Shapespyer 0.2.3__py3-none-any.whl

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Files changed (91) hide show
  1. scripts/__init__.py +0 -0
  2. scripts/ana_solution.py +1130 -0
  3. scripts/ana_solvent.py +775 -0
  4. scripts/ana_trajectory.py +659 -0
  5. scripts/bash_cli.py +72 -0
  6. scripts/convert_aa2cg.py +239 -0
  7. scripts/densities.py +43 -0
  8. scripts/dlm_ana_density.py +1178 -0
  9. scripts/dlm_ana_gyration.py +1187 -0
  10. scripts/dlm_ana_solvation.py +1147 -0
  11. scripts/dlm_atoms2beads.py +404 -0
  12. scripts/dlm_equilibrate.py +1231 -0
  13. scripts/dlm_production_run.py +1320 -0
  14. scripts/dlm_solvate.py +984 -0
  15. scripts/dlm_visualise_dcd.py +1188 -0
  16. scripts/dlm_visualise_vmd.py +1136 -0
  17. scripts/gmx-add-ions-solv.bsh +169 -0
  18. scripts/gmx-ana-clusters-for.bsh +103 -0
  19. scripts/gmx-ana-clusters-prl.bsh +334 -0
  20. scripts/gmx-ana-clusters.bsh +170 -0
  21. scripts/gmx-ana-gyration-dirs.bsh +172 -0
  22. scripts/gmx-ana-gyration-pieces.bsh +177 -0
  23. scripts/gmx-ana-gyration.bsh +309 -0
  24. scripts/gmx-ana-maxclust-for.bsh +54 -0
  25. scripts/gmx-ana-solvation.bsh +549 -0
  26. scripts/gmx-center-cluster.bsh +255 -0
  27. scripts/gmx-equilibrate.bsh +302 -0
  28. scripts/gmx-posres-gro.bsh +77 -0
  29. scripts/gmx-setup-equil.bsh +445 -0
  30. scripts/gmx-setup-multi.bsh +512 -0
  31. scripts/namd_bilayer_calculate_ndens.py +425 -0
  32. scripts/namd_bilayer_calculate_sld.py +87 -0
  33. scripts/namd_bilayer_postprocessing.py +180 -0
  34. scripts/namd_setup_equil.py +207 -0
  35. scripts/namd_setup_psf.py +270 -0
  36. scripts/namd_solvate.py +365 -0
  37. scripts/shape_structure.py +172 -0
  38. scripts/smiles.py +40 -0
  39. shapes/__init__.py +0 -0
  40. shapes/basics/__init__.py +0 -0
  41. shapes/basics/defaults.py +211 -0
  42. shapes/basics/functions.py +269 -0
  43. shapes/basics/globals.py +68 -0
  44. shapes/basics/help.py +328 -0
  45. shapes/basics/input.py +417 -0
  46. shapes/basics/mendeleyev.py +280 -0
  47. shapes/basics/options.py +2072 -0
  48. shapes/basics/temp.yaml +64 -0
  49. shapes/basics/utils.py +1674 -0
  50. shapes/cgmap/__init__.py +0 -0
  51. shapes/cgmap/coarse_grainer.py +1092 -0
  52. shapes/cgmap/martini_converter.py +260 -0
  53. shapes/cgmap/molecule_mapper.py +440 -0
  54. shapes/designs/__init__.py +0 -0
  55. shapes/designs/protolattice.py +406 -0
  56. shapes/designs/protolayer.py +500 -0
  57. shapes/designs/protoshape.py +2136 -0
  58. shapes/designs/smiles.py +4254 -0
  59. shapes/ioports/__init__.py +10 -0
  60. shapes/ioports/ioconfig.py +415 -0
  61. shapes/ioports/iodcd.py +555 -0
  62. shapes/ioports/iofield.py +360 -0
  63. shapes/ioports/iofiles.py +164 -0
  64. shapes/ioports/ioframe.py +1381 -0
  65. shapes/ioports/iogro.py +764 -0
  66. shapes/ioports/iohistory.py +740 -0
  67. shapes/ioports/iopdb.py +562 -0
  68. shapes/ioports/iotop.py +1921 -0
  69. shapes/ioports/iotraj.py +2751 -0
  70. shapes/ioports/ioxyz.py +191 -0
  71. shapes/models/__init__.py +0 -0
  72. shapes/models/topology.py +521 -0
  73. shapes/project/__init__.py +5 -0
  74. shapes/project/analysis.py +44 -0
  75. shapes/project/assets.py +48 -0
  76. shapes/project/core.py +167 -0
  77. shapes/project/files.py +207 -0
  78. shapes/project/project.py +31 -0
  79. shapes/project/sample_model.py +143 -0
  80. shapes/stage/__init__.py +0 -0
  81. shapes/stage/protoatom.py +254 -0
  82. shapes/stage/protoatomset.py +693 -0
  83. shapes/stage/protomolecularsystem.py +1169 -0
  84. shapes/stage/protomolecule.py +2252 -0
  85. shapes/stage/protomoleculeset.py +1458 -0
  86. shapes/stage/protovector.py +432 -0
  87. shapespyer-0.2.3.dist-info/METADATA +132 -0
  88. shapespyer-0.2.3.dist-info/RECORD +91 -0
  89. shapespyer-0.2.3.dist-info/WHEEL +4 -0
  90. shapespyer-0.2.3.dist-info/entry_points.txt +37 -0
  91. shapespyer-0.2.3.dist-info/licenses/LICENSE +49 -0
scripts/__init__.py ADDED
File without changes