stjames 0.0.36__tar.gz → 0.0.37__tar.gz

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Files changed (41) hide show
  1. {stjames-0.0.36/stjames.egg-info → stjames-0.0.37}/PKG-INFO +1 -1
  2. {stjames-0.0.36 → stjames-0.0.37}/pyproject.toml +1 -1
  3. {stjames-0.0.36 → stjames-0.0.37}/stjames/workflows/conformer.py +19 -6
  4. {stjames-0.0.36 → stjames-0.0.37/stjames.egg-info}/PKG-INFO +1 -1
  5. {stjames-0.0.36 → stjames-0.0.37}/LICENSE +0 -0
  6. {stjames-0.0.36 → stjames-0.0.37}/README.md +0 -0
  7. {stjames-0.0.36 → stjames-0.0.37}/setup.cfg +0 -0
  8. {stjames-0.0.36 → stjames-0.0.37}/stjames/__init__.py +0 -0
  9. {stjames-0.0.36 → stjames-0.0.37}/stjames/_deprecated_solvent_settings.py +0 -0
  10. {stjames-0.0.36 → stjames-0.0.37}/stjames/base.py +0 -0
  11. {stjames-0.0.36 → stjames-0.0.37}/stjames/basis_set.py +0 -0
  12. {stjames-0.0.36 → stjames-0.0.37}/stjames/calculation.py +0 -0
  13. {stjames-0.0.36 → stjames-0.0.37}/stjames/constraint.py +0 -0
  14. {stjames-0.0.36 → stjames-0.0.37}/stjames/correction.py +0 -0
  15. {stjames-0.0.36 → stjames-0.0.37}/stjames/diis_settings.py +0 -0
  16. {stjames-0.0.36 → stjames-0.0.37}/stjames/grid_settings.py +0 -0
  17. {stjames-0.0.36 → stjames-0.0.37}/stjames/int_settings.py +0 -0
  18. {stjames-0.0.36 → stjames-0.0.37}/stjames/message.py +0 -0
  19. {stjames-0.0.36 → stjames-0.0.37}/stjames/method.py +0 -0
  20. {stjames-0.0.36 → stjames-0.0.37}/stjames/mode.py +0 -0
  21. {stjames-0.0.36 → stjames-0.0.37}/stjames/molecule.py +0 -0
  22. {stjames-0.0.36 → stjames-0.0.37}/stjames/opt_settings.py +0 -0
  23. {stjames-0.0.36 → stjames-0.0.37}/stjames/py.typed +0 -0
  24. {stjames-0.0.36 → stjames-0.0.37}/stjames/scf_settings.py +0 -0
  25. {stjames-0.0.36 → stjames-0.0.37}/stjames/settings.py +0 -0
  26. {stjames-0.0.36 → stjames-0.0.37}/stjames/solvent.py +0 -0
  27. {stjames-0.0.36 → stjames-0.0.37}/stjames/status.py +0 -0
  28. {stjames-0.0.36 → stjames-0.0.37}/stjames/task.py +0 -0
  29. {stjames-0.0.36 → stjames-0.0.37}/stjames/thermochem_settings.py +0 -0
  30. {stjames-0.0.36 → stjames-0.0.37}/stjames/workflows/__init__.py +0 -0
  31. {stjames-0.0.36 → stjames-0.0.37}/stjames/workflows/descriptors.py +0 -0
  32. {stjames-0.0.36 → stjames-0.0.37}/stjames/workflows/fukui.py +0 -0
  33. {stjames-0.0.36 → stjames-0.0.37}/stjames/workflows/pka.py +0 -0
  34. {stjames-0.0.36 → stjames-0.0.37}/stjames/workflows/redox_potential.py +0 -0
  35. {stjames-0.0.36 → stjames-0.0.37}/stjames/workflows/scan.py +0 -0
  36. {stjames-0.0.36 → stjames-0.0.37}/stjames/workflows/tautomer.py +0 -0
  37. {stjames-0.0.36 → stjames-0.0.37}/stjames/workflows/workflow.py +0 -0
  38. {stjames-0.0.36 → stjames-0.0.37}/stjames.egg-info/SOURCES.txt +0 -0
  39. {stjames-0.0.36 → stjames-0.0.37}/stjames.egg-info/dependency_links.txt +0 -0
  40. {stjames-0.0.36 → stjames-0.0.37}/stjames.egg-info/requires.txt +0 -0
  41. {stjames-0.0.36 → stjames-0.0.37}/stjames.egg-info/top_level.txt +0 -0
{stjames-0.0.36/stjames.egg-info → stjames-0.0.37}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.1
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  Name: stjames
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- Version: 0.0.36
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+ Version: 0.0.37
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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-0.0.36 → stjames-0.0.37}/pyproject.toml RENAMED
@@ -1,6 +1,6 @@
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  [project]
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  name = "stjames"
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- version = "0.0.36"
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+ version = "0.0.37"
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  description = "standardized JSON atom/molecule encoding scheme"
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  readme = "README.md"
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  requires-python = ">=3.8"
{stjames-0.0.36 → stjames-0.0.37}/stjames/workflows/conformer.py RENAMED
@@ -45,12 +45,18 @@ class ConformerWorkflow(Workflow):
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  conformers: list[Conformer] = []
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  def model_post_init(self, __context: Any) -> None:
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- self.settings = csearch_settings_by_mode(self.mode)
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+ self.settings = csearch_settings_by_mode(self.mode, self.settings)
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- def csearch_settings_by_mode(mode: Mode) -> ConformerSettings:
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+ def csearch_settings_by_mode(mode: Mode, old_settings: Optional[ConformerSettings]) -> ConformerSettings:
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+ if mode == Mode.MANUAL:
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+ assert old_settings is not None
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+ return old_settings
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+
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+ settings: ConformerSettings
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+
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  if mode == Mode.METICULOUS:
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- return CrestConformerSettings(
