molscope 0.8.2__tar.gz → 0.8.3__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 (137) hide show
  1. {molscope-0.8.2 → molscope-0.8.3}/CITATION.cff +3 -1
  2. {molscope-0.8.2/molscope.egg-info → molscope-0.8.3}/PKG-INFO +1 -1
  3. {molscope-0.8.2 → molscope-0.8.3}/molscope/__init__.py +1 -1
  4. {molscope-0.8.2 → molscope-0.8.3/molscope.egg-info}/PKG-INFO +1 -1
  5. {molscope-0.8.2 → molscope-0.8.3}/LICENSE +0 -0
  6. {molscope-0.8.2 → molscope-0.8.3}/MANIFEST.in +0 -0
  7. {molscope-0.8.2 → molscope-0.8.3}/README.md +0 -0
  8. {molscope-0.8.2 → molscope-0.8.3}/docs/api-reference.md +0 -0
  9. {molscope-0.8.2 → molscope-0.8.3}/docs/assets/coarsegrain/1fqy-cg-mapping-comparison.png +0 -0
  10. {molscope-0.8.2 → molscope-0.8.3}/docs/assets/coarsegrain/1fqy-martini-mapping.png +0 -0
  11. {molscope-0.8.2 → molscope-0.8.3}/docs/assets/contactmaps/1aml-contact-frequency.png +0 -0
  12. {molscope-0.8.2 → molscope-0.8.3}/docs/assets/contactmaps/1fqy-ca-distance-matrix.png +0 -0
  13. {molscope-0.8.2 → molscope-0.8.3}/docs/assets/contactmaps/1fqy-residue-contact-map.png +0 -0
  14. {molscope-0.8.2 → molscope-0.8.3}/docs/assets/geometry/1aml-rmsf-profile.png +0 -0
  15. {molscope-0.8.2 → molscope-0.8.3}/docs/assets/geometry/1fqy-principal-axes.png +0 -0
  16. {molscope-0.8.2 → molscope-0.8.3}/docs/assets/graphs/1fqy-residue-contact-graph.png +0 -0
  17. {molscope-0.8.2 → molscope-0.8.3}/docs/assets/readme/aquaporin-structure-v2.png +0 -0
  18. {molscope-0.8.2 → molscope-0.8.3}/docs/assets/readme/coarse-grained-beads-v2.png +0 -0
  19. {molscope-0.8.2 → molscope-0.8.3}/docs/assets/readme/residue-contact-map.png +0 -0
  20. {molscope-0.8.2 → molscope-0.8.3}/docs/assets/readme/secondary-structure.png +0 -0
  21. {molscope-0.8.2 → molscope-0.8.3}/docs/benchmarks.md +0 -0
  22. {molscope-0.8.2 → molscope-0.8.3}/docs/contributing.md +0 -0
  23. {molscope-0.8.2 → molscope-0.8.3}/docs/examples/analyze-contacts.md +0 -0
  24. {molscope-0.8.2 → molscope-0.8.3}/docs/examples/binding-site.md +0 -0
  25. {molscope-0.8.2 → molscope-0.8.3}/docs/examples/build-molecular-graph.md +0 -0
  26. {molscope-0.8.2 → molscope-0.8.3}/docs/examples/coarse-grain-protein.md +0 -0
  27. {molscope-0.8.2 → molscope-0.8.3}/docs/examples/compare-nmr-models.md +0 -0
  28. {molscope-0.8.2 → molscope-0.8.3}/docs/examples/export-pyg.md +0 -0
  29. {molscope-0.8.2 → molscope-0.8.3}/docs/examples/geometry-tour.md +0 -0
  30. {molscope-0.8.2 → molscope-0.8.3}/docs/examples/index.md +0 -0
  31. {molscope-0.8.2 → molscope-0.8.3}/docs/examples/pdb-to-graph-cg.md +0 -0
  32. {molscope-0.8.2 → molscope-0.8.3}/docs/examples/pdb-to-pyg-ml.md +0 -0
  33. {molscope-0.8.2 → molscope-0.8.3}/docs/examples/protein-analysis-from-scratch.md +0 -0
  34. {molscope-0.8.2 → molscope-0.8.3}/docs/examples/residue-contact-graphs.md +0 -0
  35. {molscope-0.8.2 → molscope-0.8.3}/docs/index.md +0 -0
  36. {molscope-0.8.2 → molscope-0.8.3}/docs/installation.md +0 -0
  37. {molscope-0.8.2 → molscope-0.8.3}/docs/limitations.md +0 -0
  38. {molscope-0.8.2 → molscope-0.8.3}/docs/quickstart.md +0 -0
  39. {molscope-0.8.2 → molscope-0.8.3}/docs/roadmap.md +0 -0
  40. {molscope-0.8.2 → molscope-0.8.3}/docs/tutorials/index.md +0 -0
  41. {molscope-0.8.2 → molscope-0.8.3}/docs/tutorials/pdb-to-coarse-grained-beads.md +0 -0
