pytme 0.3b0__cp311-cp311-macosx_15_0_arm64.whl → 0.3b0.post1__cp311-cp311-macosx_15_0_arm64.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- {pytme-0.3b0.data → pytme-0.3b0.post1.data}/scripts/estimate_memory_usage.py +1 -5
- {pytme-0.3b0.data → pytme-0.3b0.post1.data}/scripts/match_template.py +163 -201
- {pytme-0.3b0.data → pytme-0.3b0.post1.data}/scripts/postprocess.py +48 -39
- {pytme-0.3b0.data → pytme-0.3b0.post1.data}/scripts/preprocess.py +10 -23
- {pytme-0.3b0.data → pytme-0.3b0.post1.data}/scripts/preprocessor_gui.py +3 -4
- pytme-0.3b0.post1.data/scripts/pytme_runner.py +769 -0
- {pytme-0.3b0.dist-info → pytme-0.3b0.post1.dist-info}/METADATA +14 -14
- {pytme-0.3b0.dist-info → pytme-0.3b0.post1.dist-info}/RECORD +54 -50
- {pytme-0.3b0.dist-info → pytme-0.3b0.post1.dist-info}/entry_points.txt +1 -0
- pytme-0.3b0.post1.dist-info/licenses/LICENSE +339 -0
- scripts/estimate_memory_usage.py +1 -5
- scripts/eval.py +93 -0
- scripts/match_template.py +163 -201
- scripts/match_template_filters.py +1200 -0
- scripts/postprocess.py +48 -39
- scripts/preprocess.py +10 -23
- scripts/preprocessor_gui.py +3 -4
- scripts/pytme_runner.py +769 -0
- scripts/refine_matches.py +0 -1
- tests/preprocessing/test_frequency_filters.py +19 -10
- tests/test_analyzer.py +122 -122
- tests/test_backends.py +1 -0
- tests/test_matching_cli.py +30 -30
- tests/test_matching_data.py +5 -5
- tests/test_matching_utils.py +1 -1
- tme/__version__.py +1 -1
- tme/analyzer/__init__.py +1 -1
- tme/analyzer/_utils.py +1 -4
- tme/analyzer/aggregation.py +15 -6
- tme/analyzer/base.py +25 -36
- tme/analyzer/peaks.py +39 -113
- tme/analyzer/proxy.py +1 -0
- tme/backends/_jax_utils.py +16 -15
- tme/backends/cupy_backend.py +9 -13
- tme/backends/jax_backend.py +19 -16
- tme/backends/npfftw_backend.py +27 -25
- tme/backends/pytorch_backend.py +4 -0
- tme/density.py +5 -4
- tme/filters/__init__.py +2 -2
- tme/filters/_utils.py +32 -7
- tme/filters/bandpass.py +225 -186
- tme/filters/ctf.py +117 -67
- tme/filters/reconstruction.py +38 -9
- tme/filters/wedge.py +88 -105
- tme/filters/whitening.py +1 -6
- tme/matching_data.py +24 -36
- tme/matching_exhaustive.py +14 -11
- tme/matching_scores.py +21 -12
- tme/matching_utils.py +13 -6
- tme/orientations.py +13 -3
- tme/parser.py +109 -29
- tme/preprocessor.py +2 -2
- pytme-0.3b0.dist-info/licenses/LICENSE +0 -153
- {pytme-0.3b0.dist-info → pytme-0.3b0.post1.dist-info}/WHEEL +0 -0
- {pytme-0.3b0.dist-info → pytme-0.3b0.post1.dist-info}/top_level.txt +0 -0
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@@ -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.",
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@@ -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.",
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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.",
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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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"--
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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 "
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