chilife 1.0.0.dev4__tar.gz → 1.0.0.dev6__tar.gz

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Files changed (115) hide show
  1. {chilife-1.0.0.dev4 → chilife-1.0.0.dev6}/LICENSE +0 -0
  2. {chilife-1.0.0.dev4 → chilife-1.0.0.dev6}/PKG-INFO +934 -935
  3. {chilife-1.0.0.dev4 → chilife-1.0.0.dev6}/README.md +0 -0
  4. {chilife-1.0.0.dev4 → chilife-1.0.0.dev6}/pyproject.toml +0 -1
  5. {chilife-1.0.0.dev4 → chilife-1.0.0.dev6}/scripts/oldProteinIC.py +0 -0
  6. {chilife-1.0.0.dev4 → chilife-1.0.0.dev6}/scripts/update_rotlib.py +0 -0
  7. {chilife-1.0.0.dev4 → chilife-1.0.0.dev6}/setup.cfg +4 -4
  8. {chilife-1.0.0.dev4 → chilife-1.0.0.dev6}/setup.py +0 -0
  9. {chilife-1.0.0.dev4 → chilife-1.0.0.dev6}/src/chilife/FluorLabel.py +0 -0
  10. {chilife-1.0.0.dev4 → chilife-1.0.0.dev6}/src/chilife/IntrinsicLabel.py +0 -0
  11. {chilife-1.0.0.dev4 → chilife-1.0.0.dev6}/src/chilife/MolSys.py +0 -0
  12. {chilife-1.0.0.dev4 → chilife-1.0.0.dev6}/src/chilife/MolSysIC.py +19 -3
  13. {chilife-1.0.0.dev4 → chilife-1.0.0.dev6}/src/chilife/RotamerEnsemble.py +79 -16
  14. {chilife-1.0.0.dev4 → chilife-1.0.0.dev6}/src/chilife/SpinLabel.py +5 -0
  15. {chilife-1.0.0.dev4 → chilife-1.0.0.dev6}/src/chilife/SpinLabelTraj.py +0 -0
  16. {chilife-1.0.0.dev4 → chilife-1.0.0.dev6}/src/chilife/Topology.py +18 -0
  17. {chilife-1.0.0.dev4 → chilife-1.0.0.dev6}/src/chilife/__init__.py +1 -1
  18. {chilife-1.0.0.dev4 → chilife-1.0.0.dev6}/src/chilife/alignment_methods.py +0 -0
  19. {chilife-1.0.0.dev4 → chilife-1.0.0.dev6}/src/chilife/chilife.py +2 -1
  20. {chilife-1.0.0.dev4 → chilife-1.0.0.dev6}/src/chilife/dRotamerEnsemble.py +0 -0
  21. {chilife-1.0.0.dev4 → chilife-1.0.0.dev6}/src/chilife/dSpinLabel.py +0 -0
  22. {chilife-1.0.0.dev4 → chilife-1.0.0.dev6}/src/chilife/data/BondDefs.pkl +0 -0
  23. {chilife-1.0.0.dev4 → chilife-1.0.0.dev6}/src/chilife/data/atom_dict +0 -0
  24. {chilife-1.0.0.dev4 → chilife-1.0.0.dev6}/src/chilife/data/dihedral_defs.json +0 -0
  25. {chilife-1.0.0.dev4 → chilife-1.0.0.dev6}/src/chilife/data/dihedral_defs.toml +0 -0
  26. {chilife-1.0.0.dev4 → chilife-1.0.0.dev6}/src/chilife/data/mplstyles/chiLife.mplstyle +0 -0
  27. {chilife-1.0.0.dev4 → chilife-1.0.0.dev6}/src/chilife/data/rotamer_libraries/ALL.bbdep.rotamers.lib +0 -0
  28. {chilife-1.0.0.dev4 → chilife-1.0.0.dev6}/src/chilife/data/rotamer_libraries/BBDEP2010_LICENSE +0 -0
  29. {chilife-1.0.0.dev4 → chilife-1.0.0.dev6}/src/chilife/data/rotamer_libraries/IndexBBDep.py +0 -0
  30. {chilife-1.0.0.dev4 → chilife-1.0.0.dev6}/src/chilife/data/rotamer_libraries/R1C.lib +0 -0
  31. {chilife-1.0.0.dev4 → chilife-1.0.0.dev6}/src/chilife/data/rotamer_libraries/RotlibIndexes.pkl +0 -0
  32. {chilife-1.0.0.dev4 → chilife-1.0.0.dev6}/src/chilife/data/rotamer_libraries/additional_rotlib_dirs.txt +0 -0
  33. {chilife-1.0.0.dev4 → chilife-1.0.0.dev6}/src/chilife/data/rotamer_libraries/bbdep.db +0 -0
