stjames 0.0.114__tar.gz → 0.0.115__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 (83) hide show
  1. {stjames-0.0.114/stjames.egg-info → stjames-0.0.115}/PKG-INFO +1 -1
  2. {stjames-0.0.114 → stjames-0.0.115}/pyproject.toml +1 -1
  3. {stjames-0.0.114 → stjames-0.0.115}/stjames/workflows/pka.py +4 -4
  4. {stjames-0.0.114 → stjames-0.0.115/stjames.egg-info}/PKG-INFO +1 -1
  5. {stjames-0.0.114 → stjames-0.0.115}/LICENSE +0 -0
  6. {stjames-0.0.114 → stjames-0.0.115}/README.md +0 -0
  7. {stjames-0.0.114 → stjames-0.0.115}/setup.cfg +0 -0
  8. {stjames-0.0.114 → stjames-0.0.115}/stjames/__init__.py +0 -0
  9. {stjames-0.0.114 → stjames-0.0.115}/stjames/_deprecated_solvent_settings.py +0 -0
  10. {stjames-0.0.114 → stjames-0.0.115}/stjames/atom.py +0 -0
  11. {stjames-0.0.114 → stjames-0.0.115}/stjames/atomium_stjames/__init__.py +0 -0
  12. {stjames-0.0.114 → stjames-0.0.115}/stjames/atomium_stjames/data.py +0 -0
  13. {stjames-0.0.114 → stjames-0.0.115}/stjames/atomium_stjames/mmcif.py +0 -0
  14. {stjames-0.0.114 → stjames-0.0.115}/stjames/atomium_stjames/pdb.py +0 -0
  15. {stjames-0.0.114 → stjames-0.0.115}/stjames/atomium_stjames/utilities.py +0 -0
  16. {stjames-0.0.114 → stjames-0.0.115}/stjames/base.py +0 -0
  17. {stjames-0.0.114 → stjames-0.0.115}/stjames/basis_set.py +0 -0
  18. {stjames-0.0.114 → stjames-0.0.115}/stjames/calculation.py +0 -0
  19. {stjames-0.0.114 → stjames-0.0.115}/stjames/compute_settings.py +0 -0
  20. {stjames-0.0.114 → stjames-0.0.115}/stjames/constraint.py +0 -0
  21. {stjames-0.0.114 → stjames-0.0.115}/stjames/correction.py +0 -0
  22. {stjames-0.0.114 → stjames-0.0.115}/stjames/data/__init__.py +0 -0
  23. {stjames-0.0.114 → stjames-0.0.115}/stjames/data/bragg_radii.json +0 -0
  24. {stjames-0.0.114 → stjames-0.0.115}/stjames/data/elements.py +0 -0
  25. {stjames-0.0.114 → stjames-0.0.115}/stjames/data/isotopes.json +0 -0
  26. {stjames-0.0.114 → stjames-0.0.115}/stjames/data/nist_isotopes.json +0 -0
  27. {stjames-0.0.114 → stjames-0.0.115}/stjames/data/read_nist_isotopes.py +0 -0
  28. {stjames-0.0.114 → stjames-0.0.115}/stjames/data/symbol_element.json +0 -0
  29. {stjames-0.0.114 → stjames-0.0.115}/stjames/engine.py +0 -0
  30. {stjames-0.0.114 → stjames-0.0.115}/stjames/message.py +0 -0
  31. {stjames-0.0.114 → stjames-0.0.115}/stjames/method.py +0 -0
  32. {stjames-0.0.114 → stjames-0.0.115}/stjames/mode.py +0 -0
  33. {stjames-0.0.114 → stjames-0.0.115}/stjames/molecule.py +0 -0
  34. {stjames-0.0.114 → stjames-0.0.115}/stjames/opt_settings.py +0 -0
  35. {stjames-0.0.114 → stjames-0.0.115}/stjames/optimization/__init__.py +0 -0
  36. {stjames-0.0.114 → stjames-0.0.115}/stjames/optimization/freezing_string_method.py +0 -0
  37. {stjames-0.0.114 → stjames-0.0.115}/stjames/pdb.py +0 -0
  38. {stjames-0.0.114 → stjames-0.0.115}/stjames/periodic_cell.py +0 -0
  39. {stjames-0.0.114 → stjames-0.0.115}/stjames/py.typed +0 -0
  40. {stjames-0.0.114 → stjames-0.0.115}/stjames/scf_settings.py +0 -0
  41. {stjames-0.0.114 → stjames-0.0.115}/stjames/settings.py +0 -0
  42. {stjames-0.0.114 → stjames-0.0.115}/stjames/solvent.py +0 -0
  43. {stjames-0.0.114 → stjames-0.0.115}/stjames/status.py +0 -0
  44. {stjames-0.0.114 → stjames-0.0.115}/stjames/task.py +0 -0
  45. {stjames-0.0.114 → stjames-0.0.115}/stjames/thermochem_settings.py +0 -0
  46. {stjames-0.0.114 → stjames-0.0.115}/stjames/types.py +0 -0
