stjames 0.0.104__tar.gz → 0.0.105__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 (82) hide show
  1. {stjames-0.0.104/stjames.egg-info → stjames-0.0.105}/PKG-INFO +1 -1
  2. {stjames-0.0.104 → stjames-0.0.105}/pyproject.toml +1 -1
  3. {stjames-0.0.104 → stjames-0.0.105}/stjames/workflows/nmr.py +2 -2
  4. {stjames-0.0.104 → stjames-0.0.105}/stjames/workflows/solubility.py +2 -1
  5. {stjames-0.0.104 → stjames-0.0.105/stjames.egg-info}/PKG-INFO +1 -1
  6. {stjames-0.0.104 → stjames-0.0.105}/LICENSE +0 -0
  7. {stjames-0.0.104 → stjames-0.0.105}/README.md +0 -0
  8. {stjames-0.0.104 → stjames-0.0.105}/setup.cfg +0 -0
  9. {stjames-0.0.104 → stjames-0.0.105}/stjames/__init__.py +0 -0
  10. {stjames-0.0.104 → stjames-0.0.105}/stjames/_deprecated_solvent_settings.py +0 -0
  11. {stjames-0.0.104 → stjames-0.0.105}/stjames/atom.py +0 -0
  12. {stjames-0.0.104 → stjames-0.0.105}/stjames/atomium_stjames/__init__.py +0 -0
  13. {stjames-0.0.104 → stjames-0.0.105}/stjames/atomium_stjames/data.py +0 -0
  14. {stjames-0.0.104 → stjames-0.0.105}/stjames/atomium_stjames/mmcif.py +0 -0
  15. {stjames-0.0.104 → stjames-0.0.105}/stjames/atomium_stjames/pdb.py +0 -0
  16. {stjames-0.0.104 → stjames-0.0.105}/stjames/atomium_stjames/utilities.py +0 -0
  17. {stjames-0.0.104 → stjames-0.0.105}/stjames/base.py +0 -0
  18. {stjames-0.0.104 → stjames-0.0.105}/stjames/basis_set.py +0 -0
  19. {stjames-0.0.104 → stjames-0.0.105}/stjames/calculation.py +0 -0
  20. {stjames-0.0.104 → stjames-0.0.105}/stjames/compute_settings.py +0 -0
  21. {stjames-0.0.104 → stjames-0.0.105}/stjames/constraint.py +0 -0
  22. {stjames-0.0.104 → stjames-0.0.105}/stjames/correction.py +0 -0
  23. {stjames-0.0.104 → stjames-0.0.105}/stjames/data/__init__.py +0 -0
  24. {stjames-0.0.104 → stjames-0.0.105}/stjames/data/bragg_radii.json +0 -0
  25. {stjames-0.0.104 → stjames-0.0.105}/stjames/data/elements.py +0 -0
  26. {stjames-0.0.104 → stjames-0.0.105}/stjames/data/isotopes.json +0 -0
  27. {stjames-0.0.104 → stjames-0.0.105}/stjames/data/nist_isotopes.json +0 -0
  28. {stjames-0.0.104 → stjames-0.0.105}/stjames/data/read_nist_isotopes.py +0 -0
  29. {stjames-0.0.104 → stjames-0.0.105}/stjames/data/symbol_element.json +0 -0
  30. {stjames-0.0.104 → stjames-0.0.105}/stjames/engine.py +0 -0
  31. {stjames-0.0.104 → stjames-0.0.105}/stjames/message.py +0 -0
  32. {stjames-0.0.104 → stjames-0.0.105}/stjames/method.py +0 -0
  33. {stjames-0.0.104 → stjames-0.0.105}/stjames/mode.py +0 -0
  34. {stjames-0.0.104 → stjames-0.0.105}/stjames/molecule.py +0 -0
  35. {stjames-0.0.104 → stjames-0.0.105}/stjames/opt_settings.py +0 -0
  36. {stjames-0.0.104 → stjames-0.0.105}/stjames/optimization/__init__.py +0 -0
  37. {stjames-0.0.104 → stjames-0.0.105}/stjames/optimization/freezing_string_method.py +0 -0
  38. {stjames-0.0.104 → stjames-0.0.105}/stjames/pdb.py +0 -0
  39. {stjames-0.0.104 → stjames-0.0.105}/stjames/periodic_cell.py +0 -0
  40. {stjames-0.0.104 → stjames-0.0.105}/stjames/py.typed +0 -0
  41. {stjames-0.0.104 → stjames-0.0.105}/stjames/scf_settings.py +0 -0
  42. {stjames-0.0.104 → stjames-0.0.105}/stjames/settings.py +0 -0
  43. {stjames-0.0.104 → stjames-0.0.105}/stjames/solvent.py +0 -0
  44. {stjames-0.0.104 → stjames-0.0.105}/stjames/status.py +0 -0
  45. {stjames-0.0.104 → stjames-0.0.105}/stjames/task.py +0 -0
  46. {stjames-0.0.104 → stjames-0.0.105}/stjames/thermochem_settings.py +0 -0
  47. {stjames-0.0.104 → stjames-0.0.105}/stjames/types.py +0 -0
  48. {stjames-0.0.104 → stjames-0.0.105}/stjames/workflows/__init__.py +0 -0
  49. {stjames-0.0.104 → stjames-0.0.105}/stjames/workflows/admet.py +0 -0
