EntDetect 1.2.0__py3-none-any.whl

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Files changed (45) hide show
  1. EntDetect/Jwalk/GridTools.py +567 -0
  2. EntDetect/Jwalk/PDBTools.py +532 -0
  3. EntDetect/Jwalk/SASDTools.py +543 -0
  4. EntDetect/Jwalk/SurfaceTools.py +150 -0
  5. EntDetect/Jwalk/__init__.py +19 -0
  6. EntDetect/Jwalk/naccess.config.txt +255 -0
  7. EntDetect/__init__.py +10 -0
  8. EntDetect/_logging.py +71 -0
  9. EntDetect/change_resolution.py +2361 -0
  10. EntDetect/clustering.py +2626 -0
  11. EntDetect/compare_sim2exp.py +1927 -0
  12. EntDetect/entanglement_features.py +478 -0
  13. EntDetect/gaussian_entanglement.py +2067 -0
  14. EntDetect/order_params.py +1048 -0
  15. EntDetect/resources/__init__.py +11 -0
  16. EntDetect/resources/__pycache__/__init__.cpython-311.pyc +0 -0
  17. EntDetect/resources/calc_K.pl +712 -0
  18. EntDetect/resources/calc_Q.pl +962 -0
  19. EntDetect/resources/pulchra +0 -0
  20. EntDetect/resources/shared_files/__init__.py +2 -0
  21. EntDetect/resources/shared_files/bt_contact_potential.dat +22 -0
  22. EntDetect/resources/shared_files/karanicolas_dihe_parm.dat +1600 -0
  23. EntDetect/resources/shared_files/kgs_contact_potential.dat +22 -0
  24. EntDetect/resources/shared_files/mj_contact_potential.dat +22 -0
  25. EntDetect/resources/stride +0 -0
  26. EntDetect/statistics.py +1344 -0
  27. EntDetect/utilities.py +201 -0
  28. entdetect-1.2.0.dist-info/METADATA +26 -0
  29. entdetect-1.2.0.dist-info/RECORD +45 -0
  30. entdetect-1.2.0.dist-info/WHEEL +5 -0
  31. entdetect-1.2.0.dist-info/entry_points.txt +11 -0
  32. entdetect-1.2.0.dist-info/licenses/LICENSE +674 -0
  33. entdetect-1.2.0.dist-info/top_level.txt +2 -0
  34. scripts/__init__.py +5 -0
  35. scripts/convert_cor_psf_to_pdb.py +103 -0
  36. scripts/run_Foldingpathway.py +162 -0
  37. scripts/run_MSM.py +152 -0
  38. scripts/run_OP_on_simulation_traj.py +194 -0
  39. scripts/run_change_resolution.py +63 -0
  40. scripts/run_compare_sim2exp.py +215 -0
  41. scripts/run_montecarlo.py +158 -0
  42. scripts/run_nativeNCLE.py +179 -0
  43. scripts/run_nonnative_entanglement_clustering.py +110 -0
  44. scripts/run_population_modeling.py +117 -0
  45. scripts/run_workflow4_nativeNCLE_batch.py +412 -0
EntDetect/resources/shared_files/kgs_contact_potential.dat ADDED
@@ -0,0 +1,22 @@
1
+ # units of kT KGS potential
2
+ AA: gly ala ser cys val thr ile pro met asp asn leu lys glu gln arg his phe tyr trp
3
+ 0.3
4
+ 0.1 -0.1
5
+ 0.0 -0.1 -0.6
6
+ 0.1 0.1 -0.4 -3.3