  42. {molscope-0.8.2 → molscope-0.8.3}/docs/tutorials/pdb-to-descriptors.md +0 -0
  43. {molscope-0.8.2 → molscope-0.8.3}/docs/tutorials/pdb-to-graph-gnn.md +0 -0
  44. {molscope-0.8.2 → molscope-0.8.3}/docs/user-guide/chemical-perception.md +0 -0
  45. {molscope-0.8.2 → molscope-0.8.3}/docs/user-guide/coarse-graining.md +0 -0
  46. {molscope-0.8.2 → molscope-0.8.3}/docs/user-guide/contact-maps.md +0 -0
  47. {molscope-0.8.2 → molscope-0.8.3}/docs/user-guide/coordinate-formats.md +0 -0
  48. {molscope-0.8.2 → molscope-0.8.3}/docs/user-guide/descriptors.md +0 -0
  49. {molscope-0.8.2 → molscope-0.8.3}/docs/user-guide/ensembles.md +0 -0
  50. {molscope-0.8.2 → molscope-0.8.3}/docs/user-guide/geometry.md +0 -0
  51. {molscope-0.8.2 → molscope-0.8.3}/docs/user-guide/molecular-graphs.md +0 -0
  52. {molscope-0.8.2 → molscope-0.8.3}/docs/user-guide/plotting.md +0 -0
  53. {molscope-0.8.2 → molscope-0.8.3}/docs/user-guide/protein-analysis.md +0 -0
  54. {molscope-0.8.2 → molscope-0.8.3}/docs/user-guide/reading-files.md +0 -0
  55. {molscope-0.8.2 → molscope-0.8.3}/docs/user-guide/selections.md +0 -0
  56. {molscope-0.8.2 → molscope-0.8.3}/docs/validation.md +0 -0
  57. {molscope-0.8.2 → molscope-0.8.3}/examples/binding_site.py +0 -0
  58. {molscope-0.8.2 → molscope-0.8.3}/examples/coarse_graining.py +0 -0
  59. {molscope-0.8.2 → molscope-0.8.3}/examples/data/1aml.pdb +0 -0
  60. {molscope-0.8.2 → molscope-0.8.3}/examples/data/1fqy.pdb +0 -0
  61. {molscope-0.8.2 → molscope-0.8.3}/examples/data/3ptb.pdb +0 -0
  62. {molscope-0.8.2 → molscope-0.8.3}/examples/data/helix_201.xyz +0 -0
  63. {molscope-0.8.2 → molscope-0.8.3}/examples/geometry.py +0 -0
  64. {molscope-0.8.2 → molscope-0.8.3}/examples/graph_to_gnn.py +0 -0
  65. {molscope-0.8.2 → molscope-0.8.3}/examples/legacy_utils.py +0 -0
  66. {molscope-0.8.2 → molscope-0.8.3}/examples/pdb_to_pyg_ml.py +0 -0
  67. {molscope-0.8.2 → molscope-0.8.3}/examples/protein_analysis.py +0 -0
  68. {molscope-0.8.2 → molscope-0.8.3}/examples/residue_contact_graph.py +0 -0
  69. {molscope-0.8.2 → molscope-0.8.3}/examples/tour.py +0 -0
  70. {molscope-0.8.2 → molscope-0.8.3}/mkdocs.yml +0 -0
  71. {molscope-0.8.2 → molscope-0.8.3}/molscope/__main__.py +0 -0
  72. {molscope-0.8.2 → molscope-0.8.3}/molscope/chem.py +0 -0
  73. {molscope-0.8.2 → molscope-0.8.3}/molscope/cif.py +0 -0
  74. {molscope-0.8.2 → molscope-0.8.3}/molscope/cli.py +0 -0
  75. {molscope-0.8.2 → molscope-0.8.3}/molscope/coarsegrain.py +0 -0
  76. {molscope-0.8.2 → molscope-0.8.3}/molscope/contactmap.py +0 -0
  77. {molscope-0.8.2 → molscope-0.8.3}/molscope/contacts.py +0 -0
  78. {molscope-0.8.2 → molscope-0.8.3}/molscope/descriptors.py +0 -0
  79. {molscope-0.8.2 → molscope-0.8.3}/molscope/distance.py +0 -0
  80. {molscope-0.8.2 → molscope-0.8.3}/molscope/dssp.py +0 -0
  81. {molscope-0.8.2 → molscope-0.8.3}/molscope/elements.py +0 -0
  82. {molscope-0.8.2 → molscope-0.8.3}/molscope/ensemble.py +0 -0
  83. {molscope-0.8.2 → molscope-0.8.3}/molscope/graph.py +0 -0
  84. {molscope-0.8.2 → molscope-0.8.3}/molscope/io.py +0 -0
  85. {molscope-0.8.2 → molscope-0.8.3}/molscope/molecule.py +0 -0
  86. {molscope-0.8.2 → molscope-0.8.3}/molscope/plotting.py +0 -0