  47. {stjames-0.0.114 → stjames-0.0.115}/stjames/workflows/__init__.py +0 -0
  48. {stjames-0.0.114 → stjames-0.0.115}/stjames/workflows/admet.py +0 -0
  49. {stjames-0.0.114 → stjames-0.0.115}/stjames/workflows/basic_calculation.py +0 -0
  50. {stjames-0.0.114 → stjames-0.0.115}/stjames/workflows/bde.py +0 -0
  51. {stjames-0.0.114 → stjames-0.0.115}/stjames/workflows/conformer.py +0 -0
  52. {stjames-0.0.114 → stjames-0.0.115}/stjames/workflows/conformer_search.py +0 -0
  53. {stjames-0.0.114 → stjames-0.0.115}/stjames/workflows/descriptors.py +0 -0
  54. {stjames-0.0.114 → stjames-0.0.115}/stjames/workflows/docking.py +0 -0
  55. {stjames-0.0.114 → stjames-0.0.115}/stjames/workflows/double_ended_ts_search.py +0 -0
  56. {stjames-0.0.114 → stjames-0.0.115}/stjames/workflows/electronic_properties.py +0 -0
  57. {stjames-0.0.114 → stjames-0.0.115}/stjames/workflows/fukui.py +0 -0
  58. {stjames-0.0.114 → stjames-0.0.115}/stjames/workflows/hydrogen_bond_basicity.py +0 -0
  59. {stjames-0.0.114 → stjames-0.0.115}/stjames/workflows/ion_mobility.py +0 -0
  60. {stjames-0.0.114 → stjames-0.0.115}/stjames/workflows/irc.py +0 -0
  61. {stjames-0.0.114 → stjames-0.0.115}/stjames/workflows/macropka.py +0 -0
  62. {stjames-0.0.114 → stjames-0.0.115}/stjames/workflows/molecular_dynamics.py +0 -0
  63. {stjames-0.0.114 → stjames-0.0.115}/stjames/workflows/multistage_opt.py +0 -0
  64. {stjames-0.0.114 → stjames-0.0.115}/stjames/workflows/nmr.py +0 -0
  65. {stjames-0.0.114 → stjames-0.0.115}/stjames/workflows/pose_analysis_md.py +0 -0
  66. {stjames-0.0.114 → stjames-0.0.115}/stjames/workflows/protein_cofolding.py +0 -0
  67. {stjames-0.0.114 → stjames-0.0.115}/stjames/workflows/redox_potential.py +0 -0
  68. {stjames-0.0.114 → stjames-0.0.115}/stjames/workflows/scan.py +0 -0
  69. {stjames-0.0.114 → stjames-0.0.115}/stjames/workflows/solubility.py +0 -0
  70. {stjames-0.0.114 → stjames-0.0.115}/stjames/workflows/spin_states.py +0 -0
  71. {stjames-0.0.114 → stjames-0.0.115}/stjames/workflows/strain.py +0 -0
  72. {stjames-0.0.114 → stjames-0.0.115}/stjames/workflows/tautomer.py +0 -0
  73. {stjames-0.0.114 → stjames-0.0.115}/stjames/workflows/workflow.py +0 -0
  74. {stjames-0.0.114 → stjames-0.0.115}/stjames.egg-info/SOURCES.txt +0 -0
  75. {stjames-0.0.114 → stjames-0.0.115}/stjames.egg-info/dependency_links.txt +0 -0
  76. {stjames-0.0.114 → stjames-0.0.115}/stjames.egg-info/requires.txt +0 -0
  77. {stjames-0.0.114 → stjames-0.0.115}/stjames.egg-info/top_level.txt +0 -0
  78. {stjames-0.0.114 → stjames-0.0.115}/tests/test_constraints.py +0 -0
  79. {stjames-0.0.114 → stjames-0.0.115}/tests/test_from_extxyz.py +0 -0
  80. {stjames-0.0.114 → stjames-0.0.115}/tests/test_molecule.py +0 -0
  81. {stjames-0.0.114 → stjames-0.0.115}/tests/test_pdb.py +0 -0
  82. {stjames-0.0.114 → stjames-0.0.115}/tests/test_rounding.py +0 -0
  83. {stjames-0.0.114 → stjames-0.0.115}/tests/test_settings.py +0 -0
{stjames-0.0.114/stjames.egg-info → stjames-0.0.115}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.4
2
2
  Name: stjames
3
- Version: 0.0.114
3
+ Version: 0.0.115
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-0.0.114 → stjames-0.0.115}/pyproject.toml RENAMED
@@ -1,6 +1,6 @@
1
1
  [project]
2
2
  name = "stjames"
3
- version = "0.0.114"
3
+ version = "0.0.115"
4
4
  description = "standardized JSON atom/molecule encoding scheme"
5
5