7
+ 0.2 -0.6 0.3 -0.8 -0.9
8
+ -0.0 -0.3 -0.5 0.0 0.2 -0.3
9
+ 0.3 -0.6 0.4 -1.1 -0.7 0.0 -0.8
10
+ 0.4 0.3 0.4 -0.0 0.1 0.3 0.3 0.1
11
+ 0.4 0.1 -0.0 -1.8 -0.5 0.2 -0.7 -0.2 -1.1
12
+ -0.4 0.1 -0.9 0.3 0.7 -0.6 0.6 0.6 1.0 0.3
13
+ -0.1 0.1 -0.3 0.3 0.2 -0.3 0.7 0.4 0.2 -0.6 -0.4
14
+ 0.5 -0.4 0.4 -0.5 -0.6 0.3 -0.6 0.5 -0.6 0.8 0.5 -0.6
15
+ 1.2 1.0 0.5 1.6 0.9 0.6 0.8 1.1 0.5 -0.6 0.1 1.1 1.9
16
+ 0.6 0.5 -0.2 0.8 0.4 -0.2 0.4 0.6 0.0 0.3 -0.4 0.7 -0.7 0.6
17
+ -0.1 -0.0 0.0 0.1 0.2 -0.2 0.3 -0.1 0.2 0.0 -0.4 0.4 0.4 0.2 0.0
18
+ 0.5 0.5 0.0 0.4 0.3 0.1 0.4 0.5 0.1 -1.1 0.0 0.2 1.7 -0.9 -0.5 0.2
19
+ 0.3 -0.1 -0.6 -1.2 -0.2 -0.6 -0.2 -0.5 -0.9 -1.0 -0.5 -0.3 0.3 -0.9 0.9 -0.4 -1.4
20
+ 0.1 -0.6 -0.0 -1.5 -0.8 -0.0 -0.8 -0.2 -1.1 0.4 0.2 -0.9 0.3 0.1 0.0 -0.4 -1.0 -1.5
21
+ -0.4 -0.5 -0.1 -0.1 -0.3 -0.2 -0.5 -0.9 -0.6 -0.3 -0.5 -0.1 -0.2 -0.0 -0.5 -0.4 -0.8 -0.5 -0.8
22
+ -0.3 -0.3 -0.4 2.0 -0.1 -0.6 -0.4 0.1 -0.3 -0.2 0.1 -0.4 1.3 0.6 -0.6 0.5 0.3 -0.1 -0.9 -1.2
EntDetect/resources/shared_files/mj_contact_potential.dat ADDED
@@ -0,0 +1,22 @@
1
+ # units of RT, 1999 Paper, Miyazawa-Jernigan Proteins
2
+ AA: CYS MET PHE ILE LEU VAL TRP TYR ALA GLY THR SER GLN ASN GLU ASP HIS ARG LYS PRO
3
+ -1.19
4
+ -0.61 -0.70
5
+ -0.67 -0.83 -0.88
6
+ -0.64 -0.66 -0.73 -0.74
7
+ -0.65 -0.70 -0.80 -0.81 -0.84
8
+ -0.59 -0.51 -0.67 -0.67 -0.74 -0.65
9
+ -0.66 -0.73 -0.68 -0.60 -0.62 -0.51 -0.64
10
+ -0.39 -0.56 -0.58 -0.49 -0.55 -0.38 -0.49 -0.45
11
+ -0.33 -0.27 -0.36 -0.37 -0.38 -0.32 -0.27 -0.20 -0.12
12
+ -0.31 -0.17 -0.19 -0.13 -0.16 -0.15 -0.25 -0.22 -0.08 -0.29
13
+ -0.15 -0.11 -0.15 -0.15 -0.15 -0.07 -0.02 -0.09 0.04 -0.04 0.03
14
+ -0.13 0.05 -0.12 0.03 -0.02 0.04 -0.01 -0.08 0.10 -0.01 0.04 0.05
15
+ -0.07 -0.06 -0.11 -0.01 -0.04 0.08 -0.02 -0.14 0.22 0.13 0.12 0.22 0.20
16
+ -0.01 0.04 -0.01 0.14 0.04 0.12 -0.10 -0.11 0.15 -0.01 0.04 0.09 0.06 -0.06
17
+ 0.20 0.12 0.14 0.17 0.17 0.26 -0.00 -0.08 0.38 0.32 0.16 0.18 0.27 0.12 0.46
18
+ 0.12 0.30 0.18 0.22 0.27 0.36 0.07 -0.07 0.27 0.11 0.11 0.10 0.24 0.02 0.44 0.29
19
+ -0.36 -0.29 -0.34 -0.13 -0.18 -0.06 -0.37 -0.30 0.07 0.00 -0.03 0.04 0.15 0.00 0.00 -0.10 -0.40
20
+ 0.08 0.03 -0.05 0.00 -0.04 0.08 -0.21 -0.25 0.24 0.09 0.11 0.16 0.09 0.10 -0.22 -0.24 0.05 0.19
21
+ 0.33 0.29 0.19 0.24 0.22 0.29 0.09 -0.05 0.41 0.29 0.33 0.36 0.28 0.22 -0.06 -0.01 0.38 0.66 0.76
22
+ -0.18 -0.13 -0.19 -0.05 -0.12 -0.05 -0.37 -0.25 0.15 0.02 0.13 0.20 0.17 0.18 0.37 0.33 0.01 0.17 0.47 0.11
EntDetect/resources/stride ADDED
Binary file