stjames 0.0.59__tar.gz → 0.0.62__tar.gz

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  1. {stjames-0.0.59/stjames.egg-info → stjames-0.0.62}/PKG-INFO +2 -3
  2. {stjames-0.0.59 → stjames-0.0.62}/pyproject.toml +3 -4
  3. {stjames-0.0.59 → stjames-0.0.62}/stjames/atomium_stjames/mmcif.py +216 -162
  4. {stjames-0.0.59 → stjames-0.0.62}/stjames/atomium_stjames/utilities.py +58 -46
  5. {stjames-0.0.59 → stjames-0.0.62}/stjames/molecule.py +46 -1
  6. {stjames-0.0.59 → stjames-0.0.62}/stjames/types.py +10 -1
  7. {stjames-0.0.59 → stjames-0.0.62}/stjames/workflows/__init__.py +5 -2
  8. stjames-0.0.62/stjames/workflows/admet.py +18 -0
  9. stjames-0.0.62/stjames/workflows/basic_calculation.py +24 -0
  10. {stjames-0.0.59 → stjames-0.0.62}/stjames/workflows/bde.py +5 -5
  11. {stjames-0.0.59 → stjames-0.0.62}/stjames/workflows/conformer.py +4 -2
  12. {stjames-0.0.59 → stjames-0.0.62}/stjames/workflows/conformer_search.py +3 -3
  13. stjames-0.0.62/stjames/workflows/descriptors.py +24 -0
  14. {stjames-0.0.59 → stjames-0.0.62}/stjames/workflows/docking.py +26 -11
  15. {stjames-0.0.59 → stjames-0.0.62}/stjames/workflows/electronic_properties.py +5 -2
  16. {stjames-0.0.59 → stjames-0.0.62}/stjames/workflows/fukui.py +19 -2
  17. stjames-0.0.62/stjames/workflows/hydrogen_bond_basicity.py +45 -0
  18. {stjames-0.0.59 → stjames-0.0.62}/stjames/workflows/irc.py +4 -2
  19. {stjames-0.0.59 → stjames-0.0.62}/stjames/workflows/molecular_dynamics.py +28 -3
  20. {stjames-0.0.59 → stjames-0.0.62}/stjames/workflows/multistage_opt.py +5 -3
  21. stjames-0.0.62/stjames/workflows/pka.py +66 -0
  22. {stjames-0.0.59 → stjames-0.0.62}/stjames/workflows/redox_potential.py +4 -2
  23. stjames-0.0.62/stjames/workflows/scan.py +76 -0
  24. stjames-0.0.62/stjames/workflows/solubility.py +60 -0
  25. {stjames-0.0.59 → stjames-0.0.62}/stjames/workflows/spin_states.py +4 -2
  26. stjames-0.0.62/stjames/workflows/tautomer.py +43 -0
  27. {stjames-0.0.59 → stjames-0.0.62}/stjames/workflows/workflow.py +27 -4
  28. {stjames-0.0.59 → stjames-0.0.62/stjames.egg-info}/PKG-INFO +2 -3
  29. {stjames-0.0.59 → stjames-0.0.62}/stjames.egg-info/SOURCES.txt +1 -0
  30. stjames-0.0.62/stjames.egg-info/requires.txt +4 -0
  31. {stjames-0.0.59 → stjames-0.0.62}/tests/test_pdb.py +3 -3
  32. stjames-0.0.59/stjames/workflows/admet.py +0 -7
  33. stjames-0.0.59/stjames/workflows/basic_calculation.py +0 -9
  34. stjames-0.0.59/stjames/workflows/descriptors.py +0 -11
  35. stjames-0.0.59/stjames/workflows/hydrogen_bond_basicity.py +0 -21
  36. stjames-0.0.59/stjames/workflows/pka.py +0 -32
  37. stjames-0.0.59/stjames/workflows/scan.py +0 -41
  38. stjames-0.0.59/stjames/workflows/tautomer.py +0 -21
  39. stjames-0.0.59/stjames.egg-info/requires.txt +0 -5
  40. {stjames-0.0.59 → stjames-0.0.62}/LICENSE +0 -0
  41. {stjames-0.0.59 → stjames-0.0.62}/README.md +0 -0
  42. {stjames-0.0.59 → stjames-0.0.62}/setup.cfg +0 -0
  43. {stjames-0.0.59 → stjames-0.0.62}/stjames/__init__.py +0 -0
  44. {stjames-0.0.59 → stjames-0.0.62}/stjames/_deprecated_solvent_settings.py +0 -0
  45. {stjames-0.0.59 → stjames-0.0.62}/stjames/atom.py +0 -0
  46. {stjames-0.0.59 → stjames-0.0.62}/stjames/atomium_stjames/__init__.py +0 -0
  47. {stjames-0.0.59 → stjames-0.0.62}/stjames/atomium_stjames/data.py +0 -0
  48. {stjames-0.0.59 → stjames-0.0.62}/stjames/atomium_stjames/pdb.py +0 -0
  49. {stjames-0.0.59 → stjames-0.0.62}/stjames/base.py +0 -0
  50. {stjames-0.0.59 → stjames-0.0.62}/stjames/basis_set.py +0 -0
  51. {stjames-0.0.59 → stjames-0.0.62}/stjames/calculation.py +0 -0
  52. {stjames-0.0.59 → stjames-0.0.62}/stjames/compute_settings.py +0 -0
  53. {stjames-0.0.59 → stjames-0.0.62}/stjames/constraint.py +0 -0
  54. {stjames-0.0.59 → stjames-0.0.62}/stjames/correction.py +0 -0
  55. {stjames-0.0.59 → stjames-0.0.62}/stjames/data/__init__.py +0 -0
  56. {stjames-0.0.59 → stjames-0.0.62}/stjames/data/bragg_radii.json +0 -0
  57. {stjames-0.0.59 → stjames-0.0.62}/stjames/data/elements.py +0 -0
  58. {stjames-0.0.59 → stjames-0.0.62}/stjames/data/isotopes.json +0 -0
  59. {stjames-0.0.59 → stjames-0.0.62}/stjames/data/nist_isotopes.json +0 -0
  60. {stjames-0.0.59 → stjames-0.0.62}/stjames/data/read_nist_isotopes.py +0 -0
  61. {stjames-0.0.59 → stjames-0.0.62}/stjames/data/symbol_element.json +0 -0
  62. {stjames-0.0.59 → stjames-0.0.62}/stjames/diis_settings.py +0 -0
  63. {stjames-0.0.59 → stjames-0.0.62}/stjames/grid_settings.py +0 -0
