stjames 0.0.89__tar.gz → 0.0.90__tar.gz

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  1. {stjames-0.0.89/stjames.egg-info → stjames-0.0.90}/PKG-INFO +1 -1
  2. {stjames-0.0.89 → stjames-0.0.90}/pyproject.toml +1 -1
  3. {stjames-0.0.89 → stjames-0.0.90}/stjames/workflows/ion_mobility.py +6 -0
  4. {stjames-0.0.89 → stjames-0.0.90/stjames.egg-info}/PKG-INFO +1 -1
  5. {stjames-0.0.89 → stjames-0.0.90}/LICENSE +0 -0
  6. {stjames-0.0.89 → stjames-0.0.90}/README.md +0 -0
  7. {stjames-0.0.89 → stjames-0.0.90}/setup.cfg +0 -0
  8. {stjames-0.0.89 → stjames-0.0.90}/stjames/__init__.py +0 -0
  9. {stjames-0.0.89 → stjames-0.0.90}/stjames/_deprecated_solvent_settings.py +0 -0
  10. {stjames-0.0.89 → stjames-0.0.90}/stjames/atom.py +0 -0
  11. {stjames-0.0.89 → stjames-0.0.90}/stjames/atomium_stjames/__init__.py +0 -0
  12. {stjames-0.0.89 → stjames-0.0.90}/stjames/atomium_stjames/data.py +0 -0
  13. {stjames-0.0.89 → stjames-0.0.90}/stjames/atomium_stjames/mmcif.py +0 -0
  14. {stjames-0.0.89 → stjames-0.0.90}/stjames/atomium_stjames/pdb.py +0 -0
  15. {stjames-0.0.89 → stjames-0.0.90}/stjames/atomium_stjames/utilities.py +0 -0
  16. {stjames-0.0.89 → stjames-0.0.90}/stjames/base.py +0 -0
  17. {stjames-0.0.89 → stjames-0.0.90}/stjames/basis_set.py +0 -0
  18. {stjames-0.0.89 → stjames-0.0.90}/stjames/calculation.py +0 -0
  19. {stjames-0.0.89 → stjames-0.0.90}/stjames/compute_settings.py +0 -0
  20. {stjames-0.0.89 → stjames-0.0.90}/stjames/constraint.py +0 -0
  21. {stjames-0.0.89 → stjames-0.0.90}/stjames/correction.py +0 -0
  22. {stjames-0.0.89 → stjames-0.0.90}/stjames/data/__init__.py +0 -0
  23. {stjames-0.0.89 → stjames-0.0.90}/stjames/data/bragg_radii.json +0 -0
  24. {stjames-0.0.89 → stjames-0.0.90}/stjames/data/elements.py +0 -0
  25. {stjames-0.0.89 → stjames-0.0.90}/stjames/data/isotopes.json +0 -0
  26. {stjames-0.0.89 → stjames-0.0.90}/stjames/data/nist_isotopes.json +0 -0
  27. {stjames-0.0.89 → stjames-0.0.90}/stjames/data/read_nist_isotopes.py +0 -0
  28. {stjames-0.0.89 → stjames-0.0.90}/stjames/data/symbol_element.json +0 -0
  29. {stjames-0.0.89 → stjames-0.0.90}/stjames/diis_settings.py +0 -0
  30. {stjames-0.0.89 → stjames-0.0.90}/stjames/grid_settings.py +0 -0
  31. {stjames-0.0.89 → stjames-0.0.90}/stjames/int_settings.py +0 -0
  32. {stjames-0.0.89 → stjames-0.0.90}/stjames/message.py +0 -0
  33. {stjames-0.0.89 → stjames-0.0.90}/stjames/method.py +0 -0
  34. {stjames-0.0.89 → stjames-0.0.90}/stjames/mode.py +0 -0
  35. {stjames-0.0.89 → stjames-0.0.90}/stjames/molecule.py +0 -0
  36. {stjames-0.0.89 → stjames-0.0.90}/stjames/opt_settings.py +0 -0
  37. {stjames-0.0.89 → stjames-0.0.90}/stjames/pdb.py +0 -0
  38. {stjames-0.0.89 → stjames-0.0.90}/stjames/periodic_cell.py +0 -0
  39. {stjames-0.0.89 → stjames-0.0.90}/stjames/py.typed +0 -0
  40. {stjames-0.0.89 → stjames-0.0.90}/stjames/scf_settings.py +0 -0
  41. {stjames-0.0.89 → stjames-0.0.90}/stjames/settings.py +0 -0
  42. {stjames-0.0.89 → stjames-0.0.90}/stjames/solvent.py +0 -0
  43. {stjames-0.0.89 → stjames-0.0.90}/stjames/status.py +0 -0
  44. {stjames-0.0.89 → stjames-0.0.90}/stjames/task.py +0 -0
  45. {stjames-0.0.89 → stjames-0.0.90}/stjames/thermochem_settings.py +0 -0
  46. {stjames-0.0.89 → stjames-0.0.90}/stjames/types.py +0 -0
  47. {stjames-0.0.89 → stjames-0.0.90}/stjames/workflows/__init__.py +0 -0
  48. {stjames-0.0.89 → stjames-0.0.90}/stjames/workflows/admet.py +0 -0
  49. {stjames-0.0.89 → stjames-0.0.90}/stjames/workflows/basic_calculation.py +0 -0
  50. {stjames-0.0.89 → stjames-0.0.90}/stjames/workflows/bde.py +0 -0
  51. {stjames-0.0.89 → stjames-0.0.90}/stjames/workflows/conformer.py +0 -0
  52. {stjames-0.0.89 → stjames-0.0.90}/stjames/workflows/conformer_search.py +0 -0
  53. {stjames-0.0.89 → stjames-0.0.90}/stjames/workflows/descriptors.py +0 -0
  54. {stjames-0.0.89 → stjames-0.0.90}/stjames/workflows/docking.py +0 -0
  55. {stjames-0.0.89 → stjames-0.0.90}/stjames/workflows/electronic_properties.py +0 -0
  56. {stjames-0.0.89 → stjames-0.0.90}/stjames/workflows/fukui.py +0 -0
  57. {stjames-0.0.89 → stjames-0.0.90}/stjames/workflows/hydrogen_bond_basicity.py +0 -0
  58. {stjames-0.0.89 → stjames-0.0.90}/stjames/workflows/irc.py +0 -0
  59. {stjames-0.0.89 → stjames-0.0.90}/stjames/workflows/macropka.py +0 -0
  60. {stjames-0.0.89 → stjames-0.0.90}/stjames/workflows/molecular_dynamics.py +0 -0
  61. {stjames-0.0.89 → stjames-0.0.90}/stjames/workflows/multistage_opt.py +0 -0
  62. {stjames-0.0.89 → stjames-0.0.90}/stjames/workflows/pka.py +0 -0
  63. {stjames-0.0.89 → stjames-0.0.90}/stjames/workflows/pose_analysis_md.py +0 -0
