stjames 0.0.110__py3-none-any.whl → 0.0.112__py3-none-any.whl

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/opt_settings.py

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

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/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.dist-info → stjames-0.0.112.dist-info}/METADATA

@@ -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.dist-info → stjames-0.0.112.dist-info}/RECORD

@@ -1,6 +1,6 @@
 stjames/__init__.py,sha256=i_vqziEdoBNXhD7Gjb2_1zLkSx0Ko1N8BnCk6No_T6A,522
 stjames/_deprecated_solvent_settings.py,sha256=gj5j9p3zakIwSTK5_ndqBXJx--IzjZNxZ75z-wipLOo,450
-stjames/atom.py,sha256=hQCTMu3y30dvqjyCInnSs47DkUEnwhm_M2qB2jTD4Ik,2153
+stjames/atom.py,sha256=RnlAgWsZZJEZnSBWCeoj6NtWht8mZTf4qDWfT_Ot05U,2704
 stjames/base.py,sha256=YhmNZqFdWYD_lCw8rD2fZtt17nh8g7lUFBnGMezB-u8,1837
 stjames/basis_set.py,sha256=wI3M2q9uPf9jhKpAi4E2DrsyKzloDGLRjAlk7krdYgc,949
 stjames/calculation.py,sha256=O2LwwQ_cOLmDOGXTHA9J71YbUZXigUSbvbLA-fSVm3w,915
@@ -12,7 +12,7 @@ stjames/message.py,sha256=Rq6QqmHZKecWxYH8fVyXmuoCCPZv8YinvgykSeorXSU,216
 stjames/method.py,sha256=3HJ-dSK75HG-YPzgDVT8lQ0Ttld-TF984qDDTTAJk9A,4762
 stjames/mode.py,sha256=xw46Cc7f3eTS8i35qECi-8DocAlANhayK3w4akD4HBU,496
 stjames/molecule.py,sha256=4Tsa_gRC4C-qGPop24jRIs2q07r0LGbSRb-ApOaZa5c,20839
-stjames/opt_settings.py,sha256=LEwGXUEKq5TfU5rr60Z4QQBhCqiw1Ch5w0M_lXawWo8,642
+stjames/opt_settings.py,sha256=HjKbyFWcxD10FZfbqLxx1RKT0rcXGBr8bmi4ms4U3Sw,684
 stjames/pdb.py,sha256=6ayVUUdTufkXs_nfpRQuT1yGvymuyICB4L5Wh55OsaA,26507
 stjames/periodic_cell.py,sha256=eV_mArsY_MPEFSrFEsTC-CyCc6V8ITAXdk7yhjjNI7M,1080
 stjames/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -38,7 +38,7 @@ stjames/data/symbol_element.json,sha256=vl_buFusTqBd-muYQtMLtTDLy2OtBI6KkBeqkaWR
 stjames/optimization/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 stjames/optimization/freezing_string_method.py,sha256=eEQBqbYHgJH9gVRLDIFtGuPcsHHMLAAt1hF3jtq70lo,2285
 stjames/workflows/__init__.py,sha256=I-s6f6uz7PXpeKsvQlL04wswId2mW2u7thk309TC7ng,3165
-stjames/workflows/admet.py,sha256=h8ph6oeRCxU3-_jqRRWPg3RZcheu9JzCHiWqSC9VYKY,1296
+stjames/workflows/admet.py,sha256=qFUpCFiLW-3gzuEjCMNBJ6DEG_vquJcPAsN4SVZRfdE,1289
 stjames/workflows/basic_calculation.py,sha256=sAgHBcNHE72ZbZPB9vyZShALRC4zOVw6It6cpJlbX2A,911
 stjames/workflows/bde.py,sha256=g_In-caftXiimrhfdptHjpfrYQUs3vF58qYmRnaTN8g,10825
 stjames/workflows/conformer.py,sha256=18aO6ngMBeGAmQkBdLGCCHr398RIYr1v2hD2IT1u4cc,3005
@@ -55,7 +55,7 @@ stjames/workflows/macropka.py,sha256=Krj0xXuB-u57Kqlf4bbRiHDUWCpliFr6YPiYqPmYaWk
 stjames/workflows/molecular_dynamics.py,sha256=HqWNxxPSAphfI0DdbTERFkq8UeBjEvhnA_ETv0xw_RY,3522
 stjames/workflows/multistage_opt.py,sha256=UN-4WLsT2WEjO5KqDPrcCkb708Co-ZScHx3g2bto768,16597
 stjames/workflows/nmr.py,sha256=1QEF4SB6dWIr-jzLEZ7V972UnRUOTufOJSHwIGyV3dM,2681
-stjames/workflows/pka.py,sha256=24mpGNPMc-hOaVqQFFlUdGadB65fb3DyOt4XXQvB2YY,4593
+stjames/workflows/pka.py,sha256=EaeC61dIiG_-ymA_BY0Be-pATpI2sHhYVRu4DXKRYzA,4580
 stjames/workflows/pose_analysis_md.py,sha256=ES0XlzaLpTjhLrNvcB0zFZa1b1ZHXekN72EbLsx0Skw,4723
 stjames/workflows/protein_cofolding.py,sha256=cN0WUh8trrWwzNvoU75hB-VectIer-g5sMKgibQJcfE,4293
 stjames/workflows/redox_potential.py,sha256=7S18t9Y3eynSnA3lZbRlvLfdbgeBopdiigLzt1zxg5c,3871
@@ -65,8 +65,8 @@ stjames/workflows/spin_states.py,sha256=0degmE-frovgoXweshZyjfjqL7nkbaFoO9YoJhvQ
 stjames/workflows/strain.py,sha256=paYxDDQTB1eYP_c2kLVz1-QX7Vpw0LLb3ujnFin_SOM,1834
 stjames/workflows/tautomer.py,sha256=7eYKziGPg8Km6lfowTzSkgJfJ4SHUPrAmnTf8Bi-SB0,1164
 stjames/workflows/workflow.py,sha256=OE05pt2ZOd8TzTOlBngXCVg9wv_553ZR60VNRPlq0f8,1953
-stjames-0.0.110.dist-info/licenses/LICENSE,sha256=i05z7xEhyrg6f8j0lR3XYjShnF-MJGFQ-DnpsZ8yiVI,1084
-stjames-0.0.110.dist-info/METADATA,sha256=U5ELdyppOGvFvZRXvktt8mqT-knNDdcl9wZJ2fY9h3o,1725
-stjames-0.0.110.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-stjames-0.0.110.dist-info/top_level.txt,sha256=FYCwxl6quhYOAgG-mnPQcCK8vsVM7B8rIUrO-WrQ_PI,8
-stjames-0.0.110.dist-info/RECORD,,
+stjames-0.0.112.dist-info/licenses/LICENSE,sha256=i05z7xEhyrg6f8j0lR3XYjShnF-MJGFQ-DnpsZ8yiVI,1084
+stjames-0.0.112.dist-info/METADATA,sha256=uFnIQFjjqEHxaIKFXI-WxX5521fRNUfGQZiFqZfl6Fw,1725
+stjames-0.0.112.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+stjames-0.0.112.dist-info/top_level.txt,sha256=FYCwxl6quhYOAgG-mnPQcCK8vsVM7B8rIUrO-WrQ_PI,8
+stjames-0.0.112.dist-info/RECORD,,