RNApolis 0.9.2__tar.gz → 0.10.1__tar.gz

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.
Files changed (48) hide show
  1. {rnapolis-0.9.2/src/RNApolis.egg-info → rnapolis-0.10.1}/PKG-INFO +4 -1
  2. {rnapolis-0.9.2 → rnapolis-0.10.1}/setup.py +5 -1
  3. {rnapolis-0.9.2 → rnapolis-0.10.1/src/RNApolis.egg-info}/PKG-INFO +4 -1
  4. {rnapolis-0.9.2 → rnapolis-0.10.1}/src/RNApolis.egg-info/SOURCES.txt +1 -0
  5. {rnapolis-0.9.2 → rnapolis-0.10.1}/src/RNApolis.egg-info/entry_points.txt +1 -0
  6. {rnapolis-0.9.2 → rnapolis-0.10.1}/src/RNApolis.egg-info/requires.txt +3 -0
  7. rnapolis-0.10.1/src/rnapolis/distiller.py +1119 -0
  8. {rnapolis-0.9.2 → rnapolis-0.10.1}/src/rnapolis/parser.py +7 -0
  9. {rnapolis-0.9.2 → rnapolis-0.10.1}/src/rnapolis/tertiary_v2.py +482 -18
  10. {rnapolis-0.9.2 → rnapolis-0.10.1}/LICENSE +0 -0
  11. {rnapolis-0.9.2 → rnapolis-0.10.1}/README.md +0 -0
  12. {rnapolis-0.9.2 → rnapolis-0.10.1}/pyproject.toml +0 -0
  13. {rnapolis-0.9.2 → rnapolis-0.10.1}/setup.cfg +0 -0
  14. {rnapolis-0.9.2 → rnapolis-0.10.1}/src/RNApolis.egg-info/dependency_links.txt +0 -0
  15. {rnapolis-0.9.2 → rnapolis-0.10.1}/src/RNApolis.egg-info/top_level.txt +0 -0
  16. {rnapolis-0.9.2 → rnapolis-0.10.1}/src/rnapolis/adapter.py +0 -0
  17. {rnapolis-0.9.2 → rnapolis-0.10.1}/src/rnapolis/aligner.py +0 -0
  18. {rnapolis-0.9.2 → rnapolis-0.10.1}/src/rnapolis/annotator.py +0 -0
  19. {rnapolis-0.9.2 → rnapolis-0.10.1}/src/rnapolis/clashfinder.py +0 -0
  20. {rnapolis-0.9.2 → rnapolis-0.10.1}/src/rnapolis/common.py +0 -0
  21. {rnapolis-0.9.2 → rnapolis-0.10.1}/src/rnapolis/component_A.csv +0 -0
  22. {rnapolis-0.9.2 → rnapolis-0.10.1}/src/rnapolis/component_C.csv +0 -0
  23. {rnapolis-0.9.2 → rnapolis-0.10.1}/src/rnapolis/component_G.csv +0 -0
  24. {rnapolis-0.9.2 → rnapolis-0.10.1}/src/rnapolis/component_U.csv +0 -0
  25. {rnapolis-0.9.2 → rnapolis-0.10.1}/src/rnapolis/metareader.py +0 -0
  26. {rnapolis-0.9.2 → rnapolis-0.10.1}/src/rnapolis/mmcif_pdbx_v50.dic +0 -0
  27. {rnapolis-0.9.2 → rnapolis-0.10.1}/src/rnapolis/molecule_filter.py +0 -0
  28. {rnapolis-0.9.2 → rnapolis-0.10.1}/src/rnapolis/motif_extractor.py +0 -0
  29. {rnapolis-0.9.2 → rnapolis-0.10.1}/src/rnapolis/parser_v2.py +0 -0
  30. {rnapolis-0.9.2 → rnapolis-0.10.1}/src/rnapolis/py.typed +0 -0
  31. {rnapolis-0.9.2 → rnapolis-0.10.1}/src/rnapolis/rfam_folder.py +0 -0
  32. {rnapolis-0.9.2 → rnapolis-0.10.1}/src/rnapolis/splitter.py +0 -0
  33. {rnapolis-0.9.2 → rnapolis-0.10.1}/src/rnapolis/tertiary.py +0 -0
  34. {rnapolis-0.9.2 → rnapolis-0.10.1}/src/rnapolis/transformer.py +0 -0
  35. {rnapolis-0.9.2 → rnapolis-0.10.1}/src/rnapolis/unifier.py +0 -0
  36. {rnapolis-0.9.2 → rnapolis-0.10.1}/src/rnapolis/util.py +0 -0
  37. {rnapolis-0.9.2 → rnapolis-0.10.1}/tests/test_adapter.py +0 -0
  38. {rnapolis-0.9.2 → rnapolis-0.10.1}/tests/test_annotator.py +0 -0
  39. {rnapolis-0.9.2 → rnapolis-0.10.1}/tests/test_bugfixes.py +0 -0
  40. {rnapolis-0.9.2 → rnapolis-0.10.1}/tests/test_common.py +0 -0
  41. {rnapolis-0.9.2 → rnapolis-0.10.1}/tests/test_metareader.py +0 -0
  42. {rnapolis-0.9.2 → rnapolis-0.10.1}/tests/test_molecule_filter.py +0 -0
  43. {rnapolis-0.9.2 → rnapolis-0.10.1}/tests/test_parser.py +0 -0
  44. {rnapolis-0.9.2 → rnapolis-0.10.1}/tests/test_quadruplexes.py +0 -0
  45. {rnapolis-0.9.2 → rnapolis-0.10.1}/tests/test_rfam_folder.py +0 -0
  46. {rnapolis-0.9.2 → rnapolis-0.10.1}/tests/test_tertiary.py +0 -0
  47. {rnapolis-0.9.2 → rnapolis-0.10.1}/tests/test_transformer.py +0 -0
  48. {rnapolis-0.9.2 → rnapolis-0.10.1}/tests/test_v2.py +0 -0
{rnapolis-0.9.2/src/RNApolis.egg-info → rnapolis-0.10.1}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: RNApolis
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- Version: 0.9.2
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+ Version: 0.10.1
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  Summary: A Python library containing RNA-related bioinformatics functions and classes
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  Home-page: https://github.com/tzok/rnapolis-py
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  Author: Tomasz Zok
@@ -16,6 +16,7 @@ Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
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  Description-Content-Type: text/markdown
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  License-File: LICENSE
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  Requires-Dist: appdirs
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+ Requires-Dist: faiss-cpu
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  Requires-Dist: graphviz
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  Requires-Dist: mmcif
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  Requires-Dist: numpy
@@ -24,7 +25,9 @@ Requires-Dist: orjson
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  Requires-Dist: pandas
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  Requires-Dist: pulp
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  Requires-Dist: requests
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+ Requires-Dist: scikit-learn
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  Requires-Dist: scipy
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+ Requires-Dist: tqdm
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  Requires-Dist: viennarna
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  Dynamic: author
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  Dynamic: author-email
{rnapolis-0.9.2 → rnapolis-0.10.1}/setup.py RENAMED
@@ -5,7 +5,7 @@ with open("README.md") as f:
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  setup(
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  name="RNApolis",
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- version="0.9.2",
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+ version="0.10.1",
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  packages=["rnapolis"],
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  package_dir={"": "src"},
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  author="Tomasz Zok",
