stjames 0.0.55__tar.gz → 0.0.56__tar.gz

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  1. {stjames-0.0.55/stjames.egg-info → stjames-0.0.56}/PKG-INFO +1 -1
  2. {stjames-0.0.55 → stjames-0.0.56}/pyproject.toml +1 -1
  3. {stjames-0.0.55 → stjames-0.0.56}/stjames/pdb.py +16 -16
  4. {stjames-0.0.55 → stjames-0.0.56/stjames.egg-info}/PKG-INFO +1 -1
  5. {stjames-0.0.55 → stjames-0.0.56}/LICENSE +0 -0
  6. {stjames-0.0.55 → stjames-0.0.56}/README.md +0 -0
  7. {stjames-0.0.55 → stjames-0.0.56}/setup.cfg +0 -0
  8. {stjames-0.0.55 → stjames-0.0.56}/stjames/__init__.py +0 -0
  9. {stjames-0.0.55 → stjames-0.0.56}/stjames/_deprecated_solvent_settings.py +0 -0
  10. {stjames-0.0.55 → stjames-0.0.56}/stjames/atom.py +0 -0
  11. {stjames-0.0.55 → stjames-0.0.56}/stjames/atomium_stjames/__init__.py +0 -0
  12. {stjames-0.0.55 → stjames-0.0.56}/stjames/atomium_stjames/data.py +0 -0
  13. {stjames-0.0.55 → stjames-0.0.56}/stjames/atomium_stjames/mmcif.py +0 -0
  14. {stjames-0.0.55 → stjames-0.0.56}/stjames/atomium_stjames/pdb.py +0 -0
  15. {stjames-0.0.55 → stjames-0.0.56}/stjames/atomium_stjames/utilities.py +0 -0
  16. {stjames-0.0.55 → stjames-0.0.56}/stjames/base.py +0 -0
  17. {stjames-0.0.55 → stjames-0.0.56}/stjames/basis_set.py +0 -0
  18. {stjames-0.0.55 → stjames-0.0.56}/stjames/calculation.py +0 -0
  19. {stjames-0.0.55 → stjames-0.0.56}/stjames/compute_settings.py +0 -0
  20. {stjames-0.0.55 → stjames-0.0.56}/stjames/constraint.py +0 -0
  21. {stjames-0.0.55 → stjames-0.0.56}/stjames/correction.py +0 -0
  22. {stjames-0.0.55 → stjames-0.0.56}/stjames/data/__init__.py +0 -0
  23. {stjames-0.0.55 → stjames-0.0.56}/stjames/data/bragg_radii.json +0 -0
  24. {stjames-0.0.55 → stjames-0.0.56}/stjames/data/elements.py +0 -0
  25. {stjames-0.0.55 → stjames-0.0.56}/stjames/data/isotopes.json +0 -0
  26. {stjames-0.0.55 → stjames-0.0.56}/stjames/data/nist_isotopes.json +0 -0
  27. {stjames-0.0.55 → stjames-0.0.56}/stjames/data/read_nist_isotopes.py +0 -0
  28. {stjames-0.0.55 → stjames-0.0.56}/stjames/data/symbol_element.json +0 -0
  29. {stjames-0.0.55 → stjames-0.0.56}/stjames/diis_settings.py +0 -0
  30. {stjames-0.0.55 → stjames-0.0.56}/stjames/grid_settings.py +0 -0
  31. {stjames-0.0.55 → stjames-0.0.56}/stjames/int_settings.py +0 -0
  32. {stjames-0.0.55 → stjames-0.0.56}/stjames/message.py +0 -0
  33. {stjames-0.0.55 → stjames-0.0.56}/stjames/method.py +0 -0
  34. {stjames-0.0.55 → stjames-0.0.56}/stjames/mode.py +0 -0
  35. {stjames-0.0.55 → stjames-0.0.56}/stjames/molecule.py +0 -0
  36. {stjames-0.0.55 → stjames-0.0.56}/stjames/opt_settings.py +0 -0
  37. {stjames-0.0.55 → stjames-0.0.56}/stjames/periodic_cell.py +0 -0
  38. {stjames-0.0.55 → stjames-0.0.56}/stjames/py.typed +0 -0
  39. {stjames-0.0.55 → stjames-0.0.56}/stjames/scf_settings.py +0 -0
  40. {stjames-0.0.55 → stjames-0.0.56}/stjames/settings.py +0 -0
  41. {stjames-0.0.55 → stjames-0.0.56}/stjames/solvent.py +0 -0
  42. {stjames-0.0.55 → stjames-0.0.56}/stjames/status.py +0 -0
  43. {stjames-0.0.55 → stjames-0.0.56}/stjames/task.py +0 -0
  44. {stjames-0.0.55 → stjames-0.0.56}/stjames/thermochem_settings.py +0 -0
  45. {stjames-0.0.55 → stjames-0.0.56}/stjames/types.py +0 -0
  46. {stjames-0.0.55 → stjames-0.0.56}/stjames/workflows/__init__.py +0 -0
  47. {stjames-0.0.55 → stjames-0.0.56}/stjames/workflows/admet.py +0 -0
  48. {stjames-0.0.55 → stjames-0.0.56}/stjames/workflows/basic_calculation.py +0 -0
  49. {stjames-0.0.55 → stjames-0.0.56}/stjames/workflows/bde.py +0 -0
  50. {stjames-0.0.55 → stjames-0.0.56}/stjames/workflows/conformer.py +0 -0
  51. {stjames-0.0.55 → stjames-0.0.56}/stjames/workflows/conformer_search.py +0 -0
  52. {stjames-0.0.55 → stjames-0.0.56}/stjames/workflows/descriptors.py +0 -0
  53. {stjames-0.0.55 → stjames-0.0.56}/stjames/workflows/docking.py +0 -0
  54. {stjames-0.0.55 → stjames-0.0.56}/stjames/workflows/electronic_properties.py +0 -0
  55. {stjames-0.0.55 → stjames-0.0.56}/stjames/workflows/fukui.py +0 -0
  56. {stjames-0.0.55 → stjames-0.0.56}/stjames/workflows/hydrogen_bond_basicity.py +0 -0
