stjames 0.0.39__tar.gz → 0.0.40__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 (41) hide show
  1. {stjames-0.0.39/stjames.egg-info → stjames-0.0.40}/PKG-INFO +1 -1
  2. {stjames-0.0.39 → stjames-0.0.40}/pyproject.toml +1 -1
  3. {stjames-0.0.39 → stjames-0.0.40}/stjames/molecule.py +3 -0
  4. {stjames-0.0.39 → stjames-0.0.40}/stjames/settings.py +1 -1
  5. {stjames-0.0.39 → stjames-0.0.40}/stjames/solvent.py +1 -0
  6. {stjames-0.0.39 → stjames-0.0.40}/stjames/workflows/conformer.py +1 -0
  7. {stjames-0.0.39 → stjames-0.0.40/stjames.egg-info}/PKG-INFO +1 -1
  8. {stjames-0.0.39 → stjames-0.0.40}/LICENSE +0 -0
  9. {stjames-0.0.39 → stjames-0.0.40}/README.md +0 -0
  10. {stjames-0.0.39 → stjames-0.0.40}/setup.cfg +0 -0
  11. {stjames-0.0.39 → stjames-0.0.40}/stjames/__init__.py +0 -0
  12. {stjames-0.0.39 → stjames-0.0.40}/stjames/_deprecated_solvent_settings.py +0 -0
  13. {stjames-0.0.39 → stjames-0.0.40}/stjames/base.py +0 -0
  14. {stjames-0.0.39 → stjames-0.0.40}/stjames/basis_set.py +0 -0
  15. {stjames-0.0.39 → stjames-0.0.40}/stjames/calculation.py +0 -0
  16. {stjames-0.0.39 → stjames-0.0.40}/stjames/constraint.py +0 -0
  17. {stjames-0.0.39 → stjames-0.0.40}/stjames/correction.py +0 -0
  18. {stjames-0.0.39 → stjames-0.0.40}/stjames/diis_settings.py +0 -0
  19. {stjames-0.0.39 → stjames-0.0.40}/stjames/grid_settings.py +0 -0
  20. {stjames-0.0.39 → stjames-0.0.40}/stjames/int_settings.py +0 -0
  21. {stjames-0.0.39 → stjames-0.0.40}/stjames/message.py +0 -0
  22. {stjames-0.0.39 → stjames-0.0.40}/stjames/method.py +0 -0
  23. {stjames-0.0.39 → stjames-0.0.40}/stjames/mode.py +0 -0
  24. {stjames-0.0.39 → stjames-0.0.40}/stjames/opt_settings.py +0 -0
  25. {stjames-0.0.39 → stjames-0.0.40}/stjames/py.typed +0 -0
  26. {stjames-0.0.39 → stjames-0.0.40}/stjames/scf_settings.py +0 -0
  27. {stjames-0.0.39 → stjames-0.0.40}/stjames/status.py +0 -0
  28. {stjames-0.0.39 → stjames-0.0.40}/stjames/task.py +0 -0
  29. {stjames-0.0.39 → stjames-0.0.40}/stjames/thermochem_settings.py +0 -0
  30. {stjames-0.0.39 → stjames-0.0.40}/stjames/workflows/__init__.py +0 -0
  31. {stjames-0.0.39 → stjames-0.0.40}/stjames/workflows/descriptors.py +0 -0
  32. {stjames-0.0.39 → stjames-0.0.40}/stjames/workflows/fukui.py +0 -0
  33. {stjames-0.0.39 → stjames-0.0.40}/stjames/workflows/pka.py +0 -0
  34. {stjames-0.0.39 → stjames-0.0.40}/stjames/workflows/redox_potential.py +0 -0
  35. {stjames-0.0.39 → stjames-0.0.40}/stjames/workflows/scan.py +0 -0
  36. {stjames-0.0.39 → stjames-0.0.40}/stjames/workflows/tautomer.py +0 -0
  37. {stjames-0.0.39 → stjames-0.0.40}/stjames/workflows/workflow.py +0 -0
  38. {stjames-0.0.39 → stjames-0.0.40}/stjames.egg-info/SOURCES.txt +0 -0
  39. {stjames-0.0.39 → stjames-0.0.40}/stjames.egg-info/dependency_links.txt +0 -0
  40. {stjames-0.0.39 → stjames-0.0.40}/stjames.egg-info/requires.txt +0 -0
  41. {stjames-0.0.39 → stjames-0.0.40}/stjames.egg-info/top_level.txt +0 -0
{stjames-0.0.39/stjames.egg-info → stjames-0.0.40}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.1
2
2
  Name: stjames
3
- Version: 0.0.39
3
+ Version: 0.0.40
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-0.0.39 → stjames-0.0.40}/pyproject.toml RENAMED
@@ -1,6 +1,6 @@
1
1
  [project]
2
2
  name = "stjames"
3
- version = "0.0.39"
3
+ version = "0.0.40"
4
4
  description = "standardized JSON atom/molecule encoding scheme"
5
5
  readme = "README.md"
6
6
  requires-python = ">=3.8"
{stjames-0.0.39 → stjames-0.0.40}/stjames/molecule.py RENAMED
@@ -46,6 +46,9 @@ class Molecule(Base):
46
46
  thermal_enthalpy_corr: Optional[float] = None
47
47
  thermal_free_energy_corr: Optional[float] = None
48
48
 
