fairmd-lipids 1.3.1__tar.gz

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  1. fairmd_lipids-1.3.1/AUTHORS.md +29 -0
  2. fairmd_lipids-1.3.1/LICENSE +674 -0
  3. fairmd_lipids-1.3.1/MANIFEST.in +23 -0
  4. fairmd_lipids-1.3.1/PKG-INFO +141 -0
  5. fairmd_lipids-1.3.1/README.md +103 -0
  6. fairmd_lipids-1.3.1/pyproject.toml +105 -0
  7. fairmd_lipids-1.3.1/setup.cfg +4 -0
  8. fairmd_lipids-1.3.1/src/.gitignore +1 -0
  9. fairmd_lipids-1.3.1/src/fairmd/__init__.py +0 -0
  10. fairmd_lipids-1.3.1/src/fairmd/lipids/SchemaValidation/Schema/info_template.yaml +34 -0
  11. fairmd_lipids-1.3.1/src/fairmd/lipids/SchemaValidation/Schema/info_yml_schema.json +85 -0
  12. fairmd_lipids-1.3.1/src/fairmd/lipids/SchemaValidation/ValidateYAML.py +38 -0
  13. fairmd_lipids-1.3.1/src/fairmd/lipids/SchemaValidation/__init__.py +0 -0
  14. fairmd_lipids-1.3.1/src/fairmd/lipids/__init__.py +112 -0
  15. fairmd_lipids-1.3.1/src/fairmd/lipids/_version.py +34 -0
  16. fairmd_lipids-1.3.1/src/fairmd/lipids/analyze.py +927 -0
  17. fairmd_lipids-1.3.1/src/fairmd/lipids/analyze_nmrpca.py +799 -0
  18. fairmd_lipids-1.3.1/src/fairmd/lipids/bin/__init__.py +0 -0
  19. fairmd_lipids-1.3.1/src/fairmd/lipids/bin/add_simulation.py +655 -0
  20. fairmd_lipids-1.3.1/src/fairmd/lipids/bin/compute_databank.py +169 -0
  21. fairmd_lipids-1.3.1/src/fairmd/lipids/bin/evaluate_quality.py +193 -0
  22. fairmd_lipids-1.3.1/src/fairmd/lipids/bin/initialize_data.py +140 -0
  23. fairmd_lipids-1.3.1/src/fairmd/lipids/bin/make_ranking.py +124 -0
  24. fairmd_lipids-1.3.1/src/fairmd/lipids/bin/match_experiments.py +387 -0
  25. fairmd_lipids-1.3.1/src/fairmd/lipids/core.py +201 -0
  26. fairmd_lipids-1.3.1/src/fairmd/lipids/data/ToyData/.gitignore +2 -0
  27. fairmd_lipids-1.3.1/src/fairmd/lipids/data/ToyData/Molecules/membrane/CHOL/mappingCHOLESTEROLlipid14.yaml +222 -0
  28. fairmd_lipids-1.3.1/src/fairmd/lipids/data/ToyData/Molecules/membrane/CHOL/metadata.yaml +18 -0
  29. fairmd_lipids-1.3.1/src/fairmd/lipids/data/ToyData/Molecules/membrane/DPPC/mappingDPPCberger.yaml +390 -0
  30. fairmd_lipids-1.3.1/src/fairmd/lipids/data/ToyData/Molecules/membrane/DPPC/metadata.yaml +18 -0
  31. fairmd_lipids-1.3.1/src/fairmd/lipids/data/ToyData/Molecules/membrane/POPC/mappingPOPCcharmm.yaml +402 -0
  32. fairmd_lipids-1.3.1/src/fairmd/lipids/data/ToyData/Molecules/membrane/POPC/mappingPOPClipid14.yaml +536 -0
  33. fairmd_lipids-1.3.1/src/fairmd/lipids/data/ToyData/Molecules/membrane/POPC/metadata.yaml +53 -0
  34. fairmd_lipids-1.3.1/src/fairmd/lipids/data/ToyData/Molecules/membrane/POPE/mappingPOPEGROMOS43A1-S3.yaml +375 -0
  35. fairmd_lipids-1.3.1/src/fairmd/lipids/data/ToyData/Molecules/membrane/POPE/mappingPOPEcharmm.yaml +375 -0
  36. fairmd_lipids-1.3.1/src/fairmd/lipids/data/ToyData/Molecules/membrane/POPE/metadata.yaml +19 -0
  37. fairmd_lipids-1.3.1/src/fairmd/lipids/data/ToyData/Molecules/membrane/TOCL/mappingTOCLcharmm.yaml +757 -0
  38. fairmd_lipids-1.3.1/src/fairmd/lipids/data/ToyData/Molecules/membrane/TOCL/metadata.yaml +19 -0
  39. fairmd_lipids-1.3.1/src/fairmd/lipids/data/ToyData/Molecules/solution/CLA/mappingCL.yaml +2 -0
