stjames 0.0.95__py3-none-any.whl → 0.0.97__py3-none-any.whl

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.dist-info → stjames-0.0.97.dist-info}/METADATA

@@ -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.dist-info → stjames-0.0.97.dist-info}/RECORD

@@ -51,7 +51,7 @@ stjames/workflows/irc.py,sha256=ZP7icylW8rgo_Uh7h3bmyumn0ru1IyF-61nP5Jnmq3M,3402
 stjames/workflows/macropka.py,sha256=KRIyk4gsSYL3eqyzCDndStGLwjWSo60cgCAzvAoD1Nk,3754
 stjames/workflows/molecular_dynamics.py,sha256=kxugE73Ntzpj-xpJSoQ1EwGzXXdvi_NTyeP4913EVwE,3173
 stjames/workflows/multistage_opt.py,sha256=SpbA8hNvktnlLS7C-9mBNGluBSrdVS8ygHl1C4TzWcI,16499
-stjames/workflows/nmr.py,sha256=mSmBl_kp5sWKExO-2xxfcqGtf-cot3YTcGpzBfoh68g,2023
+stjames/workflows/nmr.py,sha256=MMj91jAfq5J7AE9-eP4eiaP1GxF9r_-3AFv-SGGQXiQ,2710
 stjames/workflows/pka.py,sha256=j3vBh2YM3nJzJ1XJKPsmYahRCeaU9n3P-G-u9_moaFw,2065
 stjames/workflows/pose_analysis_md.py,sha256=ES0XlzaLpTjhLrNvcB0zFZa1b1ZHXekN72EbLsx0Skw,4723
 stjames/workflows/protein_cofolding.py,sha256=6WWbVOGzFjIRgQLMmMVODfIxo1jYFmRS1xnJmN0kOBw,3016
@@ -61,8 +61,8 @@ stjames/workflows/solubility.py,sha256=kGfVyPPGDLRpf2j6dSY7woCkfsoXSbUzdSImA4mcM
 stjames/workflows/spin_states.py,sha256=0degmE-frovgoXweshZyjfjqL7nkbaFoO9YoJhvQnaI,4748
 stjames/workflows/tautomer.py,sha256=7eYKziGPg8Km6lfowTzSkgJfJ4SHUPrAmnTf8Bi-SB0,1164
 stjames/workflows/workflow.py,sha256=OE05pt2ZOd8TzTOlBngXCVg9wv_553ZR60VNRPlq0f8,1953
-stjames-0.0.95.dist-info/licenses/LICENSE,sha256=i7ehYBS-6gGmbTcgU4mgk28pyOx2kScJ0kcx8n7bWLM,1084
-stjames-0.0.95.dist-info/METADATA,sha256=q5rJgbtmQrLOVntdIyE6pAkA3LPaKAmLyCrqZ3FUCkI,1724
-stjames-0.0.95.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-stjames-0.0.95.dist-info/top_level.txt,sha256=FYCwxl6quhYOAgG-mnPQcCK8vsVM7B8rIUrO-WrQ_PI,8
-stjames-0.0.95.dist-info/RECORD,,
+stjames-0.0.97.dist-info/licenses/LICENSE,sha256=i7ehYBS-6gGmbTcgU4mgk28pyOx2kScJ0kcx8n7bWLM,1084
+stjames-0.0.97.dist-info/METADATA,sha256=l2nJS6OssSW6Dk28HIQsfD1cPKOePXAP8Tqy2FUngCs,1724
+stjames-0.0.97.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+stjames-0.0.97.dist-info/top_level.txt,sha256=FYCwxl6quhYOAgG-mnPQcCK8vsVM7B8rIUrO-WrQ_PI,8
+stjames-0.0.97.dist-info/RECORD,,