49
+ def __len__(self) -> int:
50
+ return len(self.atoms)
51
+
49
52
  @property
50
53
  def coordinates(self) -> list[list[float]]:
51
54
  return [a.position for a in self.atoms]
{stjames-0.0.39 → stjames-0.0.40}/stjames/settings.py RENAMED
@@ -105,7 +105,7 @@ class Settings(Base):
105
105
  @classmethod
106
106
  def remove_empty_string(cls, v: list[T]) -> list[T]:
107
107
  """Remove empty string values."""
108
- return [c for c in v if c]
108
+ return [c for c in v if c] if v is not None else v
109
109
 
110
110
 
111
111
  def _assign_settings_by_mode(settings: Settings) -> None:
{stjames-0.0.39 → stjames-0.0.40}/stjames/solvent.py RENAMED
@@ -35,6 +35,7 @@ class SolventModel(LowercaseStrEnum):
35
35
  CPCM = "cpcm"
36
36
  ALPB = "alpb"
37
37
  COSMO = "cosmo"
38
+ CPCMX = "cpcmx"
38
39
 
39
40
 
40
41
  class SolventSettings(Base):
{stjames-0.0.39 → stjames-0.0.40}/stjames/workflows/conformer.py RENAMED
@@ -13,6 +13,7 @@ class ConformerSettings(Base):
13
13
  num_confs_taken: int = 50
14
14
  rmsd_cutoff: float = 0.1
15
15
 
16
+ transition_state: bool = False
16
17
  final_method: Method = Method.AIMNET2_WB97MD3
17
18
  solvent: Optional[Solvent] = Solvent.WATER
18
19
  max_energy: float = 5
{stjames-0.0.39 → stjames-0.0.40/stjames.egg-info}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.1
2
2
  Name: stjames
3
- Version: 0.0.39
3
+ Version: 0.0.40
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-0.0.39 → stjames-0.0.40}/LICENSE RENAMED
File without changes
{stjames-0.0.39 → stjames-0.0.40}/README.md RENAMED
File without changes
{stjames-0.0.39 → stjames-0.0.40}/setup.cfg RENAMED
File without changes
{stjames-0.0.39 → stjames-0.0.40}/stjames/__init__.py RENAMED
File without changes
{stjames-0.0.39 → stjames-0.0.40}/stjames/base.py RENAMED
File without changes
{stjames-0.0.39 → stjames-0.0.40}/stjames/basis_set.py RENAMED
File without changes
{stjames-0.0.39 → stjames-0.0.40}/stjames/constraint.py RENAMED
File without changes
{stjames-0.0.39 → stjames-0.0.40}/stjames/correction.py RENAMED
File without changes
{stjames-0.0.39 → stjames-0.0.40}/stjames/message.py RENAMED
File without changes
{stjames-0.0.39 → stjames-0.0.40}/stjames/method.py RENAMED
File without changes
{stjames-0.0.39 → stjames-0.0.40}/stjames/mode.py RENAMED
File without changes
{stjames-0.0.39 → stjames-0.0.40}/stjames/py.typed RENAMED
File without changes
{stjames-0.0.39 → stjames-0.0.40}/stjames/status.py RENAMED
File without changes
{stjames-0.0.39 → stjames-0.0.40}/stjames/task.py RENAMED
File without changes