Bacterial Gyrase)
ΓÜá Docking engine not available (Vina not installed), using simulated result
Γ£ô Simulated Vina Affinity: -8.07 kcal/mol
Γ£ô Consensus Affinity: -8.77 ┬▒ 0.48 kcal/mol
🧪 Docking ciprofloxacin into MUT (Mutant Gyrase (A:87:D:G))
[2026-02-18 22:03:53] [autoscan.core.prep] [INFO] Mutating pilot_study\data\receptors\3NUU_MUT.pdbqt: Chain A, Res 87 -> GLY
[2026-02-18 22:03:53] [autoscan.core.prep] [INFO] Mutated structure saved to: pilot_study\data\receptors\3NUU_MUT_mutant.pdbqt
Γ£ô Mutation applied: A:87:D:G
🔬 Minimizing mutant structure energy...
[2026-02-18 22:03:54] [autoscan.dynamics.minimizer] [INFO] Force field loaded: AMBER14 + OBC2 implicit solvent
[2026-02-18 22:03:54] [autoscan.dynamics.minimizer] [INFO] Starting energy minimization: 3NUU_MUT_mutant.pdbqt
[2026-02-18 22:03:54] [autoscan.dynamics.minimizer] [INFO] Force Field: AMBER14 + OBC2
[2026-02-18 22:03:54] [autoscan.dynamics.minimizer] [INFO] Max Iterations: 1000
[2026-02-18 22:03:54] [autoscan.dynamics.minimizer] [INFO] Convergence: 10.0 kcal/mol/Å
[2026-02-18 22:03:54] [autoscan.dynamics.minimizer] [WARNING] PDBQT file provided but PDB not found. Returning original structure.
Γ£ô Minimization complete: 3NUU_MUT_mutant.pdbqt
ΓÜá Docking engine not available (Vina not installed), using simulated result
Γ£ô Simulated Vina Affinity: -6.38 kcal/mol
Γ£ô Consensus Affinity: -5.26 ┬▒ 0.35 kcal/mol
🧪 Docking levofloxacin into WT (Wild-Type Bacterial Gyrase)
ΓÜá Docking engine not available (Vina not installed), using simulated result
Γ£ô Simulated Vina Affinity: -7.14 kcal/mol
Γ£ô Consensus Affinity: -5.14 ┬▒ 0.39 kcal/mol
🧪 Docking levofloxacin into MUT (Mutant Gyrase (A:87:D:G))
[2026-02-18 22:03:54] [autoscan.core.prep] [INFO] Mutating pilot_study\data\receptors\3NUU_MUT.pdbqt: Chain A, Res 87 -> GLY
[2026-02-18 22:03:54] [autoscan.core.prep] [INFO] Mutated structure saved to: pilot_study\data\receptors\3NUU_MUT_mutant.pdbqt
Γ£ô Mutation applied: A:87:D:G
🔬 Minimizing mutant structure energy...
[2026-02-18 22:03:54] [autoscan.dynamics.minimizer] [INFO] Force field loaded: AMBER14 + OBC2 implicit solvent
[2026-02-18 22:03:54] [autoscan.dynamics.minimizer] [INFO] Starting energy minimization: 3NUU_MUT_mutant.pdbqt
[2026-02-18 22:03:54] [autoscan.dynamics.minimizer] [INFO] Force Field: AMBER14 + OBC2
[2026-02-18 22:03:54] [autoscan.dynamics.minimizer] [INFO] Max Iterations: 1000
[2026-02-18 22:03:54] [autoscan.dynamics.minimizer] [INFO] Convergence: 10.0 kcal/mol/Å
[2026-02-18 22:03:54] [autoscan.dynamics.minimizer] [WARNING] PDBQT file provided but PDB not found. Returning original structure.
Γ£ô Minimization complete: 3NUU_MUT_mutant.pdbqt
ΓÜá Docking engine not available (Vina not installed), using simulated result
Γ£ô Simulated Vina Affinity: -6.78 kcal/mol
Γ£ô Consensus Affinity: -8.82 ┬▒ 0.26 kcal/mol
🧪 Docking moxifloxacin into WT (Wild-Type Bacterial Gyrase)
ΓÜá Docking engine not available (Vina not installed), using simulated result
Γ£ô Simulated Vina Affinity: -9.20 kcal/mol
Γ£ô Consensus Affinity: -5.82 ┬▒ 0.32 kcal/mol
🧪 Docking moxifloxacin into MUT (Mutant Gyrase (A:87:D:G))
[2026-02-18 22:03:54] [autoscan.core.prep] [INFO] Mutating pilot_study\data\receptors\3NUU_MUT.pdbqt: Chain A, Res 87 -> GLY
[2026-02-18 22:03:54] [autoscan.core.prep] [INFO] Mutated structure saved to: pilot_study\data\receptors\3NUU_MUT_mutant.pdbqt
Γ£ô Mutation applied: A:87:D:G
🔬 Minimizing mutant structure energy...
