stjames 0.0.31__py3-none-any.whl → 0.0.33__py3-none-any.whl

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/workflows/pka.py

@@ -1,5 +1,6 @@
 from typing import Optional
 
+from ..mode import Mode
 from ..base import Base
 from .workflow import DBCalculation, Workflow
 
@@ -7,11 +8,13 @@ from .workflow import DBCalculation, Workflow
 class pKaMicrostate(Base):
     atom_index: int
     structures: list[DBCalculation] = []
-    delta_G: float
-    pKa: float
+    deltaG: float
+    pka: float
 
 
 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/workflows/redox_potential.py

@@ -1,14 +1,18 @@
-from typing import Optional
+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
@@ -16,3 +20,12 @@ class RedoxPotentialWorkflow(Workflow):
 
     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/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/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/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-0.0.31.dist-info → stjames-0.0.33.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: stjames
-Version: 0.0.31
+Version: 0.0.33
 Summary: standardized JSON atom/molecule encoding scheme
 Author-email: Corin Wagen <corin@rowansci.com>
 Project-URL: Homepage, https://github.com/rowansci/stjames

{stjames-0.0.31.dist-info → stjames-0.0.33.dist-info}/RECORD

@@ -18,15 +18,15 @@ stjames/status.py,sha256=wTKNcNxStoEHrxxgr_zTyN90NITa3rxMQZzOgrCifEw,332
 stjames/task.py,sha256=TTl-iTdvDNCZTdPsyS6bYmxzY0ez9PgYlL62fztayXQ,307
 stjames/thermochem_settings.py,sha256=ZTLz31v8Ltutde5Nfm0vH5YahWjcfFWfr_R856KffxE,517
 stjames/workflows/__init__.py,sha256=TibQzeD3X3YGq9TaAzPlBMxU7zskFoa8PwPUam4TcZY,154
-stjames/workflows/conformer.py,sha256=mFqvzsLGiKWNrL0uSqxPgRPJZKKHPjIkK0MbdTqgnro,2297
+stjames/workflows/conformer.py,sha256=tqACquXy8wqIbxl3T-n4dfNNNkVdLos2dIG1u0CV8cc,2169
 stjames/workflows/fukui.py,sha256=FAabgLi_ig6Zp_jiTkuveP0wAObwv68liuumr85rb0g,366
-stjames/workflows/pka.py,sha256=oMNH_s0cdCPq8wFX5o8_5KBWXdCakW9IS1RqmI1Ezmo,720
-stjames/workflows/redox_potential.py,sha256=CCbN9VV30TkcyNQYlI319E8dyHdkzj3dZfBxXpJwJdA,466
-stjames/workflows/scan.py,sha256=qy4Y4nc_1kPXR-4_uGtmnzrQ5i9fVEnoeeiMvwpufJs,768
-stjames/workflows/tautomer.py,sha256=dJaBueUKKxnsj7A-N8ifBL97-Ecd56fPBe-uM9E5pHY,440
-stjames/workflows/workflow.py,sha256=Va1UdKScmJHZ_yfAcMY2KNO1g4eHI3ZBzEPvnLOFR8A,343
-stjames-0.0.31.dist-info/LICENSE,sha256=i7ehYBS-6gGmbTcgU4mgk28pyOx2kScJ0kcx8n7bWLM,1084
-stjames-0.0.31.dist-info/METADATA,sha256=19ec6Qmg3Zb9fgUp1fRc1lfSa-PK18QhXVllZnp0fKQ,1605
-stjames-0.0.31.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
-stjames-0.0.31.dist-info/top_level.txt,sha256=FYCwxl6quhYOAgG-mnPQcCK8vsVM7B8rIUrO-WrQ_PI,8
-stjames-0.0.31.dist-info/RECORD,,
+stjames/workflows/pka.py,sha256=r_y9sVO_lZVC9ZyRL96ANmK_xy5-xlD_ctwoxuXjK_Q,774
+stjames/workflows/redox_potential.py,sha256=uQZvgzii9SiYYxwzUTlb43uCSVaQ5C5Sg52HJ3YPhcI,897
+stjames/workflows/scan.py,sha256=d1ca1uk1nxdzlSwqMLZ0W1_DHyrQMnHJmvPfziCS0SA,773
+stjames/workflows/tautomer.py,sha256=xJMDArpsuTLmgBZHXcBGVMcP_tncQzvxUH4Kbis4opg,462
+stjames/workflows/workflow.py,sha256=jzkHO8mdmoy9zW3iD457KAXYrCCkV2OHjg6T3896nCQ,304
+stjames-0.0.33.dist-info/LICENSE,sha256=i7ehYBS-6gGmbTcgU4mgk28pyOx2kScJ0kcx8n7bWLM,1084
+stjames-0.0.33.dist-info/METADATA,sha256=BcMqbE8HOf8bGw3VQmOwezg0161D8zoMoFORxTkV4bs,1605
+stjames-0.0.33.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
+stjames-0.0.33.dist-info/top_level.txt,sha256=FYCwxl6quhYOAgG-mnPQcCK8vsVM7B8rIUrO-WrQ_PI,8
+stjames-0.0.33.dist-info/RECORD,,