  87. {molscope-0.8.2 → molscope-0.8.3}/molscope.egg-info/SOURCES.txt +0 -0
  88. {molscope-0.8.2 → molscope-0.8.3}/molscope.egg-info/dependency_links.txt +0 -0
  89. {molscope-0.8.2 → molscope-0.8.3}/molscope.egg-info/entry_points.txt +0 -0
  90. {molscope-0.8.2 → molscope-0.8.3}/molscope.egg-info/requires.txt +0 -0
  91. {molscope-0.8.2 → molscope-0.8.3}/molscope.egg-info/top_level.txt +0 -0
  92. {molscope-0.8.2 → molscope-0.8.3}/notebooks/molscope_tour.ipynb +0 -0
  93. {molscope-0.8.2 → molscope-0.8.3}/notebooks/pdb_to_gnn.ipynb +0 -0
  94. {molscope-0.8.2 → molscope-0.8.3}/notebooks/protein_analysis_from_scratch.ipynb +0 -0
  95. {molscope-0.8.2 → molscope-0.8.3}/pyproject.toml +0 -0
  96. {molscope-0.8.2 → molscope-0.8.3}/requirements.txt +0 -0
  97. {molscope-0.8.2 → molscope-0.8.3}/scripts/benchmark_core.py +0 -0
  98. {molscope-0.8.2 → molscope-0.8.3}/scripts/build_gnn_notebook.py +0 -0
  99. {molscope-0.8.2 → molscope-0.8.3}/scripts/build_protein_analysis_notebook.py +0 -0
  100. {molscope-0.8.2 → molscope-0.8.3}/scripts/build_user_guide_pdf.py +0 -0
  101. {molscope-0.8.2 → molscope-0.8.3}/scripts/render_coarsegrain_images.py +0 -0
  102. {molscope-0.8.2 → molscope-0.8.3}/scripts/render_contact_analysis_images.py +0 -0
  103. {molscope-0.8.2 → molscope-0.8.3}/scripts/render_geometry_images.py +0 -0
  104. {molscope-0.8.2 → molscope-0.8.3}/setup.cfg +0 -0
  105. {molscope-0.8.2 → molscope-0.8.3}/tests/fixtures/bad_coord.pdb +0 -0
  106. {molscope-0.8.2 → molscope-0.8.3}/tests/fixtures/bad_coord.xyz +0 -0
  107. {molscope-0.8.2 → molscope-0.8.3}/tests/fixtures/bad_counts.sdf +0 -0
  108. {molscope-0.8.2 → molscope-0.8.3}/tests/fixtures/missing_coord_col.cif +0 -0
  109. {molscope-0.8.2 → molscope-0.8.3}/tests/fixtures/no_atom_site.cif +0 -0
  110. {molscope-0.8.2 → molscope-0.8.3}/tests/fixtures/no_atoms.pdb +0 -0
  111. {molscope-0.8.2 → molscope-0.8.3}/tests/fixtures/short_atom.pdb +0 -0
  112. {molscope-0.8.2 → molscope-0.8.3}/tests/fixtures/truncated.sdf +0 -0
  113. {molscope-0.8.2 → molscope-0.8.3}/tests/fixtures/truncated.xyz +0 -0
  114. {molscope-0.8.2 → molscope-0.8.3}/tests/fixtures/v3000.sdf +0 -0
  115. {molscope-0.8.2 → molscope-0.8.3}/tests/fixtures/water.sdf +0 -0
  116. {molscope-0.8.2 → molscope-0.8.3}/tests/test_cg_mapping.py +0 -0
  117. {molscope-0.8.2 → molscope-0.8.3}/tests/test_chem.py +0 -0
  118. {molscope-0.8.2 → molscope-0.8.3}/tests/test_cif_validation.py +0 -0
  119. {molscope-0.8.2 → molscope-0.8.3}/tests/test_cli.py +0 -0
  120. {molscope-0.8.2 → molscope-0.8.3}/tests/test_cli_batch.py +0 -0
  121. {molscope-0.8.2 → molscope-0.8.3}/tests/test_clustering.py +0 -0
  122. {molscope-0.8.2 → molscope-0.8.3}/tests/test_coarsegrain.py +0 -0
  123. {molscope-0.8.2 → molscope-0.8.3}/tests/test_contactmap.py +0 -0
  124. {molscope-0.8.2 → molscope-0.8.3}/tests/test_contacts.py +0 -0
  125. {molscope-0.8.2 → molscope-0.8.3}/tests/test_descriptors.py +0 -0
  126. {molscope-0.8.2 → molscope-0.8.3}/tests/test_dssp.py +0 -0
  127. {molscope-0.8.2 → molscope-0.8.3}/tests/test_extras.py +0 -0
  128. {molscope-0.8.2 → molscope-0.8.3}/tests/test_features.py +0 -0
  129. {molscope-0.8.2 → molscope-0.8.3}/tests/test_graph.py +0 -0
  130. {molscope-0.8.2 → molscope-0.8.3}/tests/test_io.py +0 -0