  57. {stjames-0.0.55 → stjames-0.0.56}/stjames/workflows/irc.py +0 -0
  58. {stjames-0.0.55 → stjames-0.0.56}/stjames/workflows/molecular_dynamics.py +0 -0
  59. {stjames-0.0.55 → stjames-0.0.56}/stjames/workflows/multistage_opt.py +0 -0
  60. {stjames-0.0.55 → stjames-0.0.56}/stjames/workflows/pka.py +0 -0
  61. {stjames-0.0.55 → stjames-0.0.56}/stjames/workflows/redox_potential.py +0 -0
  62. {stjames-0.0.55 → stjames-0.0.56}/stjames/workflows/scan.py +0 -0
  63. {stjames-0.0.55 → stjames-0.0.56}/stjames/workflows/spin_states.py +0 -0
  64. {stjames-0.0.55 → stjames-0.0.56}/stjames/workflows/tautomer.py +0 -0
  65. {stjames-0.0.55 → stjames-0.0.56}/stjames/workflows/workflow.py +0 -0
  66. {stjames-0.0.55 → stjames-0.0.56}/stjames.egg-info/SOURCES.txt +0 -0
  67. {stjames-0.0.55 → stjames-0.0.56}/stjames.egg-info/dependency_links.txt +0 -0
  68. {stjames-0.0.55 → stjames-0.0.56}/stjames.egg-info/requires.txt +0 -0
  69. {stjames-0.0.55 → stjames-0.0.56}/stjames.egg-info/top_level.txt +0 -0
  70. {stjames-0.0.55 → stjames-0.0.56}/tests/test_constraints.py +0 -0
  71. {stjames-0.0.55 → stjames-0.0.56}/tests/test_from_extxyz.py +0 -0
  72. {stjames-0.0.55 → stjames-0.0.56}/tests/test_molecule.py +0 -0
  73. {stjames-0.0.55 → stjames-0.0.56}/tests/test_pdb.py +0 -0
  74. {stjames-0.0.55 → stjames-0.0.56}/tests/test_rounding.py +0 -0
  75. {stjames-0.0.55 → stjames-0.0.56}/tests/test_settings.py +0 -0
{stjames-0.0.55/stjames.egg-info → stjames-0.0.56}/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: 0.0.55
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+ Version: 0.0.56
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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-0.0.55 → stjames-0.0.56}/pyproject.toml RENAMED
@@ -1,6 +1,6 @@
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  [project]
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  name = "stjames"
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- version = "0.0.55"
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+ version = "0.0.56"
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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-0.0.55 → stjames-0.0.56}/stjames/pdb.py RENAMED
@@ -36,10 +36,10 @@ class PDBWater(BaseModel):
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  model_config = ConfigDict(extra=EXTRA)
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- name: str | None
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- full_name: str | None
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+ name: str | None = None
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+ full_name: str | None = None
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  atoms: dict[int, PDBAtom] = {}
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- internal_id: str | None
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+ internal_id: str | None = None
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  polymer: str
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@@ -48,7 +48,7 @@ class PDBResidue(BaseModel):
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  model_config = ConfigDict(extra=EXTRA)
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- name: str | None
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+ name: str | None = None
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  full_name: str | None = None
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  atoms: dict[int, PDBAtom] = {}
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  number: int
@@ -62,7 +62,7 @@ class PDBPolymer(BaseModel):
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  internal_id: str
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  helices: list[list[str]] = []
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  residues: dict[str, PDBResidue] = {}
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- sequence: str | None
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+ sequence: str | None = None
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  strands: list[list[str]] = []