  readme = "README.md"
6
6
  requires-python = ">=3.11"
{stjames-0.0.114 → stjames-0.0.115}/stjames/workflows/pka.py RENAMED
@@ -10,7 +10,7 @@ from ..molecule import Molecule
10
10
  from ..solvent import Solvent
11
11
  from .workflow import DBCalculation, MoleculeWorkflow, SMILESWorkflow
12
12
 
13
- CHEMPROP_NEVOLIANUS2025_ALLOWED_SOLVENTS = {
13
+ CHEMPROP_NEVOLIANIS2025_ALLOWED_SOLVENTS = {
14
14
  Solvent.WATER,
15
15
  Solvent.DIMETHYLSULFOXIDE,
16
16
  Solvent.DIMETHYLFORMAMIDE,
@@ -24,7 +24,7 @@ CHEMPROP_NEVOLIANUS2025_ALLOWED_SOLVENTS = {
24
24
 
25
25
  class MicroscopicpKaMethod(LowercaseStrEnum):
26
26
  AIMNET2_WAGEN2024 = "aimnet2_wagen2024"
27
- CHEMPROP_NEVOLIANUS2025 = "chemprop_nevolianus2025"
27
+ CHEMPROP_NEVOLIANIS2025 = "chemprop_nevolianis2025"
28
28
 
29
29
 
30
30
  class pKaMicrostate(Base):
@@ -102,8 +102,8 @@ class pKaWorkflow(SMILESWorkflow, MoleculeWorkflow):
102
102
  case MicroscopicpKaMethod.AIMNET2_WAGEN2024:
103
103
  if self.solvent is not Solvent.WATER:
104
104
  raise ValueError(f"{self.microscopic_pka_method} only supports water")
105
- case MicroscopicpKaMethod.CHEMPROP_NEVOLIANUS2025:
106
- if self.solvent not in CHEMPROP_NEVOLIANUS2025_ALLOWED_SOLVENTS:
105
+ case MicroscopicpKaMethod.CHEMPROP_NEVOLIANIS2025:
106
+ if self.solvent not in CHEMPROP_NEVOLIANIS2025_ALLOWED_SOLVENTS:
107
107
  raise ValueError(f"Solvent `{self.solvent}` is not supported by method `{self.microscopic_pka_method}`.")
108
108
  if len(self.protonate_atoms) or len(self.deprotonate_atoms):
109
109
  raise ValueError(f"Method `{self.microscopic_pka_method}` does not support selecting atoms by number.")
{stjames-0.0.114 → stjames-0.0.115/stjames.egg-info}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.4
2
2
  Name: stjames
3
- Version: 0.0.114
3
+ Version: 0.0.115
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-0.0.114 → stjames-0.0.115}/LICENSE RENAMED
File without changes
{stjames-0.0.114 → stjames-0.0.115}/README.md RENAMED
File without changes
{stjames-0.0.114 → stjames-0.0.115}/setup.cfg RENAMED
File without changes
{stjames-0.0.114 → stjames-0.0.115}/stjames/__init__.py RENAMED
File without changes
{stjames-0.0.114 → stjames-0.0.115}/stjames/atom.py RENAMED
File without changes
{stjames-0.0.114 → stjames-0.0.115}/stjames/base.py RENAMED
File without changes
{stjames-0.0.114 → stjames-0.0.115}/stjames/engine.py RENAMED
File without changes
{stjames-0.0.114 → stjames-0.0.115}/stjames/message.py RENAMED
File without changes
{stjames-0.0.114 → stjames-0.0.115}/stjames/method.py RENAMED
File without changes
{stjames-0.0.114 → stjames-0.0.115}/stjames/mode.py RENAMED
File without changes
{stjames-0.0.114 → stjames-0.0.115}/stjames/molecule.py RENAMED
File without changes
{stjames-0.0.114 → stjames-0.0.115}/stjames/pdb.py RENAMED
File without changes
{stjames-0.0.114 → stjames-0.0.115}/stjames/py.typed RENAMED
File without changes
{stjames-0.0.114 → stjames-0.0.115}/stjames/settings.py RENAMED
File without changes
{stjames-0.0.114 → stjames-0.0.115}/stjames/solvent.py RENAMED
File without changes
{stjames-0.0.114 → stjames-0.0.115}/stjames/status.py RENAMED
File without changes
{stjames-0.0.114 → stjames-0.0.115}/stjames/task.py RENAMED
File without changes
{stjames-0.0.114 → stjames-0.0.115}/stjames/types.py RENAMED
File without changes
{stjames-0.0.114 → stjames-0.0.115}/tests/test_pdb.py RENAMED
File without changes