  40. fairmd_lipids-1.3.1/src/fairmd/lipids/data/ToyData/Molecules/solution/SOD/mappingNA.yaml +2 -0
  41. fairmd_lipids-1.3.1/src/fairmd/lipids/data/ToyData/Molecules/solution/SOD/mappingSOD.yaml +2 -0
  42. fairmd_lipids-1.3.1/src/fairmd/lipids/data/ToyData/Molecules/solution/SOL/mappingSPCwater.yaml +6 -0
  43. fairmd_lipids-1.3.1/src/fairmd/lipids/data/ToyData/Molecules/solution/SOL/mappingTIP3PCHARMMgui.yaml +6 -0
  44. fairmd_lipids-1.3.1/src/fairmd/lipids/data/ToyData/Molecules/solution/SOL/mappingwaterlipid14.yaml +6 -0
  45. fairmd_lipids-1.3.1/src/fairmd/lipids/data/ToyData/Simulations.1/aa0/README.yaml +56 -0
  46. fairmd_lipids-1.3.1/src/fairmd/lipids/data/ToyData/Simulations.1/aa0/md.gro +12211 -0
  47. fairmd_lipids-1.3.1/src/fairmd/lipids/data/ToyData/Simulations.1/aa0/md.tpr +0 -0
  48. fairmd_lipids-1.3.1/src/fairmd/lipids/data/ToyData/Simulations.1/aa0/short.xtc +0 -0
  49. fairmd_lipids-1.3.1/src/fairmd/lipids/data/ToyData/Simulations.1/aa1/README.yaml +43 -0
  50. fairmd_lipids-1.3.1/src/fairmd/lipids/data/ToyData/Simulations.1/aa2/README.yaml +54 -0
  51. fairmd_lipids-1.3.1/src/fairmd/lipids/data/ToyData/Simulations.1/aa3/README.yaml +58 -0
  52. fairmd_lipids-1.3.1/src/fairmd/lipids/data/ToyData/Simulations.1/aa4/README.yaml +45 -0
  53. fairmd_lipids-1.3.1/src/fairmd/lipids/data/ToyData/Simulations.2/aa0/DPPCOrderParameters.json +67 -0
  54. fairmd_lipids-1.3.1/src/fairmd/lipids/data/ToyData/Simulations.2/aa0/FormFactor.json +1002 -0
  55. fairmd_lipids-1.3.1/src/fairmd/lipids/data/ToyData/Simulations.2/aa0/LipidDensity.json +252 -0
  56. fairmd_lipids-1.3.1/src/fairmd/lipids/data/ToyData/Simulations.2/aa0/README.yaml +56 -0
  57. fairmd_lipids-1.3.1/src/fairmd/lipids/data/ToyData/Simulations.2/aa0/TotalDensity.json +252 -0
  58. fairmd_lipids-1.3.1/src/fairmd/lipids/data/ToyData/Simulations.2/aa0/WaterDensity.json +252 -0
  59. fairmd_lipids-1.3.1/src/fairmd/lipids/data/ToyData/Simulations.2/aa0/apl.json +63 -0
  60. fairmd_lipids-1.3.1/src/fairmd/lipids/data/ToyData/Simulations.2/aa0/eq_times.json +1 -0
  61. fairmd_lipids-1.3.1/src/fairmd/lipids/data/ToyData/Simulations.2/aa1/FormFactor.json +1002 -0
  62. fairmd_lipids-1.3.1/src/fairmd/lipids/data/ToyData/Simulations.2/aa1/LipidDensity.json +210 -0
  63. fairmd_lipids-1.3.1/src/fairmd/lipids/data/ToyData/Simulations.2/aa1/POPCOrderParameters.json +248 -0
  64. fairmd_lipids-1.3.1/src/fairmd/lipids/data/ToyData/Simulations.2/aa1/README.yaml +43 -0
  65. fairmd_lipids-1.3.1/src/fairmd/lipids/data/ToyData/Simulations.2/aa1/TotalDensity.json +210 -0
  66. fairmd_lipids-1.3.1/src/fairmd/lipids/data/ToyData/Simulations.2/aa1/WaterDensity.json +210 -0
  67. fairmd_lipids-1.3.1/src/fairmd/lipids/data/ToyData/Simulations.2/aa1/apl.json +1003 -0
  68. fairmd_lipids-1.3.1/src/fairmd/lipids/data/ToyData/Simulations.2/aa1/eq_times.json +1 -0
  69. fairmd_lipids-1.3.1/src/fairmd/lipids/data/ToyData/Simulations.2/aa2/CHOLOrderParameters.json +137 -0
  70. fairmd_lipids-1.3.1/src/fairmd/lipids/data/ToyData/Simulations.2/aa2/FormFactor.json +1002 -0
  71. fairmd_lipids-1.3.1/src/fairmd/lipids/data/ToyData/Simulations.2/aa2/LipidDensity.json +218 -0