  34. {chilife-1.0.0.dev4 → chilife-1.0.0.dev6}/src/chilife/data/rotamer_libraries/defaults.toml +0 -0
  35. {chilife-1.0.0.dev4 → chilife-1.0.0.dev6}/src/chilife/data/rotamer_libraries/make_bbdep_rotlib.py +0 -0
  36. {chilife-1.0.0.dev4 → chilife-1.0.0.dev6}/src/chilife/data/rotamer_libraries/make_rotlib.py +0 -0
  37. {chilife-1.0.0.dev4 → chilife-1.0.0.dev6}/src/chilife/data/rotamer_libraries/residue_internal_coords/I1M_ic.pkl +0 -0
  38. {chilife-1.0.0.dev4 → chilife-1.0.0.dev6}/src/chilife/data/rotamer_libraries/residue_internal_coords/ala_ic.pkl +0 -0
  39. {chilife-1.0.0.dev4 → chilife-1.0.0.dev6}/src/chilife/data/rotamer_libraries/residue_internal_coords/arg_ic.pkl +0 -0
  40. {chilife-1.0.0.dev4 → chilife-1.0.0.dev6}/src/chilife/data/rotamer_libraries/residue_internal_coords/asn_ic.pkl +0 -0
  41. {chilife-1.0.0.dev4 → chilife-1.0.0.dev6}/src/chilife/data/rotamer_libraries/residue_internal_coords/asp_ic.pkl +0 -0
  42. {chilife-1.0.0.dev4 → chilife-1.0.0.dev6}/src/chilife/data/rotamer_libraries/residue_internal_coords/cys_ic.pkl +0 -0
  43. {chilife-1.0.0.dev4 → chilife-1.0.0.dev6}/src/chilife/data/rotamer_libraries/residue_internal_coords/gln_ic.pkl +0 -0
  44. {chilife-1.0.0.dev4 → chilife-1.0.0.dev6}/src/chilife/data/rotamer_libraries/residue_internal_coords/glu_ic.pkl +0 -0
  45. {chilife-1.0.0.dev4 → chilife-1.0.0.dev6}/src/chilife/data/rotamer_libraries/residue_internal_coords/gly_ic.pkl +0 -0
  46. {chilife-1.0.0.dev4 → chilife-1.0.0.dev6}/src/chilife/data/rotamer_libraries/residue_internal_coords/his_ic.pkl +0 -0
  47. {chilife-1.0.0.dev4 → chilife-1.0.0.dev6}/src/chilife/data/rotamer_libraries/residue_internal_coords/ile_ic.pkl +0 -0
  48. {chilife-1.0.0.dev4 → chilife-1.0.0.dev6}/src/chilife/data/rotamer_libraries/residue_internal_coords/leu_ic.pkl +0 -0
  49. {chilife-1.0.0.dev4 → chilife-1.0.0.dev6}/src/chilife/data/rotamer_libraries/residue_internal_coords/lys_ic.pkl +0 -0
  50. {chilife-1.0.0.dev4 → chilife-1.0.0.dev6}/src/chilife/data/rotamer_libraries/residue_internal_coords/met_ic.pkl +0 -0
  51. {chilife-1.0.0.dev4 → chilife-1.0.0.dev6}/src/chilife/data/rotamer_libraries/residue_internal_coords/phe_ic.pkl +0 -0
  52. {chilife-1.0.0.dev4 → chilife-1.0.0.dev6}/src/chilife/data/rotamer_libraries/residue_internal_coords/pro_ic.pkl +0 -0
  53. {chilife-1.0.0.dev4 → chilife-1.0.0.dev6}/src/chilife/data/rotamer_libraries/residue_internal_coords/r1c_ic.pkl +0 -0
  54. {chilife-1.0.0.dev4 → chilife-1.0.0.dev6}/src/chilife/data/rotamer_libraries/residue_internal_coords/remake_ics.py +0 -0
  55. {chilife-1.0.0.dev4 → chilife-1.0.0.dev6}/src/chilife/data/rotamer_libraries/residue_internal_coords/ser_ic.pkl +0 -0
  56. {chilife-1.0.0.dev4 → chilife-1.0.0.dev6}/src/chilife/data/rotamer_libraries/residue_internal_coords/thr_ic.pkl +0 -0
  57. {chilife-1.0.0.dev4 → chilife-1.0.0.dev6}/src/chilife/data/rotamer_libraries/residue_internal_coords/trp_ic.pkl +0 -0
