polyphys 1.0.0__py3-none-any.whl

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Files changed (69) hide show
  1. polyphys/__init__.py +7 -0
  2. polyphys/__version__.py +22 -0
  3. polyphys/analyze/__init__.py +51 -0
  4. polyphys/analyze/clusters.py +1738 -0
  5. polyphys/analyze/correlations.py +995 -0
  6. polyphys/analyze/density.py +1138 -0
  7. polyphys/analyze/measurer.py +1338 -0
  8. polyphys/analyze/pipeline.py +1868 -0
  9. polyphys/analyze/stats.py +810 -0
  10. polyphys/analyze/sumrule.py +1159 -0
  11. polyphys/manage/__init__.py +11 -0
  12. polyphys/manage/organizer.py +2188 -0
  13. polyphys/manage/parser.py +1264 -0
  14. polyphys/manage/types.py +171 -0
  15. polyphys/manage/utils.py +777 -0
  16. polyphys/probe/__init__.py +25 -0
  17. polyphys/probe/binders.py +711 -0
  18. polyphys/probe/chain_size.py +583 -0
  19. polyphys/probe/core.py +437 -0
  20. polyphys/probe/histograms.py +863 -0
  21. polyphys/probe/pairs.py +555 -0
  22. polyphys/simulate/__init__.py +48 -0
  23. polyphys/simulate/build.py +1231 -0
  24. polyphys/simulate/core.py +237 -0
  25. polyphys/simulate/data.py +977 -0
  26. polyphys/simulate/dump.py +752 -0
  27. polyphys/simulate/log.py +788 -0
  28. polyphys/spec.py +1359 -0
  29. polyphys/tests/analyze/test_clusters.py +1058 -0
  30. polyphys/tests/analyze/test_correlations.py +708 -0
  31. polyphys/tests/analyze/test_density.py +813 -0
  32. polyphys/tests/analyze/test_measurer.py +785 -0
  33. polyphys/tests/analyze/test_pipeline.py +1881 -0
  34. polyphys/tests/analyze/test_stats.py +732 -0
  35. polyphys/tests/analyze/test_sumrule.py +917 -0
  36. polyphys/tests/conftest.py +753 -0
  37. polyphys/tests/data/lammps_build/make_starts.py +70 -0
  38. polyphys/tests/manage/test_organizer.py +1495 -0
  39. polyphys/tests/manage/test_parser.py +1222 -0
  40. polyphys/tests/manage/test_utils.py +498 -0
  41. polyphys/tests/probe/conftest.py +407 -0
  42. polyphys/tests/probe/test_binders.py +686 -0
  43. polyphys/tests/probe/test_chain_size.py +557 -0
  44. polyphys/tests/probe/test_core.py +391 -0
  45. polyphys/tests/probe/test_histograms.py +779 -0
  46. polyphys/tests/probe/test_pairs.py +475 -0
  47. polyphys/tests/simulate/test_build.py +1042 -0
  48. polyphys/tests/simulate/test_core.py +106 -0
  49. polyphys/tests/simulate/test_data.py +858 -0
  50. polyphys/tests/simulate/test_dump.py +487 -0
  51. polyphys/tests/simulate/test_log.py +667 -0
  52. polyphys/tests/strategies.py +120 -0
  53. polyphys/tests/synthetic.py +410 -0
  54. polyphys/tests/test_conftest.py +414 -0
  55. polyphys/tests/test_docs.py +82 -0
  56. polyphys/tests/test_packaging.py +97 -0
  57. polyphys/tests/test_spec.py +772 -0
  58. polyphys/tests/viz/conftest.py +32 -0
  59. polyphys/tests/viz/test_colors.py +113 -0
  60. polyphys/tests/viz/test_helpers.py +292 -0
  61. polyphys/viz/__init__.py +15 -0
  62. polyphys/viz/colors.py +204 -0
  63. polyphys/viz/helpers.py +549 -0
  64. polyphys-1.0.0.dist-info/METADATA +339 -0
  65. polyphys-1.0.0.dist-info/RECORD +69 -0
  66. polyphys-1.0.0.dist-info/WHEEL +5 -0
  67. polyphys-1.0.0.dist-info/licenses/AUTHORS.rst +13 -0
  68. polyphys-1.0.0.dist-info/licenses/LICENSE +22 -0
  69. polyphys-1.0.0.dist-info/top_level.txt +1 -0
polyphys/probe/__init__.py ADDED
@@ -0,0 +1,25 @@
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+ """
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+ The probe layer: per-frame observables read from LAMMPS trajectories with
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+ MDAnalysis, which the ``mda`` extra installs
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+ (``python -m pip install 'polyphys[mda]'``). The rest of PolyPhys does not
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+ need it, so this package is imported on demand and raises :exc:`ImportError`
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+ with that hint when MDAnalysis is missing.
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+
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+ .. versionadded:: 0.7.0
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+ """
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+ try:
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+ import MDAnalysis # noqa: F401
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+ except ImportError as error: # pragma: no cover - depends on the install
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+ raise ImportError(
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+ "polyphys.probe needs MDAnalysis; install it with "
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+ "python -m pip install 'polyphys[mda]'.") from error
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+
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+ from .binders import BinderStatistics
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+ from .chain_size import ChainSize
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+ from .core import make_universe, write_stamps
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+ from .histograms import SpatialHistograms, histogram_edges
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+ from .pairs import PairDistances
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+
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+ __all__ = ['BinderStatistics', 'ChainSize', 'PairDistances',
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+ 'SpatialHistograms', 'histogram_edges', 'make_universe',
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+ 'write_stamps']