pytme 0.3b0__cp311-cp311-macosx_15_0_arm64.whl → 0.3.1__cp311-cp311-macosx_15_0_arm64.whl

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Files changed (73) hide show
  1. {pytme-0.3b0.data → pytme-0.3.1.data}/scripts/estimate_memory_usage.py +1 -5
  2. {pytme-0.3b0.data → pytme-0.3.1.data}/scripts/match_template.py +177 -226
  3. {pytme-0.3b0.data → pytme-0.3.1.data}/scripts/postprocess.py +69 -47
  4. {pytme-0.3b0.data → pytme-0.3.1.data}/scripts/preprocess.py +10 -23
  5. {pytme-0.3b0.data → pytme-0.3.1.data}/scripts/preprocessor_gui.py +98 -28
  6. pytme-0.3.1.data/scripts/pytme_runner.py +1223 -0
  7. {pytme-0.3b0.dist-info → pytme-0.3.1.dist-info}/METADATA +15 -15
  8. pytme-0.3.1.dist-info/RECORD +133 -0
  9. {pytme-0.3b0.dist-info → pytme-0.3.1.dist-info}/entry_points.txt +1 -0
  10. pytme-0.3.1.dist-info/licenses/LICENSE +339 -0
  11. scripts/estimate_memory_usage.py +1 -5
  12. scripts/eval.py +93 -0
  13. scripts/extract_candidates.py +118 -99
  14. scripts/match_template.py +177 -226
  15. scripts/match_template_filters.py +1200 -0
  16. scripts/postprocess.py +69 -47
  17. scripts/preprocess.py +10 -23
  18. scripts/preprocessor_gui.py +98 -28
  19. scripts/pytme_runner.py +1223 -0
  20. scripts/refine_matches.py +156 -387
  21. tests/data/.DS_Store +0 -0
  22. tests/data/Blurring/.DS_Store +0 -0
  23. tests/data/Maps/.DS_Store +0 -0
  24. tests/data/Raw/.DS_Store +0 -0
  25. tests/data/Structures/.DS_Store +0 -0
  26. tests/preprocessing/test_frequency_filters.py +19 -10
  27. tests/preprocessing/test_utils.py +18 -0
  28. tests/test_analyzer.py +122 -122
  29. tests/test_backends.py +4 -9
  30. tests/test_density.py +0 -1
  31. tests/test_matching_cli.py +30 -30
  32. tests/test_matching_data.py +5 -5
  33. tests/test_matching_utils.py +11 -61
  34. tests/test_rotations.py +1 -1
  35. tme/__version__.py +1 -1
  36. tme/analyzer/__init__.py +1 -1
  37. tme/analyzer/_utils.py +5 -8
  38. tme/analyzer/aggregation.py +28 -9
  39. tme/analyzer/base.py +25 -36
  40. tme/analyzer/peaks.py +49 -122
  41. tme/analyzer/proxy.py +1 -0
  42. tme/backends/_jax_utils.py +31 -28
  43. tme/backends/_numpyfftw_utils.py +270 -0
  44. tme/backends/cupy_backend.py +11 -54
  45. tme/backends/jax_backend.py +72 -48
  46. tme/backends/matching_backend.py +6 -51
  47. tme/backends/mlx_backend.py +1 -27
  48. tme/backends/npfftw_backend.py +95 -90
  49. tme/backends/pytorch_backend.py +5 -26
  50. tme/density.py +7 -10
  51. tme/extensions.cpython-311-darwin.so +0 -0
  52. tme/filters/__init__.py +2 -2
  53. tme/filters/_utils.py +32 -7
  54. tme/filters/bandpass.py +225 -186
  55. tme/filters/ctf.py +138 -87
  56. tme/filters/reconstruction.py +38 -9
  57. tme/filters/wedge.py +98 -112
  58. tme/filters/whitening.py +1 -6
  59. tme/mask.py +341 -0
  60. tme/matching_data.py +20 -44
  61. tme/matching_exhaustive.py +46 -56
  62. tme/matching_optimization.py +2 -1
  63. tme/matching_scores.py +216 -412
  64. tme/matching_utils.py +82 -424
  65. tme/memory.py +1 -1
  66. tme/orientations.py +16 -8
  67. tme/parser.py +109 -29
  68. tme/preprocessor.py +2 -2
  69. tme/rotations.py +1 -1
  70. pytme-0.3b0.dist-info/RECORD +0 -122
  71. pytme-0.3b0.dist-info/licenses/LICENSE +0 -153
  72. {pytme-0.3b0.dist-info → pytme-0.3.1.dist-info}/WHEEL +0 -0
  73. {pytme-0.3b0.dist-info → pytme-0.3.1.dist-info}/top_level.txt +0 -0
{pytme-0.3b0.data → pytme-0.3.1.data}/scripts/estimate_memory_usage.py RENAMED
@@ -20,7 +20,6 @@ def parse_args():
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  parser.add_argument(
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  "-m",
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  "--target",
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- dest="target",
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  type=str,
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  required=True,
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  help="Path to a target in CCP4/MRC format.",
@@ -28,7 +27,6 @@ def parse_args():
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  parser.add_argument(
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  "-i",
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  "--template",
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- dest="template",
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  type=str,
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  required=True,
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  help="Path to a template in PDB/MMCIF or CCP4/MRC format.",
@@ -36,7 +34,6 @@ def parse_args():
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  parser.add_argument(
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  "-s",
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  "--score",
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- dest="score",
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  type=str,
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  default="FLCSphericalMask",
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  help="Template matching scoring function.",
@@ -46,8 +43,7 @@ def parse_args():
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  "--ncores", type=int, help="Number of cores for parallelization.", required=True
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  )
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  parser.add_argument(
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- "--pad_edges",
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- dest="pad_edges",
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+ "--pad-edges",
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  action="store_true",
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  default=False,
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  help="Whether to pad the edges of the target. Useful if the target does not "