SOURSOP 2.0.0__py3-none-any.whl

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Files changed (117) hide show
  1. soursop/__init__.py +42 -0
  2. soursop/_internal_data.py +1408 -0
  3. soursop/_version.py +1 -0
  4. soursop/configs.py +33 -0
  5. soursop/data/SASA_SUMMARY.csv +20 -0
  6. soursop/data/bbseg2.dat +36 -0
  7. soursop/data/phi_excluded_volume_tripeptides.pickle +0 -0
  8. soursop/data/psi_excluded_volume_tripeptides.pickle +0 -0
  9. soursop/data/test_data/all_residues_AA.pdb +339 -0
  10. soursop/data/test_data/all_residues_AA.xtc +0 -0
  11. soursop/data/test_data/cap_tests/ACD_start_1.pdb +48 -0
  12. soursop/data/test_data/cap_tests/ACD_start_10.pdb +48 -0
  13. soursop/data/test_data/cap_tests/ACE_NH2.pdb +87 -0
  14. soursop/data/test_data/cap_tests/ACE_NME.pdb +90 -0
  15. soursop/data/test_data/cap_tests/ACE_NME_multichain.pdb +264 -0
  16. soursop/data/test_data/cap_tests/ACE_NME_start_at_5.pdb +90 -0
  17. soursop/data/test_data/cap_tests/ACE_UCAP.pdb +85 -0
  18. soursop/data/test_data/cap_tests/FOR_NH2.pdb +84 -0
  19. soursop/data/test_data/cap_tests/FOR_NME.pdb +87 -0
  20. soursop/data/test_data/cap_tests/FOR_UCAP.pdb +82 -0
  21. soursop/data/test_data/cap_tests/UCAP_NH2.pdb +83 -0
  22. soursop/data/test_data/cap_tests/UCAP_NME.pdb +86 -0
  23. soursop/data/test_data/cap_tests/UCAP_UCAP.pdb +81 -0
  24. soursop/data/test_data/cap_tests/__START.pdb +48 -0
  25. soursop/data/test_data/ctl9_AA.pdb +1486 -0
  26. soursop/data/test_data/ctl9_AA.xtc +0 -0
  27. soursop/data/test_data/ctl9_AA_reference.pkl +0 -0
  28. soursop/data/test_data/gromacs1chain/top.pdb +945 -0
  29. soursop/data/test_data/gromacs1chain/traj.xtc +0 -0
  30. soursop/data/test_data/gromacs2chains/top.pdb +964 -0
  31. soursop/data/test_data/gromacs2chains/traj.xtc +0 -0
  32. soursop/data/test_data/gs6_AA.dcd +0 -0
  33. soursop/data/test_data/gs6_AA.pdb +86 -0
  34. soursop/data/test_data/gs6_AA.xtc +0 -0
  35. soursop/data/test_data/gs6_AA_reference.pkl +0 -0
  36. soursop/data/test_data/gs6_distance_map_mean.npy +0 -0
  37. soursop/data/test_data/gs6_distance_map_std.npy +0 -0
  38. soursop/data/test_data/gs6_invalid_r1.pdb +86 -0
  39. soursop/data/test_data/ntl9_AA.pdb +914 -0
  40. soursop/data/test_data/ntl9_AA.xtc +0 -0
  41. soursop/data/test_data/ntl9_AA_reference.pkl +0 -0
  42. soursop/data/test_data/ntl9_distance_map_mean.npy +0 -0
  43. soursop/data/test_data/ntl9_distance_map_std.npy +0 -0
  44. soursop/data/test_data/pre_data/PRE_109_unweighted.csv +92 -0
  45. soursop/data/test_data/pre_data/PRE_119_unweighted.csv +92 -0
  46. soursop/data/test_data/pre_data/PRE_149_unweighted.csv +92 -0
  47. soursop/data/test_data/pre_data/PRE_61_unweighted.csv +92 -0
  48. soursop/data/test_data/pre_data/PRE_74_unweighted.csv +92 -0
  49. soursop/data/test_data/pre_data/PRE_96_unweighted.csv +92 -0
  50. soursop/data/test_data/sampling_quality/EV/1/__START.pdb +35 -0
  51. soursop/data/test_data/sampling_quality/EV/1/__traj.xtc +0 -0
  52. soursop/data/test_data/sampling_quality/EV/2/__START.pdb +35 -0
  53. soursop/data/test_data/sampling_quality/EV/2/__traj.xtc +0 -0
  54. soursop/data/test_data/sampling_quality/EV/3/__START.pdb +35 -0
  55. soursop/data/test_data/sampling_quality/EV/3/__traj.xtc +0 -0
  56. soursop/data/test_data/sampling_quality/WT/1/__START.pdb +35 -0
  57. soursop/data/test_data/sampling_quality/WT/1/__traj.xtc +0 -0
  58. soursop/data/test_data/sampling_quality/WT/2/__START.pdb +35 -0
  59. soursop/data/test_data/sampling_quality/WT/2/__traj.xtc +0 -0
  60. soursop/data/test_data/sampling_quality/WT/3/__START.pdb +35 -0
  61. soursop/data/test_data/sampling_quality/WT/3/__traj.xtc +0 -0
  62. soursop/data/test_data/sigA_CG.pdb +206 -0
  63. soursop/data/test_data/sigA_CG.xtc +0 -0
  64. soursop/data/test_data/sigA_CG_reference.pkl +0 -0
  65. soursop/data/test_data/swan_trajectories/Ash1.pdb +328 -0
  66. soursop/data/test_data/swan_trajectories/Ash1.xtc +0 -0
  67. soursop/data/test_data/swan_trajectories/alpha_syn.pdb +528 -0
  68. soursop/data/test_data/swan_trajectories/alpha_syn.xtc +0 -0
  69. soursop/data/test_data/swan_trajectories/helix.pdb +190 -0
  70. soursop/data/test_data/swan_trajectories/helix.xtc +0 -0
  71. soursop/data/test_data/synth_1_CG.pdb +78 -0
  72. soursop/data/test_data/synth_1_CG.xtc +0 -0
  73. soursop/data/test_data/synth_1_CG_reference.pkl +0 -0
  74. soursop/plugins/__init__.py +4 -0
  75. soursop/plugins/sparrow_plugin/__init__.py +94 -0
  76. soursop/soursop.py +86 -0
  77. soursop/ssbme.py +1805 -0
  78. soursop/sscoper.py +1507 -0
  79. soursop/ssdata.py +202 -0
  80. soursop/ssexceptions.py +52 -0
  81. soursop/sshdx.py +359 -0
  82. soursop/ssio.py +62 -0
  83. soursop/ssmutualinformation.py +170 -0
  84. soursop/ssnmr.py +2272 -0
  85. soursop/sspolymer.py +53 -0
  86. soursop/sspre.py +286 -0
  87. soursop/ssprotein.py +6110 -0
  88. soursop/sssampling.py +1684 -0
  89. soursop/sstools.py +346 -0
  90. soursop/sstrajectory.py +1467 -0
