stjames 0.0.69__tar.gz → 0.0.70__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.

Potentially problematic release.

This version of stjames might be problematic. Click here for more details.

Files changed (78) hide show
  1. {stjames-0.0.69/stjames.egg-info → stjames-0.0.70}/PKG-INFO +1 -1
  2. {stjames-0.0.69 → stjames-0.0.70}/pyproject.toml +1 -1
  3. {stjames-0.0.69 → stjames-0.0.70}/stjames/opt_settings.py +1 -0
  4. {stjames-0.0.69 → stjames-0.0.70}/stjames/workflows/macropka.py +7 -0
  5. {stjames-0.0.69 → stjames-0.0.70/stjames.egg-info}/PKG-INFO +1 -1
  6. {stjames-0.0.69 → stjames-0.0.70}/LICENSE +0 -0
  7. {stjames-0.0.69 → stjames-0.0.70}/README.md +0 -0
  8. {stjames-0.0.69 → stjames-0.0.70}/setup.cfg +0 -0
  9. {stjames-0.0.69 → stjames-0.0.70}/stjames/__init__.py +0 -0
  10. {stjames-0.0.69 → stjames-0.0.70}/stjames/_deprecated_solvent_settings.py +0 -0
  11. {stjames-0.0.69 → stjames-0.0.70}/stjames/atom.py +0 -0
  12. {stjames-0.0.69 → stjames-0.0.70}/stjames/atomium_stjames/__init__.py +0 -0
  13. {stjames-0.0.69 → stjames-0.0.70}/stjames/atomium_stjames/data.py +0 -0
  14. {stjames-0.0.69 → stjames-0.0.70}/stjames/atomium_stjames/mmcif.py +0 -0
  15. {stjames-0.0.69 → stjames-0.0.70}/stjames/atomium_stjames/pdb.py +0 -0
  16. {stjames-0.0.69 → stjames-0.0.70}/stjames/atomium_stjames/utilities.py +0 -0
  17. {stjames-0.0.69 → stjames-0.0.70}/stjames/base.py +0 -0
  18. {stjames-0.0.69 → stjames-0.0.70}/stjames/basis_set.py +0 -0
  19. {stjames-0.0.69 → stjames-0.0.70}/stjames/calculation.py +0 -0
  20. {stjames-0.0.69 → stjames-0.0.70}/stjames/compute_settings.py +0 -0
  21. {stjames-0.0.69 → stjames-0.0.70}/stjames/constraint.py +0 -0
  22. {stjames-0.0.69 → stjames-0.0.70}/stjames/correction.py +0 -0
  23. {stjames-0.0.69 → stjames-0.0.70}/stjames/data/__init__.py +0 -0
  24. {stjames-0.0.69 → stjames-0.0.70}/stjames/data/bragg_radii.json +0 -0
  25. {stjames-0.0.69 → stjames-0.0.70}/stjames/data/elements.py +0 -0
  26. {stjames-0.0.69 → stjames-0.0.70}/stjames/data/isotopes.json +0 -0
  27. {stjames-0.0.69 → stjames-0.0.70}/stjames/data/nist_isotopes.json +0 -0
  28. {stjames-0.0.69 → stjames-0.0.70}/stjames/data/read_nist_isotopes.py +0 -0
  29. {stjames-0.0.69 → stjames-0.0.70}/stjames/data/symbol_element.json +0 -0
  30. {stjames-0.0.69 → stjames-0.0.70}/stjames/diis_settings.py +0 -0
  31. {stjames-0.0.69 → stjames-0.0.70}/stjames/grid_settings.py +0 -0
  32. {stjames-0.0.69 → stjames-0.0.70}/stjames/int_settings.py +0 -0
  33. {stjames-0.0.69 → stjames-0.0.70}/stjames/message.py +0 -0
  34. {stjames-0.0.69 → stjames-0.0.70}/stjames/method.py +0 -0
  35. {stjames-0.0.69 → stjames-0.0.70}/stjames/mode.py +0 -0
  36. {stjames-0.0.69 → stjames-0.0.70}/stjames/molecule.py +0 -0
  37. {stjames-0.0.69 → stjames-0.0.70}/stjames/pdb.py +0 -0
  38. {stjames-0.0.69 → stjames-0.0.70}/stjames/periodic_cell.py +0 -0
  39. {stjames-0.0.69 → stjames-0.0.70}/stjames/py.typed +0 -0
  40. {stjames-0.0.69 → stjames-0.0.70}/stjames/scf_settings.py +0 -0
  41. {stjames-0.0.69 → stjames-0.0.70}/stjames/settings.py +0 -0
  42. {stjames-0.0.69 → stjames-0.0.70}/stjames/solvent.py +0 -0
  43. {stjames-0.0.69 → stjames-0.0.70}/stjames/status.py +0 -0
  44. {stjames-0.0.69 → stjames-0.0.70}/stjames/task.py +0 -0
  45. {stjames-0.0.69 → stjames-0.0.70}/stjames/thermochem_settings.py +0 -0
  46. {stjames-0.0.69 → stjames-0.0.70}/stjames/types.py +0 -0
