stjames 0.0.30__tar.gz → 0.0.32__tar.gz

{stjames-0.0.30/stjames.egg-info → stjames-0.0.32}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: stjames
-Version: 0.0.30
+Version: 0.0.32
 Summary: standardized JSON atom/molecule encoding scheme
 Author-email: Corin Wagen <corin@rowansci.com>
 Project-URL: Homepage, https://github.com/rowansci/stjames

{stjames-0.0.30 → stjames-0.0.32}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "stjames"
-version = "0.0.30"
+version = "0.0.32"
 description = "standardized JSON atom/molecule encoding scheme"
 readme = "README.md"
 requires-python = ">=3.8"

{stjames-0.0.30 → stjames-0.0.32}/stjames/__init__.py

@@ -8,7 +8,6 @@ from .scf_settings import *
 from .int_settings import *
 from .opt_settings import *
 from .diis_settings import *
-from .solvent_settings import *
 from .thermochem_settings import *
 from .grid_settings import *
 from .settings import *

{stjames-0.0.30 → stjames-0.0.32}/stjames/workflows/conformer.py

@@ -18,19 +18,12 @@ class ConformerSettings(Base):
 
 
 class RdkitConformerSettings(ConformerSettings):
-    csearch_program: str = "rdkit"
-
     num_initial_confs: int = 100
     max_mmff_energy: float = 10
     max_mmff_iterations: int = 500
-    num_confs_considered: float = 10
-    num_confs_taken: float = 3
-    rmsd_cutoff: float = 0.1
 
 
 class CrestConformerSettings(ConformerSettings):
-    csearch_program: str = "crest"
-
     flags: str = "--quick --ewin 10"
     gfn: int | str = "ff"
 
@@ -44,6 +37,7 @@ class Conformer(Base):
 
 
 class ConformerWorkflow(Workflow):
+    mode: Mode = Mode.RAPID
     settings: ConformerSettings = ConformerSettings()
     conformers: list[Conformer] = []
 
@@ -69,7 +63,7 @@ def csearch_settings_by_mode(mode: Mode) -> ConformerSettings:
             num_confs_taken=50,
         )
 
-    elif mode == Mode.RAPID:
+    elif mode == Mode.RAPID or Mode.AUTO:
         return RdkitConformerSettings(
             num_initial_confs=300,
             max_mmff_energy=15,

{stjames-0.0.30 → stjames-0.0.32}/stjames/workflows/pka.py

@@ -1,5 +1,6 @@
 from typing import Optional
 
+from ..mode import Mode
 from ..base import Base
 from .workflow import DBCalculation, Workflow
 
@@ -12,6 +13,8 @@ class pKaMicrostate(Base):
 
 
 class pKaWorkflow(Workflow):
+    mode: Mode = Mode.CAREFUL
+
     pka_range: tuple[float, float] = (2, 12)
     deprotonate_elements: list[int] = [7, 8, 16]
     deprotonate_atoms: list[int] = []

stjames-0.0.32/stjames/workflows/redox_potential.py

@@ -0,0 +1,31 @@
+from typing import Optional, Any
+
+from ..mode import Mode
+from ..solvent import Solvent
+from .workflow import Workflow
+
+
+class RedoxPotentialWorkflow(Workflow):
+    mode: Mode = Mode.RAPID
+    solvent: Solvent = Solvent.ACETONITRILE
+    reduction: bool = True
+    oxidation: bool = True
+
+    redox_type: Optional[str] = None
+
+    # uuids
+    neutral_molecule: Optional[str] = None
+    anion_molecule: Optional[str] = None
+    cation_molecule: Optional[str] = None
+
+    reduction_potential: Optional[float] = None
+    oxidation_potential: Optional[float] = None
+
+    def model_post_init(self, __context: Any) -> None:
+        """ Keep back-compatible with old schema. """
+        if self.redox_type == "oxidation":
+            self.oxidation = True
+            self.reduction = False
+        elif self.redox_type == "reduction":
+            self.oxidation = False
+            self.reduction = True

{stjames-0.0.30 → stjames-0.0.32}/stjames/workflows/scan.py

@@ -32,7 +32,7 @@ class ScanSettings(Base):
 class ScanWorkflow(Workflow):
     scan_settings: ScanSettings
     calc_settings: Settings
-    engine: str
+    calc_engine: str
 
     # uuids of scan points
     scan_points: list[str] = []

{stjames-0.0.30 → stjames-0.0.32}/stjames/workflows/tautomer.py

@@ -1,6 +1,7 @@
 from typing import Optional
 
 from ..base import Base
+from ..mode import Mode
 from .conformer import ConformerSettings
 from .workflow import DBCalculation, Workflow
 
@@ -15,5 +16,5 @@ class Tautomer(Base):
 
 
 class TautomerWorkflow(Workflow):
-    settings: ConformerSettings
+    mode: Mode = Mode.CAREFUL
     tautomers: list[Tautomer] = []

{stjames-0.0.30 → stjames-0.0.32}/stjames/workflows/workflow.py

@@ -1,5 +1,4 @@
 from ..base import Base
-from ..mode import Mode
 from ..molecule import Molecule
 
 
@@ -7,7 +6,6 @@ class Workflow(Base):
     """All workflows should have these properties."""
 
     initial_molecule: Molecule
-    mode: Mode
 
 
 class DBCalculation(Base):

{stjames-0.0.30 → stjames-0.0.32/stjames.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: stjames
-Version: 0.0.30
+Version: 0.0.32
 Summary: standardized JSON atom/molecule encoding scheme
 Author-email: Corin Wagen <corin@rowansci.com>
 Project-URL: Homepage, https://github.com/rowansci/stjames

stjames-0.0.30/stjames/workflows/redox_potential.py

@@ -1,18 +0,0 @@
-from typing import Optional
-
-from ..solvent import Solvent
-from .workflow import Workflow
-
-
-class RedoxPotentialWorkflow(Workflow):
-    solvent: Solvent = Solvent.ACETONITRILE
-    reduction: bool = True
-    oxidation: bool = True
-
-    # uuids
-    neutral_molecule: Optional[str] = None
-    anion_molecule: Optional[str] = None
-    cation_molecule: Optional[str] = None
-
-    reduction_potential: Optional[float] = None
-    oxidation_potential: Optional[float] = None