  58. {chilife-1.0.0.dev4 → chilife-1.0.0.dev6}/src/chilife/data/rotamer_libraries/residue_internal_coords/tyr_ic.pkl +0 -0
  59. {chilife-1.0.0.dev4 → chilife-1.0.0.dev6}/src/chilife/data/rotamer_libraries/residue_internal_coords/val_ic.pkl +0 -0
  60. {chilife-1.0.0.dev4 → chilife-1.0.0.dev6}/src/chilife/data/rotamer_libraries/residue_pdbs/I1M.pdb +0 -0
  61. {chilife-1.0.0.dev4 → chilife-1.0.0.dev6}/src/chilife/data/rotamer_libraries/residue_pdbs/R1C.pdb +0 -0
  62. {chilife-1.0.0.dev4 → chilife-1.0.0.dev6}/src/chilife/data/rotamer_libraries/residue_pdbs/ala.pdb +0 -0
  63. {chilife-1.0.0.dev4 → chilife-1.0.0.dev6}/src/chilife/data/rotamer_libraries/residue_pdbs/arg.pdb +0 -0
  64. {chilife-1.0.0.dev4 → chilife-1.0.0.dev6}/src/chilife/data/rotamer_libraries/residue_pdbs/asn.pdb +0 -0
  65. {chilife-1.0.0.dev4 → chilife-1.0.0.dev6}/src/chilife/data/rotamer_libraries/residue_pdbs/asp.pdb +0 -0
  66. {chilife-1.0.0.dev4 → chilife-1.0.0.dev6}/src/chilife/data/rotamer_libraries/residue_pdbs/cys.pdb +0 -0
  67. {chilife-1.0.0.dev4 → chilife-1.0.0.dev6}/src/chilife/data/rotamer_libraries/residue_pdbs/gln.pdb +0 -0
  68. {chilife-1.0.0.dev4 → chilife-1.0.0.dev6}/src/chilife/data/rotamer_libraries/residue_pdbs/glu.pdb +0 -0
  69. {chilife-1.0.0.dev4 → chilife-1.0.0.dev6}/src/chilife/data/rotamer_libraries/residue_pdbs/gly.pdb +0 -0
  70. {chilife-1.0.0.dev4 → chilife-1.0.0.dev6}/src/chilife/data/rotamer_libraries/residue_pdbs/his.pdb +0 -0
  71. {chilife-1.0.0.dev4 → chilife-1.0.0.dev6}/src/chilife/data/rotamer_libraries/residue_pdbs/ile.pdb +0 -0
  72. {chilife-1.0.0.dev4 → chilife-1.0.0.dev6}/src/chilife/data/rotamer_libraries/residue_pdbs/leu.pdb +0 -0
  73. {chilife-1.0.0.dev4 → chilife-1.0.0.dev6}/src/chilife/data/rotamer_libraries/residue_pdbs/lys.pdb +0 -0
  74. {chilife-1.0.0.dev4 → chilife-1.0.0.dev6}/src/chilife/data/rotamer_libraries/residue_pdbs/met.pdb +0 -0
  75. {chilife-1.0.0.dev4 → chilife-1.0.0.dev6}/src/chilife/data/rotamer_libraries/residue_pdbs/phe.pdb +0 -0
  76. {chilife-1.0.0.dev4 → chilife-1.0.0.dev6}/src/chilife/data/rotamer_libraries/residue_pdbs/pro.pdb +0 -0
  77. {chilife-1.0.0.dev4 → chilife-1.0.0.dev6}/src/chilife/data/rotamer_libraries/residue_pdbs/ser.pdb +0 -0
  78. {chilife-1.0.0.dev4 → chilife-1.0.0.dev6}/src/chilife/data/rotamer_libraries/residue_pdbs/thr.pdb +0 -0
  79. {chilife-1.0.0.dev4 → chilife-1.0.0.dev6}/src/chilife/data/rotamer_libraries/residue_pdbs/trp.pdb +0 -0
  80. {chilife-1.0.0.dev4 → chilife-1.0.0.dev6}/src/chilife/data/rotamer_libraries/residue_pdbs/tyr.pdb +0 -0
  81. {chilife-1.0.0.dev4 → chilife-1.0.0.dev6}/src/chilife/data/rotamer_libraries/residue_pdbs/val.pdb +0 -0
  82. {chilife-1.0.0.dev4 → chilife-1.0.0.dev6}/src/chilife/data/rotamer_libraries/spin_atoms.json +0 -0
  83. {chilife-1.0.0.dev4 → chilife-1.0.0.dev6}/src/chilife/data/rotamer_libraries/user_rotlibs/DCNip2_drotlib.zip +0 -0