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+ settings = CrestConformerSettings(
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  gfn=2,
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  flags="--ewin 15 --noreftopo",
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  max_energy=10,
@@ -59,7 +65,7 @@ def csearch_settings_by_mode(mode: Mode) -> ConformerSettings:
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  )
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  elif mode == Mode.CAREFUL:
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- return CrestConformerSettings(
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+ settings = CrestConformerSettings(
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  gfn="ff",
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  flags="--quick --ewin 10 --noreftopo",
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  num_confs_considered=150,
@@ -67,7 +73,7 @@ def csearch_settings_by_mode(mode: Mode) -> ConformerSettings:
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  )
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  elif mode == Mode.RAPID or Mode.AUTO:
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- return RdkitConformerSettings(
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+ settings = RdkitConformerSettings(
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  num_initial_confs=300,
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  max_mmff_energy=15,
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  num_confs_considered=100,
@@ -75,7 +81,7 @@ def csearch_settings_by_mode(mode: Mode) -> ConformerSettings:
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  )
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  elif mode == Mode.RECKLESS:
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- return RdkitConformerSettings(
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+ settings = RdkitConformerSettings(
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  num_initial_confs=200,
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  max_mmff_energy=10,
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  num_confs_considered=50,
@@ -85,3 +91,10 @@ def csearch_settings_by_mode(mode: Mode) -> ConformerSettings:
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  else:
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  raise ValueError(f"invalid mode ``{mode.value}`` for conformer settings")
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+
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+ if old_settings is not None:
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+ settings.final_method = old_settings.final_method
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+ settings.solvent = old_settings.solvent
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+ settings.constraints = old_settings.constraints
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+
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+ return settings
{stjames-0.0.36 → stjames-0.0.37/stjames.egg-info}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.1
2
2
  Name: stjames
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- Version: 0.0.36
3
+ Version: 0.0.37
4
4
  Summary: standardized JSON atom/molecule encoding scheme
5
5
  Author-email: Corin Wagen <corin@rowansci.com>
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  Project-URL: Homepage, https://github.com/rowansci/stjames
{stjames-0.0.36 → stjames-0.0.37}/LICENSE RENAMED
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{stjames-0.0.36 → stjames-0.0.37}/README.md RENAMED
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{stjames-0.0.36 → stjames-0.0.37}/setup.cfg RENAMED
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{stjames-0.0.36 → stjames-0.0.37}/stjames/__init__.py RENAMED
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{stjames-0.0.36 → stjames-0.0.37}/stjames/base.py RENAMED
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{stjames-0.0.36 → stjames-0.0.37}/stjames/basis_set.py RENAMED
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{stjames-0.0.36 → stjames-0.0.37}/stjames/constraint.py RENAMED
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{stjames-0.0.36 → stjames-0.0.37}/stjames/correction.py RENAMED
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{stjames-0.0.36 → stjames-0.0.37}/stjames/message.py RENAMED
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{stjames-0.0.36 → stjames-0.0.37}/stjames/method.py RENAMED
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{stjames-0.0.36 → stjames-0.0.37}/stjames/mode.py RENAMED
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{stjames-0.0.36 → stjames-0.0.37}/stjames/molecule.py RENAMED
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{stjames-0.0.36 → stjames-0.0.37}/stjames/py.typed RENAMED
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{stjames-0.0.36 → stjames-0.0.37}/stjames/settings.py RENAMED
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{stjames-0.0.36 → stjames-0.0.37}/stjames/solvent.py RENAMED
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{stjames-0.0.36 → stjames-0.0.37}/stjames/status.py RENAMED
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{stjames-0.0.36 → stjames-0.0.37}/stjames/task.py RENAMED
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