  47. {stjames-0.0.69 → stjames-0.0.70}/stjames/workflows/__init__.py +0 -0
  48. {stjames-0.0.69 → stjames-0.0.70}/stjames/workflows/admet.py +0 -0
  49. {stjames-0.0.69 → stjames-0.0.70}/stjames/workflows/basic_calculation.py +0 -0
  50. {stjames-0.0.69 → stjames-0.0.70}/stjames/workflows/bde.py +0 -0
  51. {stjames-0.0.69 → stjames-0.0.70}/stjames/workflows/conformer.py +0 -0
  52. {stjames-0.0.69 → stjames-0.0.70}/stjames/workflows/conformer_search.py +0 -0
  53. {stjames-0.0.69 → stjames-0.0.70}/stjames/workflows/descriptors.py +0 -0
  54. {stjames-0.0.69 → stjames-0.0.70}/stjames/workflows/docking.py +0 -0
  55. {stjames-0.0.69 → stjames-0.0.70}/stjames/workflows/electronic_properties.py +0 -0
  56. {stjames-0.0.69 → stjames-0.0.70}/stjames/workflows/fukui.py +0 -0
  57. {stjames-0.0.69 → stjames-0.0.70}/stjames/workflows/hydrogen_bond_basicity.py +0 -0
  58. {stjames-0.0.69 → stjames-0.0.70}/stjames/workflows/ion_mobility.py +0 -0
  59. {stjames-0.0.69 → stjames-0.0.70}/stjames/workflows/irc.py +0 -0
  60. {stjames-0.0.69 → stjames-0.0.70}/stjames/workflows/molecular_dynamics.py +0 -0
  61. {stjames-0.0.69 → stjames-0.0.70}/stjames/workflows/multistage_opt.py +0 -0
  62. {stjames-0.0.69 → stjames-0.0.70}/stjames/workflows/pka.py +0 -0
  63. {stjames-0.0.69 → stjames-0.0.70}/stjames/workflows/redox_potential.py +0 -0
  64. {stjames-0.0.69 → stjames-0.0.70}/stjames/workflows/scan.py +0 -0
  65. {stjames-0.0.69 → stjames-0.0.70}/stjames/workflows/solubility.py +0 -0
  66. {stjames-0.0.69 → stjames-0.0.70}/stjames/workflows/spin_states.py +0 -0
  67. {stjames-0.0.69 → stjames-0.0.70}/stjames/workflows/tautomer.py +0 -0
  68. {stjames-0.0.69 → stjames-0.0.70}/stjames/workflows/workflow.py +0 -0
  69. {stjames-0.0.69 → stjames-0.0.70}/stjames.egg-info/SOURCES.txt +0 -0
  70. {stjames-0.0.69 → stjames-0.0.70}/stjames.egg-info/dependency_links.txt +0 -0
  71. {stjames-0.0.69 → stjames-0.0.70}/stjames.egg-info/requires.txt +0 -0
  72. {stjames-0.0.69 → stjames-0.0.70}/stjames.egg-info/top_level.txt +0 -0
  73. {stjames-0.0.69 → stjames-0.0.70}/tests/test_constraints.py +0 -0
  74. {stjames-0.0.69 → stjames-0.0.70}/tests/test_from_extxyz.py +0 -0
  75. {stjames-0.0.69 → stjames-0.0.70}/tests/test_molecule.py +0 -0
  76. {stjames-0.0.69 → stjames-0.0.70}/tests/test_pdb.py +0 -0
  77. {stjames-0.0.69 → stjames-0.0.70}/tests/test_rounding.py +0 -0
  78. {stjames-0.0.69 → stjames-0.0.70}/tests/test_settings.py +0 -0
{stjames-0.0.69/stjames.egg-info → stjames-0.0.70}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.4
2
2
  Name: stjames
3
- Version: 0.0.69
3
+ Version: 0.0.70
4
4
  Summary: standardized JSON atom/molecule encoding scheme
5
5
  Author-email: Corin Wagen <corin@rowansci.com>
6
6
  Project-URL: Homepage, https://github.com/rowansci/stjames
{stjames-0.0.69 → stjames-0.0.70}/pyproject.toml RENAMED
@@ -1,6 +1,6 @@
1
1
  [project]
2
2
  name = "stjames"
3
- version = "0.0.69"
3
+ version = "0.0.70"
4
4
  description = "standardized JSON atom/molecule encoding scheme"
5
5
  readme = "README.md"
6
6
  requires-python = ">=3.11"
{stjames-0.0.69 → stjames-0.0.70}/stjames/opt_settings.py RENAMED
@@ -9,6 +9,7 @@ from .constraint import Constraint
9
9
  class OptimizationSettings(Base):
10
10
  max_steps: PositiveInt = 250
11
11
  transition_state: bool = False
12
+ recalc_hess_every: int = 0 # Recalculate the hessian every `n` steps (or never with 0)
12
13
 
