stjames 0.0.110__tar.gz → 0.0.112__tar.gz

{stjames-0.0.110/stjames.egg-info → stjames-0.0.112}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: stjames
-Version: 0.0.110
+Version: 0.0.112
 Summary: standardized JSON atom/molecule encoding scheme
 Author-email: Corin Wagen <corin@rowansci.com>
 Project-URL: Homepage, https://github.com/rowansci/stjames

{stjames-0.0.110 → stjames-0.0.112}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "stjames"
-version = "0.0.110"
+version = "0.0.112"
 description = "standardized JSON atom/molecule encoding scheme"
 readme = "README.md"
 requires-python = ">=3.11"

{stjames-0.0.110 → stjames-0.0.112}/stjames/atom.py

@@ -2,14 +2,23 @@ from typing import Annotated, Self, Sequence
 
 from pydantic import AfterValidator, NonNegativeInt
 
-from .base import Base
+from .base import Base, round_optional_float
 from .data import ELEMENT_SYMBOL, SYMBOL_ELEMENT
 from .types import Vector3D, round_vector3d
 
 
 class Atom(Base):
+    """
+    A single atom.
+
+    :param atomic_number: the atomic number
+    :param position: the Cartesian coordinates in Å
+    :param mass: the mass, in Daltons. If `None` the most common isotopologue will be employed.
+    """
+
     atomic_number: NonNegativeInt
-    position: Annotated[Vector3D, AfterValidator(round_vector3d(8))]  # in Å
+    position: Annotated[Vector3D, AfterValidator(round_vector3d(8))]
+    mass: Annotated[float | None, AfterValidator(round_optional_float(3))] = None
 
     def __repr__(self) -> str:
         """
@@ -17,6 +26,8 @@ class Atom(Base):
         Atom(2, [0.00000, 1.00000, 2.00000])
         """
         x, y, z = self.position
+        if self.mass is not None:
+            return f"Atom({self.atomic_number}, [{x:.5f}, {y:.5f}, {z:.5f}], mass={self.mass:.3f})"
         return f"Atom({self.atomic_number}, [{x:.5f}, {y:.5f}, {z:.5f}])"
 
     def __str__(self) -> str:
@@ -35,7 +46,7 @@ class Atom(Base):
         """
         return ELEMENT_SYMBOL[self.atomic_number]
 
-    def edited(self, atomic_number: int | None = None, position: Sequence[float] | None = None) -> Self:
+    def edited(self, atomic_number: int | None = None, position: Sequence[float] | None = None, mass: float | None = None) -> Self:
         """
         Create a new Atom with the specified changes.
 
@@ -50,8 +61,10 @@ class Atom(Base):
             atomic_number = self.atomic_number
         if position is None:
             position = list(self.position)
+        if mass is None:
+            mass = self.mass
 
-        return self.__class__(atomic_number=atomic_number, position=position)
+        return self.__class__(atomic_number=atomic_number, position=position, mass=mass)
 
     @classmethod
     def from_xyz(cls: type[Self], xyz_line: str) -> Self:

{stjames-0.0.110 → stjames-0.0.112}/stjames/opt_settings.py

@@ -20,3 +20,5 @@ class OptimizationSettings(Base):
     optimize_cell: bool = False
 
     constraints: Sequence[Constraint] = tuple()
+
+    save_intermediate_steps: bool = True

{stjames-0.0.110 → stjames-0.0.112}/stjames/workflows/admet.py

@@ -31,7 +31,7 @@ class ADMETWorkflow(SMILESWorkflow, MoleculeWorkflow):
         """Ensure that only one of initial_molecule or initial_smiles is set."""
 
         if not (bool(self.initial_smiles) ^ bool(self.initial_molecule)):
-            raise ValueError("Can only set one of initial_molecule should and initial_smiles")
+            raise ValueError("Can only set one of initial_molecule and initial_smiles")
 
         if self.initial_molecule is not None:
             warnings.warn(DeprecationWarning("initial_molecule is deprecated. Use initial_smiles instead."))

{stjames-0.0.110 → stjames-0.0.112}/stjames/workflows/pka.py

@@ -79,7 +79,7 @@ class pKaWorkflow(SMILESWorkflow, MoleculeWorkflow):
 
     mode: Mode = Mode.CAREFUL
 
-    microscopic_pka_method: MicroscopicpKaMethod = MicroscopicpKaMethod.CHEMPROP_NEVOLIANUS2025
+    microscopic_pka_method: MicroscopicpKaMethod = MicroscopicpKaMethod.AIMNET2_WAGEN2024
     solvent: Solvent = Solvent.WATER
     pka_range: tuple[float, float] = (2, 12)
     deprotonate_elements: list[int] = [7, 8, 16]
@@ -114,6 +114,6 @@ class pKaWorkflow(SMILESWorkflow, MoleculeWorkflow):
         """Ensure that only one of initial_molecule or initial_smiles is set."""
 
         if not (bool(self.initial_smiles) ^ bool(self.initial_molecule)):
-            raise ValueError("Can only set one of initial_molecule should and initial_smiles")
+            raise ValueError("Can only set one of initial_molecule and initial_smiles")
 
         return self

{stjames-0.0.110 → stjames-0.0.112/stjames.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: stjames
-Version: 0.0.110
+Version: 0.0.112
 Summary: standardized JSON atom/molecule encoding scheme
 Author-email: Corin Wagen <corin@rowansci.com>
 Project-URL: Homepage, https://github.com/rowansci/stjames