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/pulchra ADDED
Binary file
EntDetect/resources/shared_files/__init__.py ADDED
@@ -0,0 +1,2 @@
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+ """Data files bundled with EntDetect."""
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+ """Data files used by EntDetect resource-based workflows."""
EntDetect/resources/shared_files/bt_contact_potential.dat ADDED
@@ -0,0 +1,22 @@
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+ # units of kT Bentancourt-Thirumalai potential
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+ AA: cys phe leu trp val ile met his tyr ala gly pro asn thr ser arg gln asp lys glu
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+ -1.34
4
+ -0.53 -0.82
5
+ -0.50 -0.78 -0.81
6
+ -0.74 -0.78 -0.70 -0.74
7
+ -0.51 -0.67 -0.80 -0.62 -0.72
8
+ -0.48 -0.65 -0.79 -0.65 -0.68 -0.60
9
+ -0.49 -0.89 -0.68 -0.94 -0.47 -0.60 -0.56
10
+ -0.19 -0.19 0.10 -0.46 0.18 0.19 -0.17 -0.33
11
+ -0.16 -0.49 -0.44 -0.55 -0.27 -0.33 -0.51 -0.21 -0.27
12
+ -0.26 -0.33 -0.37 -0.40 -0.38 -0.35 -0.23 0.21 -0.15 -0.20
13
+ -0.09 0.11 0.14 -0.24 0.04 0.21 0.08 0.23 -0.04 -0.03 -0.20
14
+ -0.18 -0.19 -0.08 -0.73 -0.08 0.05 -0.16 -0.05 -0.40 0.07 -0.01 -0.07
15
+ 0.28 0.29 0.36 -0.09 0.39 0.55 0.32 0.10 0.01 0.24 0.10 0.13 -0.04
16
+ 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
17
+ 0.09 0.10 0.26 0.07 0.25 0.35 0.32 0.15 0.07 0.15 0.10 0.17 0.14 0.00 0.13
18
+ 0.32 0.08 0.09 -0.41 0.17 0.18 0.17 0.04 -0.37 0.27 0.14 -0.02 0.02 0.00 0.12 0.13
19
+ 0.04 -0.04 0.08 -0.11 0.17 0.14 -0.01 0.22 -0.18 0.21 0.20 -0.05 -0.05 0.00 0.25 -0.12 0.14
20
+ 0.38 0.48 0.62 0.06 0.66 0.54 0.62 -0.22 -0.07 0.30 0.17 0.25 -0.12 0.00 0.01 -0.71 0.12 0.27
21
+ 0.35 0.11 0.16 -0.28 0.16 0.21 0.22 0.26 -0.40 0.20 0.12 0.12 -0.14 0.00 0.10 0.50 -0.20 -0.69 0.38
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+ 0.46 0.34 0.37 -0.15 0.41 0.38 0.24 -0.11 -0.16 0.43 0.48 0.26 -0.01 0.00 0.10 -0.75 0.10 0.40 -0.87 0.45