bfee2 3.1.1.post1__py3-none-any.whl

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Files changed (68) hide show
  1. BFEE2/__init__.py +0 -0
  2. BFEE2/commonTools/__init__.py +0 -0
  3. BFEE2/commonTools/commonSlots.py +48 -0
  4. BFEE2/commonTools/fileParser.py +327 -0
  5. BFEE2/commonTools/ploter.py +218 -0
  6. BFEE2/doc/Doc.pdf +0 -0
  7. BFEE2/doc/__init__.py +1 -0
  8. BFEE2/gui.py +2785 -0
  9. BFEE2/inputGenerator.py +2949 -0
  10. BFEE2/postTreatment.py +676 -0
  11. BFEE2/templates_gromacs/000.colvars.template +37 -0
  12. BFEE2/templates_gromacs/000.generate_tpr_sh.template +31 -0
  13. BFEE2/templates_gromacs/000.mdp.template +74 -0
  14. BFEE2/templates_gromacs/001.colvars.template +76 -0
  15. BFEE2/templates_gromacs/001.generate_tpr_sh.template +31 -0
  16. BFEE2/templates_gromacs/001.mdp.template +73 -0
  17. BFEE2/templates_gromacs/001.readme.template +1 -0
  18. BFEE2/templates_gromacs/002.colvars.template +101 -0
  19. BFEE2/templates_gromacs/002.generate_tpr_sh.template +31 -0
  20. BFEE2/templates_gromacs/002.mdp.template +73 -0
  21. BFEE2/templates_gromacs/003.colvars.template +125 -0
  22. BFEE2/templates_gromacs/003.generate_tpr_sh.template +36 -0
  23. BFEE2/templates_gromacs/003.mdp.template +73 -0
  24. BFEE2/templates_gromacs/004.colvars.template +148 -0
  25. BFEE2/templates_gromacs/004.generate_tpr_sh.template +37 -0
  26. BFEE2/templates_gromacs/004.mdp.template +74 -0
  27. BFEE2/templates_gromacs/005.colvars.template +170 -0
  28. BFEE2/templates_gromacs/005.generate_tpr_sh.template +38 -0
  29. BFEE2/templates_gromacs/005.mdp.template +74 -0
  30. BFEE2/templates_gromacs/006.colvars.template +192 -0
  31. BFEE2/templates_gromacs/006.generate_tpr_sh.template +39 -0
  32. BFEE2/templates_gromacs/006.mdp.template +74 -0
  33. BFEE2/templates_gromacs/007.colvars.template +210 -0
  34. BFEE2/templates_gromacs/007.generate_tpr_sh.template +40 -0
  35. BFEE2/templates_gromacs/007.mdp.template +73 -0
  36. BFEE2/templates_gromacs/007_eq.colvars.template +169 -0
  37. BFEE2/templates_gromacs/007_eq.generate_tpr_sh.template +64 -0
  38. BFEE2/templates_gromacs/007_min.mdp.template +62 -0
  39. BFEE2/templates_gromacs/008.colvars.template +42 -0
  40. BFEE2/templates_gromacs/008.generate_tpr_sh.template +31 -0
  41. BFEE2/templates_gromacs/008.mdp.template +74 -0
  42. BFEE2/templates_gromacs/008_eq.colvars.template +14 -0
  43. BFEE2/templates_gromacs/008_eq.generate_tpr_sh.template +31 -0
  44. BFEE2/templates_gromacs/BFEEGromacs.py +1268 -0
  45. BFEE2/templates_gromacs/__init__.py +0 -0
  46. BFEE2/templates_gromacs/find_min_max.awk +27 -0
  47. BFEE2/templates_namd/__init__.py +0 -0
  48. BFEE2/templates_namd/configTemplate.py +1152 -0
  49. BFEE2/templates_namd/fep.tcl +299 -0
  50. BFEE2/templates_namd/fep_lddm.tcl +312 -0
  51. BFEE2/templates_namd/scriptTemplate.py +304 -0
  52. BFEE2/templates_namd/solvate.tcl +9 -0
  53. BFEE2/templates_namd/solvate_mem.tcl +9 -0
  54. BFEE2/templates_namd/updateCenters.py +312 -0
  55. BFEE2/templates_readme/Readme_Gromacs_Geometrical.txt +25 -0
  56. BFEE2/templates_readme/Readme_NAMD_Alchemical.txt +20 -0
  57. BFEE2/templates_readme/Readme_NAMD_Geometrical.txt +34 -0
  58. BFEE2/templates_readme/__init__.py +1 -0
  59. BFEE2/templates_readme/rags.py +187 -0
  60. BFEE2/third_party/__init__.py +0 -0
  61. BFEE2/third_party/py_bar.py +585 -0
  62. BFEE2/version.py +4 -0
  63. bfee2-3.1.1.post1.data/scripts/BFEE2Gui.py +19 -0
  64. bfee2-3.1.1.post1.dist-info/METADATA +86 -0
  65. bfee2-3.1.1.post1.dist-info/RECORD +68 -0
  66. bfee2-3.1.1.post1.dist-info/WHEEL +5 -0
  67. bfee2-3.1.1.post1.dist-info/licenses/LICENSE +677 -0
  68. bfee2-3.1.1.post1.dist-info/top_level.txt +1 -0
BFEE2/templates_gromacs/__init__.py ADDED
File without changes
BFEE2/templates_gromacs/find_min_max.awk ADDED
@@ -0,0 +1,27 @@
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+ BEGIN {
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+ first = 0
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+ }
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+
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+ !/^#/ && NF > 0 {
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+ if (first == 0) {
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+ max = $NF
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+ min = $NF
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+ first = 1
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+ argmax = $1
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+ argmin = $1
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+ }
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+ if (first > 0) {
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+ if (max < $NF) {
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+ max = $NF
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+ argmax = $1
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+ }
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+ if (min > $NF) {
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+ min = $NF
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+ argmin = $1
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+ }
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+ }
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+ }
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+
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+ END {
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+ printf("%.7f\n", argmin)
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+ }
BFEE2/templates_namd/__init__.py ADDED
File without changes