  50. {stjames-0.0.104 → stjames-0.0.105}/stjames/workflows/basic_calculation.py +0 -0
  51. {stjames-0.0.104 → stjames-0.0.105}/stjames/workflows/bde.py +0 -0
  52. {stjames-0.0.104 → stjames-0.0.105}/stjames/workflows/conformer.py +0 -0
  53. {stjames-0.0.104 → stjames-0.0.105}/stjames/workflows/conformer_search.py +0 -0
  54. {stjames-0.0.104 → stjames-0.0.105}/stjames/workflows/descriptors.py +0 -0
  55. {stjames-0.0.104 → stjames-0.0.105}/stjames/workflows/docking.py +0 -0
  56. {stjames-0.0.104 → stjames-0.0.105}/stjames/workflows/double_ended_ts_search.py +0 -0
  57. {stjames-0.0.104 → stjames-0.0.105}/stjames/workflows/electronic_properties.py +0 -0
  58. {stjames-0.0.104 → stjames-0.0.105}/stjames/workflows/fukui.py +0 -0
  59. {stjames-0.0.104 → stjames-0.0.105}/stjames/workflows/hydrogen_bond_basicity.py +0 -0
  60. {stjames-0.0.104 → stjames-0.0.105}/stjames/workflows/ion_mobility.py +0 -0
  61. {stjames-0.0.104 → stjames-0.0.105}/stjames/workflows/irc.py +0 -0
  62. {stjames-0.0.104 → stjames-0.0.105}/stjames/workflows/macropka.py +0 -0
  63. {stjames-0.0.104 → stjames-0.0.105}/stjames/workflows/molecular_dynamics.py +0 -0
  64. {stjames-0.0.104 → stjames-0.0.105}/stjames/workflows/multistage_opt.py +0 -0
  65. {stjames-0.0.104 → stjames-0.0.105}/stjames/workflows/pka.py +0 -0
  66. {stjames-0.0.104 → stjames-0.0.105}/stjames/workflows/pose_analysis_md.py +0 -0
  67. {stjames-0.0.104 → stjames-0.0.105}/stjames/workflows/protein_cofolding.py +0 -0
  68. {stjames-0.0.104 → stjames-0.0.105}/stjames/workflows/redox_potential.py +0 -0
  69. {stjames-0.0.104 → stjames-0.0.105}/stjames/workflows/scan.py +0 -0
  70. {stjames-0.0.104 → stjames-0.0.105}/stjames/workflows/spin_states.py +0 -0
  71. {stjames-0.0.104 → stjames-0.0.105}/stjames/workflows/tautomer.py +0 -0
  72. {stjames-0.0.104 → stjames-0.0.105}/stjames/workflows/workflow.py +0 -0
  73. {stjames-0.0.104 → stjames-0.0.105}/stjames.egg-info/SOURCES.txt +0 -0
  74. {stjames-0.0.104 → stjames-0.0.105}/stjames.egg-info/dependency_links.txt +0 -0
  75. {stjames-0.0.104 → stjames-0.0.105}/stjames.egg-info/requires.txt +0 -0
  76. {stjames-0.0.104 → stjames-0.0.105}/stjames.egg-info/top_level.txt +0 -0
  77. {stjames-0.0.104 → stjames-0.0.105}/tests/test_constraints.py +0 -0
  78. {stjames-0.0.104 → stjames-0.0.105}/tests/test_from_extxyz.py +0 -0
  79. {stjames-0.0.104 → stjames-0.0.105}/tests/test_molecule.py +0 -0
  80. {stjames-0.0.104 → stjames-0.0.105}/tests/test_pdb.py +0 -0
  81. {stjames-0.0.104 → stjames-0.0.105}/tests/test_rounding.py +0 -0
  82. {stjames-0.0.104 → stjames-0.0.105}/tests/test_settings.py +0 -0
{stjames-0.0.104/stjames.egg-info → stjames-0.0.105}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.4
2
2
  Name: stjames
3
- Version: 0.0.104
3
+ Version: 0.0.105
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-0.0.104 → stjames-0.0.105}/pyproject.toml RENAMED
@@ -1,6 +1,6 @@
1
1
  [project]
2
2
  name = "stjames"
3
- version = "0.0.104"
3
+ version = "0.0.105"
4
4
  description = "standardized JSON atom/molecule encoding scheme"
5
5
  readme = "README.md"
6
6
  requires-python = ">=3.11"
{stjames-0.0.104 → stjames-0.0.105}/stjames/workflows/nmr.py RENAMED
@@ -9,7 +9,7 @@ from ..mode import Mode
9
9
  from ..settings import Settings
10
10
  from ..solvent import Solvent
11
11
  from ..types import UUID, round_list
12
- from .conformer_search import ConformerGenSettings, iMTDSettings
12
+ from .conformer_search import ConformerGenSettingsUnion, iMTDSettings
13
13
  from .multistage_opt import MultiStageOptSettings
14
14
  from .workflow import MoleculeWorkflow
15
15
 