  72. fairmd_lipids-1.3.1/src/fairmd/lipids/data/ToyData/Simulations.2/aa2/POPCOrderParameters.json +248 -0
  73. fairmd_lipids-1.3.1/src/fairmd/lipids/data/ToyData/Simulations.2/aa2/README.yaml +53 -0
  74. fairmd_lipids-1.3.1/src/fairmd/lipids/data/ToyData/Simulations.2/aa2/TotalDensity.json +218 -0
  75. fairmd_lipids-1.3.1/src/fairmd/lipids/data/ToyData/Simulations.2/aa2/WaterDensity.json +218 -0
  76. fairmd_lipids-1.3.1/src/fairmd/lipids/data/ToyData/Simulations.2/aa2/apl.json +403 -0
  77. fairmd_lipids-1.3.1/src/fairmd/lipids/data/ToyData/Simulations.2/aa2/eq_times.json +1 -0
  78. fairmd_lipids-1.3.1/src/fairmd/lipids/data/ToyData/Simulations.2/aa2/thickness.json +1 -0
  79. fairmd_lipids-1.3.1/src/fairmd/lipids/data/ToyData/Simulations.2/aa3/README.yaml +58 -0
  80. fairmd_lipids-1.3.1/src/fairmd/lipids/data/ToyData/Simulations.2/aa3/apl.json +903 -0
  81. fairmd_lipids-1.3.1/src/fairmd/lipids/data/ToyData/Simulations.2/aa4/FormFactor.json +1002 -0
  82. fairmd_lipids-1.3.1/src/fairmd/lipids/data/ToyData/Simulations.2/aa4/LipidDensity.json +218 -0
  83. fairmd_lipids-1.3.1/src/fairmd/lipids/data/ToyData/Simulations.2/aa4/POPEOrderParameters.json +203 -0
  84. fairmd_lipids-1.3.1/src/fairmd/lipids/data/ToyData/Simulations.2/aa4/README.yaml +45 -0
  85. fairmd_lipids-1.3.1/src/fairmd/lipids/data/ToyData/Simulations.2/aa4/TotalDensity.json +218 -0
  86. fairmd_lipids-1.3.1/src/fairmd/lipids/data/ToyData/Simulations.2/aa4/WaterDensity.json +218 -0
  87. fairmd_lipids-1.3.1/src/fairmd/lipids/data/ToyData/Simulations.2/aa4/apl.json +203 -0
  88. fairmd_lipids-1.3.1/src/fairmd/lipids/data/ToyData/Simulations.2/aa4/eq_times.json +1 -0
  89. fairmd_lipids-1.3.1/src/fairmd/lipids/data/ToyData/Simulations.2/aa4/thickness.json +1 -0
  90. fairmd_lipids-1.3.1/src/fairmd/lipids/data/ToyData/info/info566.yaml +32 -0
  91. fairmd_lipids-1.3.1/src/fairmd/lipids/data/ToyData/info/info566_uf.yaml +33 -0
  92. fairmd_lipids-1.3.1/src/fairmd/lipids/data/ToyData/lipid_json_buildH/Berger_DPPC.json +41 -0
  93. fairmd_lipids-1.3.1/src/fairmd/lipids/data/ToyData/lipid_json_buildH/GROMOS43A1-S3_POPE.json +40 -0
  94. fairmd_lipids-1.3.1/src/fairmd/lipids/databankLibrary.py +714 -0
  95. fairmd_lipids-1.3.1/src/fairmd/lipids/databankio.py +415 -0
  96. fairmd_lipids-1.3.1/src/fairmd/lipids/databankop.py +306 -0
  97. fairmd_lipids-1.3.1/src/fairmd/lipids/jpyroutines.py +48 -0
  98. fairmd_lipids-1.3.1/src/fairmd/lipids/jsonEncoders.py +129 -0
  99. fairmd_lipids-1.3.1/src/fairmd/lipids/maicos.py +389 -0
  100. fairmd_lipids-1.3.1/src/fairmd/lipids/openmm_parser.py +67 -0
  101. fairmd_lipids-1.3.1/src/fairmd/lipids/plottings.py +307 -0
  102. fairmd_lipids-1.3.1/src/fairmd/lipids/quality.py +450 -0
  103. fairmd_lipids-1.3.1/src/fairmd/lipids/settings/READMEexplanations.yaml +62 -0
  104. fairmd_lipids-1.3.1/src/fairmd/lipids/settings/__init__.py +1 -0
  105. fairmd_lipids-1.3.1/src/fairmd/lipids/settings/dic_lipids_UA.py +326 -0
  106. fairmd_lipids-1.3.1/src/fairmd/lipids/settings/elements.py +96 -0
  107. fairmd_lipids-1.3.1/src/fairmd/lipids/settings/engines.py +558 -0
  108. fairmd_lipids-1.3.1/src/fairmd/lipids/settings/molecules.py +345 -0