  64. {stjames-0.0.89 → stjames-0.0.90}/stjames/workflows/protein_cofolding.py +0 -0
  65. {stjames-0.0.89 → stjames-0.0.90}/stjames/workflows/redox_potential.py +0 -0
  66. {stjames-0.0.89 → stjames-0.0.90}/stjames/workflows/scan.py +0 -0
  67. {stjames-0.0.89 → stjames-0.0.90}/stjames/workflows/solubility.py +0 -0
  68. {stjames-0.0.89 → stjames-0.0.90}/stjames/workflows/spin_states.py +0 -0
  69. {stjames-0.0.89 → stjames-0.0.90}/stjames/workflows/tautomer.py +0 -0
  70. {stjames-0.0.89 → stjames-0.0.90}/stjames/workflows/workflow.py +0 -0
  71. {stjames-0.0.89 → stjames-0.0.90}/stjames.egg-info/SOURCES.txt +0 -0
  72. {stjames-0.0.89 → stjames-0.0.90}/stjames.egg-info/dependency_links.txt +0 -0
  73. {stjames-0.0.89 → stjames-0.0.90}/stjames.egg-info/requires.txt +0 -0
  74. {stjames-0.0.89 → stjames-0.0.90}/stjames.egg-info/top_level.txt +0 -0
  75. {stjames-0.0.89 → stjames-0.0.90}/tests/test_constraints.py +0 -0
  76. {stjames-0.0.89 → stjames-0.0.90}/tests/test_from_extxyz.py +0 -0
  77. {stjames-0.0.89 → stjames-0.0.90}/tests/test_molecule.py +0 -0
  78. {stjames-0.0.89 → stjames-0.0.90}/tests/test_pdb.py +0 -0
  79. {stjames-0.0.89 → stjames-0.0.90}/tests/test_rounding.py +0 -0
  80. {stjames-0.0.89 → stjames-0.0.90}/tests/test_settings.py +0 -0
{stjames-0.0.89/stjames.egg-info → stjames-0.0.90}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: stjames
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- Version: 0.0.89
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+ Version: 0.0.90
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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
{stjames-0.0.89 → stjames-0.0.90}/pyproject.toml RENAMED
@@ -1,6 +1,6 @@
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  [project]
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  name = "stjames"
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- version = "0.0.89"
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+ version = "0.0.90"
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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"
{stjames-0.0.89 → stjames-0.0.90}/stjames/workflows/ion_mobility.py RENAMED
@@ -13,10 +13,13 @@ class IonMobilityWorkflow(MoleculeWorkflow):
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  :param mode: Mode for workflow (currently unused)
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  New:
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+ :param protonate: automatically protonate the molecule
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+ :param temperature: the temperature, in Kelvin
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  :param do_csearch: whether to perform a conformational search
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  :param do_optimization: whether to perform an optimization
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  Results:
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+ :param conformers: the UUIDs of the conformers
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  :param conformer_ccs: the collision cross section (Å**2) per conformer
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  :param conformer_ccs_stdev: the uncertainty in the same
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  :param conformer_weights: the Boltzmann weights at RT
@@ -24,8 +27,11 @@ class IonMobilityWorkflow(MoleculeWorkflow):
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  :param average_ccs_stdev: the uncertainty in the same
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  """
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+ protonate: bool = False
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+ temperature: float = 300
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  do_csearch: bool = True
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  do_optimization: bool = True
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+
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  conformers: list[UUID] = []
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  conformer_ccs: list[float] = []
{stjames-0.0.89 → stjames-0.0.90/stjames.egg-info}/PKG-INFO RENAMED
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  Metadata-Version: 2.4
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  Name: stjames
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- Version: 0.0.89
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+ Version: 0.0.90
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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
{stjames-0.0.89 → stjames-0.0.90}/LICENSE RENAMED
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