  91. soursop/ssutils.py +1050 -0
  92. soursop/tests/__init__.py +3 -0
  93. soursop/tests/build_reference/__init__.py +0 -0
  94. soursop/tests/build_reference/build_references.py +797 -0
  95. soursop/tests/conftest.py +173 -0
  96. soursop/tests/test_caps.py +88 -0
  97. soursop/tests/test_reference_observables.py +294 -0
  98. soursop/tests/test_scratchpad.ipynb +892 -0
  99. soursop/tests/test_soursop.py +47 -0
  100. soursop/tests/test_ssbme.py +368 -0
  101. soursop/tests/test_sscoper.py +319 -0
  102. soursop/tests/test_sshdx.py +133 -0
  103. soursop/tests/test_ssmutual_information.py +28 -0
  104. soursop/tests/test_ssnmr.py +917 -0
  105. soursop/tests/test_ssnmr_extended.py +61 -0
  106. soursop/tests/test_sspre.py +35 -0
  107. soursop/tests/test_ssproteins.py +1191 -0
  108. soursop/tests/test_sssampling.py +109 -0
  109. soursop/tests/test_sstrajectory.py +1045 -0
  110. soursop/tests/test_ssutils.py +43 -0
  111. soursop/tests/test_swan.py +195 -0
  112. soursop/tests/test_weights.py +787 -0
  113. soursop-2.0.0.dist-info/METADATA +198 -0
  114. soursop-2.0.0.dist-info/RECORD +117 -0
  115. soursop-2.0.0.dist-info/WHEEL +5 -0
  116. soursop-2.0.0.dist-info/licenses/LICENSE +57 -0
  117. soursop-2.0.0.dist-info/top_level.txt +1 -0
soursop/__init__.py ADDED
@@ -0,0 +1,42 @@
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+ ## _____ ____ _ _ _____ _____ ____ _____
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+ ## / ____|/ __ \| | | | __ \ / ____|/ __ \| __ \
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+ ## | (___ | | | | | | | |__) | (___ | | | | |__) |
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+ ## \___ \| | | | | | | _ / \___ \| | | | ___/
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+ ## ____) | |__| | |__| | | \ \ ____) | |__| | |
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+ ## |_____/ \____/ \____/|_| \_\_____/ \____/|_|
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+
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+ ## Alex Holehouse (Pappu Lab and Holehouse Lab) and Jared Lalmansing (Pappu lab)
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+ ## Simulation analysis package
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+ ## Copyright 2014 - 2026
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+ ##
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+
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+ import os
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+
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+ # Generate _version.py if missing and in the Read the Docs environment
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+ if os.getenv("READTHEDOCS") == "True" and not os.path.isfile("../soursop/_version.py"):
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+ import versioningit
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+
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+ __version__ = versioningit.get_version("../")
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+ else:
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+ from soursop._version import __version__
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+
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+ # The git revision is derived from the version string written by versioningit
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+ # (see soursop.soursop.version_git_revision). Guarded so a partially-built or
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+ # source checkout still imports cleanly.
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+ try:
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+ from soursop.soursop import version_git_revision as _version_git_revision
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+
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+ __git_revision__ = _version_git_revision()
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+ except Exception: # pragma: no cover - defensive fallback
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+ __git_revision__ = "unknown"
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+
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+ # code that allows access to the data directory
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+ _ROOT = os.path.abspath(os.path.dirname(__file__))
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+
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+
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+ def get_data(path):
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+ return os.path.join(_ROOT, "data", path)
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+
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+
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+ def get_version():
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+ return "%s - %s" % (str(__version__), str(__git_revision__))