  109. fairmd_lipids-1.3.1/src/fairmd/lipids/utils.py +70 -0
  110. fairmd_lipids-1.3.1/src/fairmd_lipids.egg-info/PKG-INFO +141 -0
  111. fairmd_lipids-1.3.1/src/fairmd_lipids.egg-info/SOURCES.txt +113 -0
  112. fairmd_lipids-1.3.1/src/fairmd_lipids.egg-info/dependency_links.txt +1 -0
  113. fairmd_lipids-1.3.1/src/fairmd_lipids.egg-info/entry_points.txt +7 -0
  114. fairmd_lipids-1.3.1/src/fairmd_lipids.egg-info/requires.txt +11 -0
  115. fairmd_lipids-1.3.1/src/fairmd_lipids.egg-info/top_level.txt +1 -0
fairmd_lipids-1.3.1/AUTHORS.md ADDED
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+ # General credits
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+
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+ NMRlipids project is run by [NMRlipids research collaboration](https://nmrlipids.blogspot.com/) since 2013.
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+
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+ # Contributors
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+
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+ Since June 2025 (v.1.1.0), FAIRMD Lipids separates codespace from [Data](https://github.com/NMRLipids/BilayerData). Below we list contributors of the code part only; contributors of the bilayer-data part are listed at [BilayerData/AUTHORS.md](https://github.com/NMRLipids/BilayerData/blob/main/AUTHORS.md).
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+
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+ Alphabetical list of contributors:
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+
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+ - @MelbourneFL
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+ - Alexey M. Nesterenko (@comcon1)
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+ - Anika Wurl (@awurl)
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+ - Anne Kiirikki (@akiirik)
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+ - Batuhan Kav (@batukav)
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+ - Cedric Mingham (@thraindk)
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+ - Fabián Suárez-Lestón (@fsuarezleston)
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+ - Julianne Hoeflich (@JHoeflich1)
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+ - Hanne Susanna Antila (@hsantila)
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+ - Hector Martinez-Seara Monne (@hseara)
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+ - Lara Dautzenberg (@larabort)
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+ - Magnus-Elias Sletten (@MagnusSletten)
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+ - Markus Miettinen (@markussmiettinen)
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+ - Patrick Frankel (@PEFrankel)
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+ - Pavel Buslaev (@pbuslaev)
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+ - Philip Robin Loche (@PicoCentauri)
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+ - Samuli O.H. Ollila (@ohsOlilla)
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+ - Suvi Heinonen (@suviheinonen)
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+