stjames 0.0.66__tar.gz → 0.0.68__tar.gz

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  1. {stjames-0.0.66/stjames.egg-info → stjames-0.0.68}/PKG-INFO +1 -1
  2. {stjames-0.0.66 → stjames-0.0.68}/pyproject.toml +1 -1
  3. {stjames-0.0.66 → stjames-0.0.68}/stjames/pdb.py +1 -1
  4. {stjames-0.0.66 → stjames-0.0.68}/stjames/status.py +4 -1
  5. {stjames-0.0.66 → stjames-0.0.68}/stjames/workflows/scan.py +2 -0
  6. {stjames-0.0.66 → stjames-0.0.68/stjames.egg-info}/PKG-INFO +1 -1
  7. {stjames-0.0.66 → stjames-0.0.68}/LICENSE +0 -0
  8. {stjames-0.0.66 → stjames-0.0.68}/README.md +0 -0
  9. {stjames-0.0.66 → stjames-0.0.68}/setup.cfg +0 -0
  10. {stjames-0.0.66 → stjames-0.0.68}/stjames/__init__.py +0 -0
  11. {stjames-0.0.66 → stjames-0.0.68}/stjames/_deprecated_solvent_settings.py +0 -0
  12. {stjames-0.0.66 → stjames-0.0.68}/stjames/atom.py +0 -0
  13. {stjames-0.0.66 → stjames-0.0.68}/stjames/atomium_stjames/__init__.py +0 -0
  14. {stjames-0.0.66 → stjames-0.0.68}/stjames/atomium_stjames/data.py +0 -0
  15. {stjames-0.0.66 → stjames-0.0.68}/stjames/atomium_stjames/mmcif.py +0 -0
  16. {stjames-0.0.66 → stjames-0.0.68}/stjames/atomium_stjames/pdb.py +0 -0
  17. {stjames-0.0.66 → stjames-0.0.68}/stjames/atomium_stjames/utilities.py +0 -0
  18. {stjames-0.0.66 → stjames-0.0.68}/stjames/base.py +0 -0
  19. {stjames-0.0.66 → stjames-0.0.68}/stjames/basis_set.py +0 -0
  20. {stjames-0.0.66 → stjames-0.0.68}/stjames/calculation.py +0 -0
  21. {stjames-0.0.66 → stjames-0.0.68}/stjames/compute_settings.py +0 -0
  22. {stjames-0.0.66 → stjames-0.0.68}/stjames/constraint.py +0 -0
  23. {stjames-0.0.66 → stjames-0.0.68}/stjames/correction.py +0 -0
  24. {stjames-0.0.66 → stjames-0.0.68}/stjames/data/__init__.py +0 -0
  25. {stjames-0.0.66 → stjames-0.0.68}/stjames/data/bragg_radii.json +0 -0
  26. {stjames-0.0.66 → stjames-0.0.68}/stjames/data/elements.py +0 -0
  27. {stjames-0.0.66 → stjames-0.0.68}/stjames/data/isotopes.json +0 -0
  28. {stjames-0.0.66 → stjames-0.0.68}/stjames/data/nist_isotopes.json +0 -0
  29. {stjames-0.0.66 → stjames-0.0.68}/stjames/data/read_nist_isotopes.py +0 -0
  30. {stjames-0.0.66 → stjames-0.0.68}/stjames/data/symbol_element.json +0 -0
  31. {stjames-0.0.66 → stjames-0.0.68}/stjames/diis_settings.py +0 -0
  32. {stjames-0.0.66 → stjames-0.0.68}/stjames/grid_settings.py +0 -0
  33. {stjames-0.0.66 → stjames-0.0.68}/stjames/int_settings.py +0 -0
  34. {stjames-0.0.66 → stjames-0.0.68}/stjames/message.py +0 -0
  35. {stjames-0.0.66 → stjames-0.0.68}/stjames/method.py +0 -0
  36. {stjames-0.0.66 → stjames-0.0.68}/stjames/mode.py +0 -0
  37. {stjames-0.0.66 → stjames-0.0.68}/stjames/molecule.py +0 -0
  38. {stjames-0.0.66 → stjames-0.0.68}/stjames/opt_settings.py +0 -0
  39. {stjames-0.0.66 → stjames-0.0.68}/stjames/periodic_cell.py +0 -0
  40. {stjames-0.0.66 → stjames-0.0.68}/stjames/py.typed +0 -0
  41. {stjames-0.0.66 → stjames-0.0.68}/stjames/scf_settings.py +0 -0
  42. {stjames-0.0.66 → stjames-0.0.68}/stjames/settings.py +0 -0
  43. {stjames-0.0.66 → stjames-0.0.68}/stjames/solvent.py +0 -0
  44. {stjames-0.0.66 → stjames-0.0.68}/stjames/task.py +0 -0
  45. {stjames-0.0.66 → stjames-0.0.68}/stjames/thermochem_settings.py +0 -0
  46. {stjames-0.0.66 → stjames-0.0.68}/stjames/types.py +0 -0
  47. {stjames-0.0.66 → stjames-0.0.68}/stjames/workflows/__init__.py +0 -0
  48. {stjames-0.0.66 → stjames-0.0.68}/stjames/workflows/admet.py +0 -0
  49. {stjames-0.0.66 → stjames-0.0.68}/stjames/workflows/basic_calculation.py +0 -0
  50. {stjames-0.0.66 → stjames-0.0.68}/stjames/workflows/bde.py +0 -0
  51. {stjames-0.0.66 → stjames-0.0.68}/stjames/workflows/conformer.py +0 -0
  52. {stjames-0.0.66 → stjames-0.0.68}/stjames/workflows/conformer_search.py +0 -0
  53. {stjames-0.0.66 → stjames-0.0.68}/stjames/workflows/descriptors.py +0 -0
  54. {stjames-0.0.66 → stjames-0.0.68}/stjames/workflows/docking.py +0 -0
  55. {stjames-0.0.66 → stjames-0.0.68}/stjames/workflows/electronic_properties.py +0 -0
  56. {stjames-0.0.66 → stjames-0.0.68}/stjames/workflows/fukui.py +0 -0
  57. {stjames-0.0.66 → stjames-0.0.68}/stjames/workflows/hydrogen_bond_basicity.py +0 -0
  58. {stjames-0.0.66 → stjames-0.0.68}/stjames/workflows/ion_mobility.py +0 -0
  59. {stjames-0.0.66 → stjames-0.0.68}/stjames/workflows/irc.py +0 -0
  60. {stjames-0.0.66 → stjames-0.0.68}/stjames/workflows/macropka.py +0 -0
  61. {stjames-0.0.66 → stjames-0.0.68}/stjames/workflows/molecular_dynamics.py +0 -0
  62. {stjames-0.0.66 → stjames-0.0.68}/stjames/workflows/multistage_opt.py +0 -0
  63. {stjames-0.0.66 → stjames-0.0.68}/stjames/workflows/pka.py +0 -0
  64. {stjames-0.0.66 → stjames-0.0.68}/stjames/workflows/redox_potential.py +0 -0
  65. {stjames-0.0.66 → stjames-0.0.68}/stjames/workflows/solubility.py +0 -0
  66. {stjames-0.0.66 → stjames-0.0.68}/stjames/workflows/spin_states.py +0 -0
  67. {stjames-0.0.66 → stjames-0.0.68}/stjames/workflows/tautomer.py +0 -0
  68. {stjames-0.0.66 → stjames-0.0.68}/stjames/workflows/workflow.py +0 -0
  69. {stjames-0.0.66 → stjames-0.0.68}/stjames.egg-info/SOURCES.txt +0 -0