@@ -58,7 +58,7 @@ class NMRSpectroscopyWorkflow(MoleculeWorkflow):
58
58
  nmr_method: NMRMethod = NMRMethod.MAGNETZERO
59
59
  solvent: Solvent = Solvent.CHLOROFORM
60
60
 
61
- conf_gen_settings: ConformerGenSettings | None = iMTDSettings(mode="careful")
61
+ conf_gen_settings: ConformerGenSettingsUnion | None = iMTDSettings(mode="careful")
62
62
  multistage_opt_settings: MultiStageOptSettings | None = MultiStageOptSettings(
63
63
  mode=Mode.MANUAL,
64
64
  optimization_settings=[Settings(method="aimnet2_wb97md3", tasks=["optimize"])],
{stjames-0.0.104 → stjames-0.0.105}/stjames/workflows/solubility.py RENAMED
@@ -41,6 +41,7 @@ class SolubilityWorkflow(SMILESWorkflow):
41
41
 
42
42
  Inputs:
43
43
  :param initial_smiles: SMILES string of the molecule
44
+ :param solubility_method: model used for solubility prediction
44
45
  :param solvents: list of solvent SMILES strings
45
46
  :param temperatures: temperatures in K
46
47
 
@@ -48,8 +49,8 @@ class SolubilityWorkflow(SMILESWorkflow):
48
49
  :param solubilities: {solvent: SolubilityResult}
49
50
  """
50
51
 
51
- solubility_method: SolubilityMethod = SolubilityMethod.FASTSOLV
52
52
  initial_smiles: str
53
+ solubility_method: SolubilityMethod = SolubilityMethod.FASTSOLV
53
54
  solvents: list[str] = ["O"]
54
55
  temperatures: list[float] = [298.15]
55
56
 
{stjames-0.0.104 → stjames-0.0.105/stjames.egg-info}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.4
2
2
  Name: stjames
3
- Version: 0.0.104
3
+ Version: 0.0.105
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-0.0.104 → stjames-0.0.105}/LICENSE RENAMED
File without changes
{stjames-0.0.104 → stjames-0.0.105}/README.md RENAMED
File without changes
{stjames-0.0.104 → stjames-0.0.105}/setup.cfg RENAMED
File without changes
{stjames-0.0.104 → stjames-0.0.105}/stjames/__init__.py RENAMED
File without changes
{stjames-0.0.104 → stjames-0.0.105}/stjames/atom.py RENAMED
File without changes
{stjames-0.0.104 → stjames-0.0.105}/stjames/base.py RENAMED
File without changes
{stjames-0.0.104 → stjames-0.0.105}/stjames/engine.py RENAMED
File without changes
{stjames-0.0.104 → stjames-0.0.105}/stjames/message.py RENAMED
File without changes
{stjames-0.0.104 → stjames-0.0.105}/stjames/method.py RENAMED
File without changes
{stjames-0.0.104 → stjames-0.0.105}/stjames/mode.py RENAMED
File without changes
{stjames-0.0.104 → stjames-0.0.105}/stjames/molecule.py RENAMED
File without changes
{stjames-0.0.104 → stjames-0.0.105}/stjames/pdb.py RENAMED
File without changes
{stjames-0.0.104 → stjames-0.0.105}/stjames/py.typed RENAMED
File without changes
{stjames-0.0.104 → stjames-0.0.105}/stjames/settings.py RENAMED
File without changes
{stjames-0.0.104 → stjames-0.0.105}/stjames/solvent.py RENAMED
File without changes
{stjames-0.0.104 → stjames-0.0.105}/stjames/status.py RENAMED
File without changes
{stjames-0.0.104 → stjames-0.0.105}/stjames/task.py RENAMED
File without changes
{stjames-0.0.104 → stjames-0.0.105}/stjames/types.py RENAMED
File without changes
{stjames-0.0.104 → stjames-0.0.105}/tests/test_pdb.py RENAMED
File without changes