stjames 0.0.95__tar.gz → 0.0.97__tar.gz

{stjames-0.0.95/stjames.egg-info → stjames-0.0.97}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: stjames
-Version: 0.0.95
+Version: 0.0.97
 Summary: standardized JSON atom/molecule encoding scheme
 Author-email: Corin Wagen <corin@rowansci.com>
 Project-URL: Homepage, https://github.com/rowansci/stjames

{stjames-0.0.95 → stjames-0.0.97}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "stjames"
-version = "0.0.95"
+version = "0.0.97"
 description = "standardized JSON atom/molecule encoding scheme"
 readme = "README.md"
 requires-python = ">=3.11"

{stjames-0.0.95 → stjames-0.0.97}/stjames/workflows/nmr.py

@@ -4,11 +4,11 @@ from typing import Annotated
 
 from pydantic import AfterValidator
 
-from ..base import LowercaseStrEnum
+from ..base import Base, LowercaseStrEnum, round_float
 from ..mode import Mode
 from ..settings import Settings
 from ..solvent import Solvent
-from ..types import UUID, round_list
+from ..types import UUID, round_list, round_optional_list
 from .conformer_search import ConformerGenSettings, iMTDSettings
 from .multistage_opt import MultiStageOptSettings
 from .workflow import MoleculeWorkflow
@@ -18,6 +18,20 @@ class NMRMethod(LowercaseStrEnum):
     MAGNETZERO = "magnet-zero"
 
 
+class NMRPeak(Base):
+    """
+    Represents a single NMR peak.
+
+    :param nucleus: the atomic number of the nucleus in question
+    :param shift: the chemical shift of the peak
+    :param atom_indices: the zero-indices of the atoms giving rise to the peak
+    """
+
+    nucleus: int
+    shift: Annotated[float, AfterValidator(round_float(3))]
+    atom_indices: set[int]
+
+
 class NMRSpectroscopyWorkflow(MoleculeWorkflow):
     """
     Workflow for calculating NMR spectra.
@@ -35,8 +49,10 @@ class NMRSpectroscopyWorkflow(MoleculeWorkflow):
     Results:
     :param conformers: list of conformer UUIDs
     :param boltzmann_weights: the boltzmann weights for each conformer
-    :param per_conformer_isotopic_shieldings: the per-atom shieldings for each conformer
-    :param isotopic_shieldings: the per-atom shieldings
+    :param per_conformer_chemical_shifts: the per-atom shifts for each conformer
+    :param chemical_shifts: the per-atom shifts
+    :param symmetry_equivalent_nuclei: 0-indexed atoms which are equivalent to one another
+    :param predicted_peaks: the predicted NMR peaks
     """
 
     nmr_method: NMRMethod = NMRMethod.MAGNETZERO
@@ -45,10 +61,13 @@ class NMRSpectroscopyWorkflow(MoleculeWorkflow):
     conf_gen_settings: ConformerGenSettings | None = iMTDSettings(mode="careful")
     multistage_opt_settings: MultiStageOptSettings | None = MultiStageOptSettings(
         mode=Mode.MANUAL,
-        optimization_settings=[Settings(method="aimnet2_wb97md3")],
+        optimization_settings=[Settings(method="aimnet2_wb97md3", tasks=["optimize"])],
     )
 
     conformers: list[UUID] = []
     boltzmann_weights: Annotated[list[float], AfterValidator(round_list(3))] = []
-    per_conformer_isotropic_shieldings: list[Annotated[list[float], AfterValidator(round_list(3))]] = []
-    isotropic_shieldings: Annotated[list[float], AfterValidator(round_list(3))] = []
+    per_conformer_chemical_shifts: list[Annotated[list[float | None], AfterValidator(round_optional_list(3))]] = []
+    chemical_shifts: Annotated[list[float | None], AfterValidator(round_optional_list(3))] = []
+    symmetry_equivalent_nuclei: set[set[int]] = set()
+
+    predicted_peaks: dict[int, list[NMRPeak]] = {}

{stjames-0.0.95 → stjames-0.0.97/stjames.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: stjames
-Version: 0.0.95
+Version: 0.0.97
 Summary: standardized JSON atom/molecule encoding scheme
 Author-email: Corin Wagen <corin@rowansci.com>
 Project-URL: Homepage, https://github.com/rowansci/stjames