pytme 0.2.9__cp311-cp311-macosx_15_0_arm64.whl

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Files changed (119) hide show
  1. pytme-0.2.9.data/scripts/estimate_ram_usage.py +97 -0
  2. pytme-0.2.9.data/scripts/match_template.py +1135 -0
  3. pytme-0.2.9.data/scripts/postprocess.py +622 -0
  4. pytme-0.2.9.data/scripts/preprocess.py +209 -0
  5. pytme-0.2.9.data/scripts/preprocessor_gui.py +1227 -0
  6. pytme-0.2.9.dist-info/METADATA +95 -0
  7. pytme-0.2.9.dist-info/RECORD +119 -0
  8. pytme-0.2.9.dist-info/WHEEL +5 -0
  9. pytme-0.2.9.dist-info/entry_points.txt +6 -0
  10. pytme-0.2.9.dist-info/licenses/LICENSE +153 -0
  11. pytme-0.2.9.dist-info/top_level.txt +3 -0
  12. scripts/__init__.py +0 -0
  13. scripts/estimate_ram_usage.py +97 -0
  14. scripts/match_template.py +1135 -0
  15. scripts/postprocess.py +622 -0
  16. scripts/preprocess.py +209 -0
  17. scripts/preprocessor_gui.py +1227 -0
  18. tests/__init__.py +0 -0
  19. tests/data/Blurring/blob_width18.npy +0 -0
  20. tests/data/Blurring/edgegaussian_sigma3.npy +0 -0
  21. tests/data/Blurring/gaussian_sigma2.npy +0 -0
  22. tests/data/Blurring/hamming_width6.npy +0 -0
  23. tests/data/Blurring/kaiserb_width18.npy +0 -0
  24. tests/data/Blurring/localgaussian_sigma0510.npy +0 -0
  25. tests/data/Blurring/mean_size5.npy +0 -0
  26. tests/data/Blurring/ntree_sigma0510.npy +0 -0
  27. tests/data/Blurring/rank_rank3.npy +0 -0
  28. tests/data/Maps/.DS_Store +0 -0
  29. tests/data/Maps/emd_8621.mrc.gz +0 -0
  30. tests/data/README.md +2 -0
  31. tests/data/Raw/em_map.map +0 -0
  32. tests/data/Structures/.DS_Store +0 -0
  33. tests/data/Structures/1pdj.cif +3339 -0
  34. tests/data/Structures/1pdj.pdb +1429 -0
  35. tests/data/Structures/5khe.cif +3685 -0
  36. tests/data/Structures/5khe.ent +2210 -0
  37. tests/data/Structures/5khe.pdb +2210 -0
  38. tests/data/Structures/5uz4.cif +70548 -0
  39. tests/preprocessing/__init__.py +0 -0
  40. tests/preprocessing/test_compose.py +76 -0
  41. tests/preprocessing/test_frequency_filters.py +178 -0
  42. tests/preprocessing/test_preprocessor.py +136 -0
  43. tests/preprocessing/test_utils.py +79 -0
  44. tests/test_analyzer.py +216 -0
  45. tests/test_backends.py +446 -0
  46. tests/test_density.py +503 -0
  47. tests/test_extensions.py +130 -0
  48. tests/test_matching_cli.py +283 -0
  49. tests/test_matching_data.py +162 -0
  50. tests/test_matching_exhaustive.py +124 -0
  51. tests/test_matching_memory.py +30 -0
  52. tests/test_matching_optimization.py +226 -0
  53. tests/test_matching_utils.py +189 -0
  54. tests/test_orientations.py +175 -0
  55. tests/test_parser.py +33 -0
  56. tests/test_rotations.py +153 -0
  57. tests/test_structure.py +247 -0
  58. tme/__init__.py +6 -0
  59. tme/__version__.py +1 -0
  60. tme/analyzer/__init__.py +2 -0
  61. tme/analyzer/_utils.py +186 -0
  62. tme/analyzer/aggregation.py +577 -0
  63. tme/analyzer/peaks.py +953 -0
  64. tme/backends/__init__.py +171 -0
  65. tme/backends/_cupy_utils.py +734 -0
  66. tme/backends/_jax_utils.py +188 -0
  67. tme/backends/cupy_backend.py +294 -0
  68. tme/backends/jax_backend.py +314 -0
  69. tme/backends/matching_backend.py +1270 -0
  70. tme/backends/mlx_backend.py +241 -0
  71. tme/backends/npfftw_backend.py +583 -0
  72. tme/backends/pytorch_backend.py +430 -0
  73. tme/data/__init__.py +0 -0
  74. tme/data/c48n309.npy +0 -0
  75. tme/data/c48n527.npy +0 -0
  76. tme/data/c48n9.npy +0 -0
  77. tme/data/c48u1.npy +0 -0
  78. tme/data/c48u1153.npy +0 -0
  79. tme/data/c48u1201.npy +0 -0
  80. tme/data/c48u1641.npy +0 -0
  81. tme/data/c48u181.npy +0 -0
  82. tme/data/c48u2219.npy +0 -0
  83. tme/data/c48u27.npy +0 -0
  84. tme/data/c48u2947.npy +0 -0
  85. tme/data/c48u3733.npy +0 -0
  86. tme/data/c48u4749.npy +0 -0
  87. tme/data/c48u5879.npy +0 -0
  88. tme/data/c48u7111.npy +0 -0
  89. tme/data/c48u815.npy +0 -0
  90. tme/data/c48u83.npy +0 -0
  91. tme/data/c48u8649.npy +0 -0
  92. tme/data/c600v.npy +0 -0
  93. tme/data/c600vc.npy +0 -0
  94. tme/data/metadata.yaml +80 -0
  95. tme/data/quat_to_numpy.py +42 -0
  96. tme/data/scattering_factors.pickle +0 -0
  97. tme/density.py +2263 -0
  98. tme/extensions.cpython-311-darwin.so +0 -0
  99. tme/external/bindings.cpp +332 -0
  100. tme/filters/__init__.py +6 -0
  101. tme/filters/_utils.py +311 -0
  102. tme/filters/bandpass.py +230 -0
  103. tme/filters/compose.py +81 -0
  104. tme/filters/ctf.py +393 -0
  105. tme/filters/reconstruction.py +160 -0
  106. tme/filters/wedge.py +542 -0
  107. tme/filters/whitening.py +191 -0
  108. tme/matching_data.py +863 -0
  109. tme/matching_exhaustive.py +497 -0
  110. tme/matching_optimization.py +1311 -0
  111. tme/matching_scores.py +1183 -0
  112. tme/matching_utils.py +1188 -0
  113. tme/memory.py +337 -0
  114. tme/orientations.py +598 -0
  115. tme/parser.py +685 -0
  116. tme/preprocessor.py +1329 -0
  117. tme/rotations.py +350 -0
  118. tme/structure.py +1864 -0
  119. tme/types.py +13 -0
tme/types.py ADDED
@@ -0,0 +1,13 @@
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+ from typing import Union, TypeVar, Tuple
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+
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+ BackendArray = TypeVar("backend_array")
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+ NDArray = TypeVar("numpy.ndarray")
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+ CupyArray = TypeVar("cupy.ndarray")
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+ TorchTensor = TypeVar("torch.Tensor")
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+ MlxArray = TypeVar("mlx.core.array")
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+ ArrayLike = TypeVar("array_like")
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+
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+ Scalar = Union[int, float, complex]
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+ shm_type = Union[Tuple[type, Tuple[int], type], BackendArray]
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+ MatchingData = TypeVar("MatchingData")
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+ CallbackClass = TypeVar("callback_class")