13
14
  # when are we converged? (Hartree and Hartree/Å)
14
15
  max_gradient_threshold: PositiveFloat = 7e-4
{stjames-0.0.69 → stjames-0.0.70}/stjames/workflows/macropka.py RENAMED
@@ -79,6 +79,13 @@ class MacropKaWorkflow(SMILESWorkflow):
79
79
  ]
80
80
  ] = []
81
81
 
82
+ aqueous_solubility_by_pH: list[
83
+ tuple[
84
+ Annotated[float, AfterValidator(round_float(3))],
85
+ Annotated[float, AfterValidator(round_float(3))],
86
+ ]
87
+ ] = []
88
+
82
89
  @model_validator(mode="after")
83
90
  def check_weights(self) -> Self:
84
91
  for _, weights in self.microstate_weights_by_pH:
{stjames-0.0.69 → stjames-0.0.70/stjames.egg-info}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.4
2
2
  Name: stjames
3
- Version: 0.0.69
3
+ Version: 0.0.70
4
4
  Summary: standardized JSON atom/molecule encoding scheme
5
5
  Author-email: Corin Wagen <corin@rowansci.com>
6
6
  Project-URL: Homepage, https://github.com/rowansci/stjames
{stjames-0.0.69 → stjames-0.0.70}/LICENSE RENAMED
File without changes
{stjames-0.0.69 → stjames-0.0.70}/README.md RENAMED
File without changes
{stjames-0.0.69 → stjames-0.0.70}/setup.cfg RENAMED
File without changes
{stjames-0.0.69 → stjames-0.0.70}/stjames/__init__.py RENAMED
File without changes
{stjames-0.0.69 → stjames-0.0.70}/stjames/atom.py RENAMED
File without changes
{stjames-0.0.69 → stjames-0.0.70}/stjames/base.py RENAMED
File without changes
{stjames-0.0.69 → stjames-0.0.70}/stjames/basis_set.py RENAMED
File without changes
{stjames-0.0.69 → stjames-0.0.70}/stjames/constraint.py RENAMED
File without changes
{stjames-0.0.69 → stjames-0.0.70}/stjames/correction.py RENAMED
File without changes
{stjames-0.0.69 → stjames-0.0.70}/stjames/message.py RENAMED
File without changes
{stjames-0.0.69 → stjames-0.0.70}/stjames/method.py RENAMED
File without changes
{stjames-0.0.69 → stjames-0.0.70}/stjames/mode.py RENAMED
File without changes
{stjames-0.0.69 → stjames-0.0.70}/stjames/molecule.py RENAMED
File without changes
{stjames-0.0.69 → stjames-0.0.70}/stjames/pdb.py RENAMED
File without changes
{stjames-0.0.69 → stjames-0.0.70}/stjames/py.typed RENAMED
File without changes
{stjames-0.0.69 → stjames-0.0.70}/stjames/settings.py RENAMED
File without changes
{stjames-0.0.69 → stjames-0.0.70}/stjames/solvent.py RENAMED
File without changes
{stjames-0.0.69 → stjames-0.0.70}/stjames/status.py RENAMED
File without changes
{stjames-0.0.69 → stjames-0.0.70}/stjames/task.py RENAMED
File without changes
{stjames-0.0.69 → stjames-0.0.70}/stjames/types.py RENAMED
File without changes
{stjames-0.0.69 → stjames-0.0.70}/tests/test_pdb.py RENAMED
File without changes