  64. {stjames-0.0.59 → stjames-0.0.62}/stjames/int_settings.py +0 -0
  65. {stjames-0.0.59 → stjames-0.0.62}/stjames/message.py +0 -0
  66. {stjames-0.0.59 → stjames-0.0.62}/stjames/method.py +0 -0
  67. {stjames-0.0.59 → stjames-0.0.62}/stjames/mode.py +0 -0
  68. {stjames-0.0.59 → stjames-0.0.62}/stjames/opt_settings.py +0 -0
  69. {stjames-0.0.59 → stjames-0.0.62}/stjames/pdb.py +0 -0
  70. {stjames-0.0.59 → stjames-0.0.62}/stjames/periodic_cell.py +0 -0
  71. {stjames-0.0.59 → stjames-0.0.62}/stjames/py.typed +0 -0
  72. {stjames-0.0.59 → stjames-0.0.62}/stjames/scf_settings.py +0 -0
  73. {stjames-0.0.59 → stjames-0.0.62}/stjames/settings.py +0 -0
  74. {stjames-0.0.59 → stjames-0.0.62}/stjames/solvent.py +0 -0
  75. {stjames-0.0.59 → stjames-0.0.62}/stjames/status.py +0 -0
  76. {stjames-0.0.59 → stjames-0.0.62}/stjames/task.py +0 -0
  77. {stjames-0.0.59 → stjames-0.0.62}/stjames/thermochem_settings.py +0 -0
  78. {stjames-0.0.59 → stjames-0.0.62}/stjames.egg-info/dependency_links.txt +0 -0
  79. {stjames-0.0.59 → stjames-0.0.62}/stjames.egg-info/top_level.txt +0 -0
  80. {stjames-0.0.59 → stjames-0.0.62}/tests/test_constraints.py +0 -0
  81. {stjames-0.0.59 → stjames-0.0.62}/tests/test_from_extxyz.py +0 -0
  82. {stjames-0.0.59 → stjames-0.0.62}/tests/test_molecule.py +0 -0
  83. {stjames-0.0.59 → stjames-0.0.62}/tests/test_rounding.py +0 -0
  84. {stjames-0.0.59 → stjames-0.0.62}/tests/test_settings.py +0 -0
{stjames-0.0.59/stjames.egg-info → stjames-0.0.62}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.2
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  Name: stjames
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- Version: 0.0.59
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+ Version: 0.0.62
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  Summary: standardized JSON atom/molecule encoding scheme
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  Author-email: Corin Wagen <corin@rowansci.com>
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  Project-URL: Homepage, https://github.com/rowansci/stjames
@@ -8,11 +8,10 @@ Project-URL: Bug Tracker, https://github.com/rowansci/stjames/issues
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  Requires-Python: >=3.11
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  Description-Content-Type: text/markdown
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  License-File: LICENSE
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- Requires-Dist: atomium<2,>=1
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  Requires-Dist: pydantic>=2.4
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  Requires-Dist: numpy
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- Requires-Dist: atomium<2.0,>=1.0
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  Requires-Dist: requests
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+ Requires-Dist: rdkit
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  # stjames
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{stjames-0.0.59 → stjames-0.0.62}/pyproject.toml RENAMED
@@ -1,6 +1,6 @@
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  [project]
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  name = "stjames"
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- version = "0.0.59"
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+ version = "0.0.62"
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  description = "standardized JSON atom/molecule encoding scheme"
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  readme = "README.md"
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  requires-python = ">=3.11"
@@ -9,11 +9,10 @@ authors = [
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  ]
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  dependencies = [
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- "atomium>=1,<2",
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  "pydantic>=2.4",
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  "numpy",
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- "atomium>=1.0,<2.0",
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- "requests"
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+ "requests",
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+ "rdkit",
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  ]
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  [build-system]