  70. {stjames-0.0.66 → stjames-0.0.68}/stjames.egg-info/dependency_links.txt +0 -0
  71. {stjames-0.0.66 → stjames-0.0.68}/stjames.egg-info/requires.txt +0 -0
  72. {stjames-0.0.66 → stjames-0.0.68}/stjames.egg-info/top_level.txt +0 -0
  73. {stjames-0.0.66 → stjames-0.0.68}/tests/test_constraints.py +0 -0
  74. {stjames-0.0.66 → stjames-0.0.68}/tests/test_from_extxyz.py +0 -0
  75. {stjames-0.0.66 → stjames-0.0.68}/tests/test_molecule.py +0 -0
  76. {stjames-0.0.66 → stjames-0.0.68}/tests/test_pdb.py +0 -0
  77. {stjames-0.0.66 → stjames-0.0.68}/tests/test_rounding.py +0 -0
  78. {stjames-0.0.66 → stjames-0.0.68}/tests/test_settings.py +0 -0
{stjames-0.0.66/stjames.egg-info → stjames-0.0.68}/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: 0.0.66
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+ Version: 0.0.68
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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-0.0.66 → stjames-0.0.68}/pyproject.toml RENAMED
@@ -1,6 +1,6 @@
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  [project]
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  name = "stjames"
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- version = "0.0.66"
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+ version = "0.0.68"
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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-0.0.66 → stjames-0.0.68}/stjames/pdb.py RENAMED
@@ -292,7 +292,7 @@ def pdb_object_to_pdb_filestring(
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  )
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  pdb_lines.append(line)
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- pdb_lines.append(f"TER {_atom_id + 1:>5} {residue.name:>3} {this_chain_id}{int(_residue_id[2:]):>4}")
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+ pdb_lines.append(f"TER {_atom_id + 1:>5} {residue.name:>3} {this_chain_id}{_residue_id[2:]:>4}")
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  # === 2) Non-polymers (e.g. ligands, ions) ===
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  for _np_id, nonpoly in model.non_polymer.items():
{stjames-0.0.66 → stjames-0.0.68}/stjames/status.py RENAMED
@@ -2,7 +2,7 @@ from enum import Enum
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  class Status(int, Enum):
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- # what a job gets when it's created
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+ # what a job gets when it's created if user is below max_concurrency
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  QUEUED = 0
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  # still running...
@@ -16,3 +16,6 @@ class Status(int, Enum):
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  # job was stopped externally, maybe timed out or something
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  STOPPED = 4
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+
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+ # Status if a user has exceeded their allowed max_concurrency
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+ AWAITING_QUEUE = 5
{stjames-0.0.66 → stjames-0.0.68}/stjames/workflows/scan.py RENAMED
@@ -18,12 +18,14 @@ class ScanPoint(Base):
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  A point in a scan.
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  :param index: index of the point
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+ :param index_2d: index of the point in 2nd dimension, if applicable
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  :param molecule: Molecule at the point
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  :param energy: energy of the point
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  :param uuid: UUID of the calculation
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  """
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  index: int
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+ index_2d: int = 0
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  molecule: Molecule
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  energy: Annotated[float | None, AfterValidator(round_optional_float(6))] = None
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  uuid: UUID | None = None
{stjames-0.0.66 → stjames-0.0.68/stjames.egg-info}/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: 0.0.66
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+ Version: 0.0.68
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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-0.0.66 → stjames-0.0.68}/LICENSE RENAMED
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{stjames-0.0.66 → stjames-0.0.68}/stjames/task.py RENAMED
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{stjames-0.0.66 → stjames-0.0.68}/stjames/types.py RENAMED
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{stjames-0.0.66 → stjames-0.0.68}/tests/test_pdb.py RENAMED
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