  131. {molscope-0.8.2 → molscope-0.8.3}/tests/test_molecule.py +0 -0
  132. {molscope-0.8.2 → molscope-0.8.3}/tests/test_protein_workflows.py +0 -0
  133. {molscope-0.8.2 → molscope-0.8.3}/tests/validation/test_bonds_ref.py +0 -0
  134. {molscope-0.8.2 → molscope-0.8.3}/tests/validation/test_chem_ref.py +0 -0
  135. {molscope-0.8.2 → molscope-0.8.3}/tests/validation/test_dssp_ref.py +0 -0
  136. {molscope-0.8.2 → molscope-0.8.3}/tests/validation/test_geometry_ref.py +0 -0
  137. {molscope-0.8.2 → molscope-0.8.3}/tests/validation/test_invariants.py +0 -0
{molscope-0.8.2 → molscope-0.8.3}/CITATION.cff RENAMED
@@ -5,7 +5,9 @@ title: "MolScope: lightweight molecular structure analysis, visualisation, graph
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  authors:
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  - family-names: Shrestha
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  given-names: Roshan
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- version: 0.8.2
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+ orcid: "https://orcid.org/0000-0002-9356-5136"
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+ affiliation: "Independent Researcher"
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+ version: 0.8.3
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  date-released: "2026-05-28"
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  license: MIT
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  repository-code: "https://github.com/roshan2004/molscope"
{molscope-0.8.2/molscope.egg-info → molscope-0.8.3}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: molscope
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- Version: 0.8.2
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+ Version: 0.8.3
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  Summary: Lightweight molecular coordinate workflows for descriptors, graph ML, and coarse-grained beads.
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  Author-email: Roshan Shrestha <roshanpra@gmail.com>
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  License-Expression: MIT
{molscope-0.8.2 → molscope-0.8.3}/molscope/__init__.py RENAMED
@@ -155,4 +155,4 @@ __all__ = [
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  "write_pdb",
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  "write_xyz",
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  ]
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- __version__ = "0.8.2"
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+ __version__ = "0.8.3"
{molscope-0.8.2 → molscope-0.8.3/molscope.egg-info}/PKG-INFO RENAMED
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  Metadata-Version: 2.4
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  Name: molscope
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- Version: 0.8.2
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  Summary: Lightweight molecular coordinate workflows for descriptors, graph ML, and coarse-grained beads.
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  Author-email: Roshan Shrestha <roshanpra@gmail.com>
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  License-Expression: MIT
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