@@ -30,6 +30,7 @@ setup(
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  "adapter=rnapolis.adapter:main",
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  "aligner=rnapolis.aligner:main",
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  "clashfinder=rnapolis.clashfinder:main",
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+ "distiller=rnapolis.distiller:main",
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  "metareader=rnapolis.metareader:main",
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  "molecule-filter=rnapolis.molecule_filter:main",
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  "motif-extractor=rnapolis.motif_extractor:main",
@@ -51,6 +52,7 @@ setup(
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  },
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  install_requires=[
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  "appdirs",
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+ "faiss-cpu",
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  "graphviz",
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  "mmcif",
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  "numpy",
@@ -59,7 +61,9 @@ setup(
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  "pandas",
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  "pulp",
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  "requests",
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+ "scikit-learn",
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  "scipy",
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+ "tqdm",
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  "viennarna",
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  ],
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  )
{rnapolis-0.9.2 → rnapolis-0.10.1/src/RNApolis.egg-info}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: RNApolis
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- Version: 0.9.2
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+ Version: 0.10.1
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  Summary: A Python library containing RNA-related bioinformatics functions and classes
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  Home-page: https://github.com/tzok/rnapolis-py
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  Author: Tomasz Zok
@@ -16,6 +16,7 @@ Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
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  Description-Content-Type: text/markdown
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  License-File: LICENSE
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  Requires-Dist: appdirs
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+ Requires-Dist: faiss-cpu
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  Requires-Dist: graphviz
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  Requires-Dist: mmcif
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  Requires-Dist: numpy
@@ -24,7 +25,9 @@ Requires-Dist: orjson
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  Requires-Dist: pandas
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  Requires-Dist: pulp
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  Requires-Dist: requests
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+ Requires-Dist: scikit-learn
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  Requires-Dist: scipy
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+ Requires-Dist: tqdm
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  Requires-Dist: viennarna
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  Dynamic: author
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  Dynamic: author-email
{rnapolis-0.9.2 → rnapolis-0.10.1}/src/RNApolis.egg-info/SOURCES.txt RENAMED
@@ -17,6 +17,7 @@ src/rnapolis/component_A.csv
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  src/rnapolis/component_C.csv
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  src/rnapolis/component_G.csv
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  src/rnapolis/component_U.csv
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+ src/rnapolis/distiller.py
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  src/rnapolis/metareader.py
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  src/rnapolis/mmcif_pdbx_v50.dic
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  src/rnapolis/molecule_filter.py
{rnapolis-0.9.2 → rnapolis-0.10.1}/src/RNApolis.egg-info/entry_points.txt RENAMED
@@ -3,6 +3,7 @@ adapter = rnapolis.adapter:main
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  aligner = rnapolis.aligner:main
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  annotator = rnapolis.annotator:main
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  clashfinder = rnapolis.clashfinder:main
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+ distiller = rnapolis.distiller:main
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  metareader = rnapolis.metareader:main
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  molecule-filter = rnapolis.molecule_filter:main
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  motif-extractor = rnapolis.motif_extractor:main
{rnapolis-0.9.2 → rnapolis-0.10.1}/src/RNApolis.egg-info/requires.txt RENAMED
@@ -1,4 +1,5 @@
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  appdirs
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+ faiss-cpu
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  graphviz
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  mmcif
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  numpy
@@ -7,5 +8,7 @@ orjson
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  pandas
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  pulp
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  requests
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+ scikit-learn
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  scipy
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+ tqdm
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  viennarna