  84. {chilife-1.0.0.dev4 → chilife-1.0.0.dev6}/src/chilife/data/rotamer_libraries/user_rotlibs/DCNip4_drotlib.zip +0 -0
  85. {chilife-1.0.0.dev4 → chilife-1.0.0.dev6}/src/chilife/data/rotamer_libraries/user_rotlibs/I1M_rotlib.npz +0 -0
  86. {chilife-1.0.0.dev4 → chilife-1.0.0.dev6}/src/chilife/data/rotamer_libraries/user_rotlibs/M1M_rotlib.npz +0 -0
  87. {chilife-1.0.0.dev4 → chilife-1.0.0.dev6}/src/chilife/data/rotamer_libraries/user_rotlibs/R1M_rotlib.npz +0 -0
  88. {chilife-1.0.0.dev4 → chilife-1.0.0.dev6}/src/chilife/data/rotamer_libraries/user_rotlibs/R7M_rotlib.npz +0 -0
  89. {chilife-1.0.0.dev4 → chilife-1.0.0.dev6}/src/chilife/data/rotamer_libraries/user_rotlibs/TOC_rotlib.npz +0 -0
  90. {chilife-1.0.0.dev4 → chilife-1.0.0.dev6}/src/chilife/data/rotamer_libraries/user_rotlibs/TRT_rotlib.npz +0 -0
  91. {chilife-1.0.0.dev4 → chilife-1.0.0.dev6}/src/chilife/data/rotamer_libraries/user_rotlibs/V1M_rotlib.npz +0 -0
  92. {chilife-1.0.0.dev4 → chilife-1.0.0.dev6}/src/chilife/io.py +8 -4
  93. chilife-1.0.0.dev6/src/chilife/math_utils.py +31 -0
  94. {chilife-1.0.0.dev4 → chilife-1.0.0.dev6}/src/chilife/numba_utils.py +0 -0
  95. {chilife-1.0.0.dev4 → chilife-1.0.0.dev6}/src/chilife/protein_utils.py +0 -0
  96. {chilife-1.0.0.dev4 → chilife-1.0.0.dev6}/src/chilife/scoring.py +0 -0
  97. {chilife-1.0.0.dev4 → chilife-1.0.0.dev6}/src/chilife.egg-info/PKG-INFO +934 -935
  98. {chilife-1.0.0.dev4 → chilife-1.0.0.dev6}/src/chilife.egg-info/SOURCES.txt +2 -0
  99. {chilife-1.0.0.dev4 → chilife-1.0.0.dev6}/src/chilife.egg-info/dependency_links.txt +0 -0
  100. {chilife-1.0.0.dev4 → chilife-1.0.0.dev6}/src/chilife.egg-info/requires.txt +0 -1
  101. {chilife-1.0.0.dev4 → chilife-1.0.0.dev6}/src/chilife.egg-info/top_level.txt +0 -0
  102. {chilife-1.0.0.dev4 → chilife-1.0.0.dev6}/tests/test_IntrinsicLabels.py +0 -0
  103. chilife-1.0.0.dev6/tests/test_MathUtils.py +23 -0
  104. {chilife-1.0.0.dev4 → chilife-1.0.0.dev6}/tests/test_MolSys.py +0 -0
  105. {chilife-1.0.0.dev4 → chilife-1.0.0.dev6}/tests/test_MolSysIC.py +0 -0
  106. {chilife-1.0.0.dev4 → chilife-1.0.0.dev6}/tests/test_NumbaUtils.py +0 -0
  107. {chilife-1.0.0.dev4 → chilife-1.0.0.dev6}/tests/test_ProteinUtils.py +2 -2
  108. {chilife-1.0.0.dev4 → chilife-1.0.0.dev6}/tests/test_RotamerEnsemble.py +70 -9
  109. {chilife-1.0.0.dev4 → chilife-1.0.0.dev6}/tests/test_Scoring.py +2 -2
  110. {chilife-1.0.0.dev4 → chilife-1.0.0.dev6}/tests/test_SpinLabel.py +0 -0
  111. {chilife-1.0.0.dev4 → chilife-1.0.0.dev6}/tests/test_SpinLabelTraj.py +0 -0
  112. {chilife-1.0.0.dev4 → chilife-1.0.0.dev6}/tests/test_Topology.py +22 -0
  113. {chilife-1.0.0.dev4 → chilife-1.0.0.dev6}/tests/test_chiLife.py +0 -0
  114. {chilife-1.0.0.dev4 → chilife-1.0.0.dev6}/tests/test_dSpinLabel.py +0 -0
  115. {chilife-1.0.0.dev4 → chilife-1.0.0.dev6}/tests/test_io.py +1 -1
{chilife-1.0.0.dev4 → chilife-1.0.0.dev6}/LICENSE RENAMED
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