[2026-02-18 22:03:54] [autoscan.dynamics.minimizer] [INFO] Force field loaded: AMBER14 + OBC2 implicit solvent
[2026-02-18 22:03:54] [autoscan.dynamics.minimizer] [INFO] Starting energy minimization: 3NUU_MUT_mutant.pdbqt
[2026-02-18 22:03:54] [autoscan.dynamics.minimizer] [INFO] Force Field: AMBER14 + OBC2
[2026-02-18 22:03:54] [autoscan.dynamics.minimizer] [INFO] Max Iterations: 1000
[2026-02-18 22:03:54] [autoscan.dynamics.minimizer] [INFO] Convergence: 10.0 kcal/mol/Å
[2026-02-18 22:03:54] [autoscan.dynamics.minimizer] [WARNING] PDBQT file provided but PDB not found. Returning original structure.
Γ£ô Minimization complete: 3NUU_MUT_mutant.pdbqt
ΓÜá Docking engine not available (Vina not installed), using simulated result
Γ£ô Simulated Vina Affinity: -6.74 kcal/mol
Γ£ô Consensus Affinity: -5.51 ┬▒ 0.12 kcal/mol
🧪 Docking nalidixic_acid into WT (Wild-Type Bacterial Gyrase)
ΓÜá Docking engine not available (Vina not installed), using simulated result
Γ£ô Simulated Vina Affinity: -5.33 kcal/mol
Γ£ô Consensus Affinity: -6.37 ┬▒ 0.11 kcal/mol
🧪 Docking nalidixic_acid into MUT (Mutant Gyrase (A:87:D:G))
[2026-02-18 22:03:54] [autoscan.core.prep] [INFO] Mutating pilot_study\data\receptors\3NUU_MUT.pdbqt: Chain A, Res 87 -> GLY
[2026-02-18 22:03:54] [autoscan.core.prep] [INFO] Mutated structure saved to: pilot_study\data\receptors\3NUU_MUT_mutant.pdbqt
Γ£ô Mutation applied: A:87:D:G
🔬 Minimizing mutant structure energy...
[2026-02-18 22:03:54] [autoscan.dynamics.minimizer] [INFO] Force field loaded: AMBER14 + OBC2 implicit solvent
[2026-02-18 22:03:54] [autoscan.dynamics.minimizer] [INFO] Starting energy minimization: 3NUU_MUT_mutant.pdbqt
[2026-02-18 22:03:54] [autoscan.dynamics.minimizer] [INFO] Force Field: AMBER14 + OBC2
[2026-02-18 22:03:54] [autoscan.dynamics.minimizer] [INFO] Max Iterations: 1000
[2026-02-18 22:03:54] [autoscan.dynamics.minimizer] [INFO] Convergence: 10.0 kcal/mol/Å
[2026-02-18 22:03:54] [autoscan.dynamics.minimizer] [WARNING] PDBQT file provided but PDB not found. Returning original structure.
Γ£ô Minimization complete: 3NUU_MUT_mutant.pdbqt
ΓÜá Docking engine not available (Vina not installed), using simulated result
Γ£ô Simulated Vina Affinity: -7.30 kcal/mol
Γ£ô Consensus Affinity: -9.15 ┬▒ 0.47 kcal/mol
🧪 Docking novobiocin into WT (Wild-Type Bacterial Gyrase)
ΓÜá Docking engine not available (Vina not installed), using simulated result
Γ£ô Simulated Vina Affinity: -8.82 kcal/mol
Γ£ô Consensus Affinity: -6.29 ┬▒ 0.18 kcal/mol
🧪 Docking novobiocin into MUT (Mutant Gyrase (A:87:D:G))
[2026-02-18 22:03:54] [autoscan.core.prep] [INFO] Mutating pilot_study\data\receptors\3NUU_MUT.pdbqt: Chain A, Res 87 -> GLY
[2026-02-18 22:03:54] [autoscan.core.prep] [INFO] Mutated structure saved to: pilot_study\data\receptors\3NUU_MUT_mutant.pdbqt
Γ£ô Mutation applied: A:87:D:G
🔬 Minimizing mutant structure energy...
[2026-02-18 22:03:54] [autoscan.dynamics.minimizer] [INFO] Force field loaded: AMBER14 + OBC2 implicit solvent
[2026-02-18 22:03:54] [autoscan.dynamics.minimizer] [INFO] Starting energy minimization: 3NUU_MUT_mutant.pdbqt
[2026-02-18 22:03:54] [autoscan.dynamics.minimizer] [INFO] Force Field: AMBER14 + OBC2
[2026-02-18 22:03:54] [autoscan.dynamics.minimizer] [INFO] Max Iterations: 1000
[2026-02-18 22:03:54] [autoscan.dynamics.minimizer] [INFO] Convergence: 10.0 kcal/mol/Å
[2026-02-18 22:03:54] [autoscan.dynamics.minimizer] [WARNING] PDBQT file provided but PDB not found. Returning original structure.
Γ£ô Minimization complete: 3NUU_MUT_mutant.pdbqt
ΓÜá Docking engine not available (Vina not installed), using simulated result
Γ£ô Simulated Vina Affinity: -8.25 kcal/mol
Γ£ô Consensus Affinity: -7.80 ┬▒ 0.33 kcal/mol
[Step 5] Generating analysis report...
Γ£ô Report saved to: pilot_study\results\PILOT_STUDY_REPORT.md
Γ£ô Results CSV saved to: pilot_study\results\docking_results.csv
================================================================================
PILOT STUDY COMPLETE
================================================================================
📁 Project Directory: pilot_study
📊 Results: pilot_study\results
📋 Report: pilot_study\results\PILOT_STUDY_REPORT.md
📈 CSV Data: pilot_study\results\docking_results.csv