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@@ -105,10 +105,10 @@ class PDBAssembly(BaseModel):
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  model_config = ConfigDict(extra=EXTRA)
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  transformations: list[PDBTransformations]
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- software: str | None
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- buried_surface_area: float | None
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- surface_area: float | None
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- delta_energy: float | None
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+ software: str | None = None
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+ buried_surface_area: float | None = None
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+ surface_area: float | None = None
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+ delta_energy: float | None = None
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  id: int
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@@ -152,10 +152,10 @@ class PDBExperiment(BaseModel):
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  model_config = ConfigDict(extra=EXTRA)
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- expression_system: str | None
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+ expression_system: str | None = None
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  missing_residues: list[PDBMissingResidue] = []
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- source_organism: str | None
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- technique: str | None
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+ source_organism: str | None = None
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+ technique: str | None = None
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  class PDBDescription(BaseModel):
@@ -163,11 +163,11 @@ class PDBDescription(BaseModel):
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  model_config = ConfigDict(extra=EXTRA)
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- code: str | None
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- title: str | None
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+ code: str | None = None
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+ title: str | None = None
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  authors: list[str] = []
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- classification: str | None
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- deposition_date: str | None
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+ classification: str | None = None
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+ deposition_date: str | None = None
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  keywords: list[str] = []
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  @field_validator("deposition_date", mode="before")
{stjames-0.0.55 → stjames-0.0.56/stjames.egg-info}/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: 0.0.55
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+ Version: 0.0.56
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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-0.0.55 → stjames-0.0.56}/LICENSE RENAMED
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{stjames-0.0.55 → stjames-0.0.56}/stjames/__init__.py RENAMED
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{stjames-0.0.55 → stjames-0.0.56}/stjames/method.py RENAMED
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{stjames-0.0.55 → stjames-0.0.56}/stjames/mode.py RENAMED
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{stjames-0.0.55 → stjames-0.0.56}/stjames/molecule.py RENAMED
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{stjames-0.0.55 → stjames-0.0.56}/stjames/settings.py RENAMED
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{stjames-0.0.55 → stjames-0.0.56}/stjames/solvent.py RENAMED
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