stjames 0.0.94__tar.gz → 0.0.95__tar.gz

{stjames-0.0.94/stjames.egg-info → stjames-0.0.95}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: stjames
-Version: 0.0.94
+Version: 0.0.95
 Summary: standardized JSON atom/molecule encoding scheme
 Author-email: Corin Wagen <corin@rowansci.com>
 Project-URL: Homepage, https://github.com/rowansci/stjames

{stjames-0.0.94 → stjames-0.0.95}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "stjames"
-version = "0.0.94"
+version = "0.0.95"
 description = "standardized JSON atom/molecule encoding scheme"
 readme = "README.md"
 requires-python = ">=3.11"

stjames-0.0.95/stjames/scf_settings.py

@@ -0,0 +1,19 @@
+from .base import Base, LowercaseStrEnum
+
+
+class UseSOSCF(LowercaseStrEnum):
+    ALWAYS = "always"
+    UPON_FAILURE = "upon_failure"
+    NEVER = "never"
+
+
+class SCFSettings(Base):
+    """
+    Settings for SCF convergence.
+
+    :param max_iters: the maximum number of SCF iterations to permit
+    :param soscf: whether or not to use SOSCF (second-order SCF).
+    """
+
+    max_iters: int = 250
+    soscf: UseSOSCF = UseSOSCF.UPON_FAILURE

{stjames-0.0.94 → stjames-0.0.95}/stjames/workflows/__init__.py

@@ -17,6 +17,7 @@ from .irc import *
 from .macropka import *
 from .molecular_dynamics import *
 from .multistage_opt import *
+from .nmr import *
 from .pka import *
 from .pose_analysis_md import *
 from .protein_cofolding import *
@@ -43,6 +44,7 @@ WORKFLOW_NAME = Literal[
     "macropka",
     "molecular_dynamics",
     "multistage_opt",
+    "nmr",
     "pka",
     "pose_analysis_md",
     "protein_cofolding",
@@ -69,6 +71,7 @@ WORKFLOW_MAPPING: dict[WORKFLOW_NAME, Workflow] = {
     "macropka": MacropKaWorkflow,  # type: ignore [dict-item]
     "molecular_dynamics": MolecularDynamicsWorkflow,  # type: ignore [dict-item]
     "multistage_opt": MultiStageOptWorkflow,  # type: ignore [dict-item]
+    "nmr": NMRSpectroscopyWorkflow,  # type: ignore [dict-item]
     "pka": pKaWorkflow,  # type: ignore [dict-item]
     "pose_analysis_md": PoseAnalysisMolecularDynamicsWorkflow,  # type: ignore [dict-item]
     "protein_cofolding": ProteinCofoldingWorkflow,  # type: ignore [dict-item]

{stjames-0.0.94 → stjames-0.0.95}/stjames/workflows/ion_mobility.py

@@ -1,6 +1,11 @@
 """Ion mobility workflow."""
 
-from ..types import UUID
+from typing import Annotated
+
+from pydantic import AfterValidator
+
+from ..base import round_optional_float
+from ..types import UUID, round_list
 from .workflow import MoleculeWorkflow
 
 
@@ -34,9 +39,9 @@ class IonMobilityWorkflow(MoleculeWorkflow):
 
     conformers: list[UUID] = []
 
-    conformer_ccs: list[float] = []
-    conformer_ccs_stdev: list[float] = []
-    boltzmann_weights: list[float] = []
+    conformer_ccs: Annotated[list[float], AfterValidator(round_list(3))] = []
+    conformer_ccs_stdev: Annotated[list[float], AfterValidator(round_list(3))] = []
+    boltzmann_weights: Annotated[list[float], AfterValidator(round_list(3))] = []
 
-    average_ccs: float | None = None
-    average_ccs_stdev: float | None = None
+    average_ccs: Annotated[float | None, AfterValidator(round_optional_float(3))] = None
+    average_ccs_stdev: Annotated[float | None, AfterValidator(round_optional_float(3))] = None

stjames-0.0.95/stjames/workflows/nmr.py

@@ -0,0 +1,54 @@
+"""Nuclear-magnetic-resonance spectroscopy workflow."""
+
+from typing import Annotated
+
+from pydantic import AfterValidator
+
+from ..base import LowercaseStrEnum
+from ..mode import Mode
+from ..settings import Settings
+from ..solvent import Solvent
+from ..types import UUID, round_list
+from .conformer_search import ConformerGenSettings, iMTDSettings
+from .multistage_opt import MultiStageOptSettings
+from .workflow import MoleculeWorkflow
+
+
+class NMRMethod(LowercaseStrEnum):
+    MAGNETZERO = "magnet-zero"
+
+
+class NMRSpectroscopyWorkflow(MoleculeWorkflow):
+    """
+    Workflow for calculating NMR spectra.
+
+    Inherited:
+    :param initial_molecule: Molecule of interest
+    :param mode: Mode for workflow (currently unused)
+
+    New:
+    :param nmr_method: how to run the NMR calculations
+    :param solvent: the solvent in which to run the calculations
+    :param conf_gen_settings : the conformer-search settings. if `None`, no conformer search will be performed
+    :param multistage_opt_settings: the optimization settings. if `None`, no optimization will be performed
+
+    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
+    """
+
+    nmr_method: NMRMethod = NMRMethod.MAGNETZERO
+    solvent: Solvent = Solvent.CHLOROFORM
+
+    conf_gen_settings: ConformerGenSettings | None = iMTDSettings(mode="careful")
+    multistage_opt_settings: MultiStageOptSettings | None = MultiStageOptSettings(
+        mode=Mode.MANUAL,
+        optimization_settings=[Settings(method="aimnet2_wb97md3")],
+    )
+
+    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))] = []

{stjames-0.0.94 → stjames-0.0.95/stjames.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: stjames
-Version: 0.0.94
+Version: 0.0.95
 Summary: standardized JSON atom/molecule encoding scheme
 Author-email: Corin Wagen <corin@rowansci.com>
 Project-URL: Homepage, https://github.com/rowansci/stjames

{stjames-0.0.94 → stjames-0.0.95}/stjames.egg-info/SOURCES.txt

@@ -59,6 +59,7 @@ stjames/workflows/irc.py
 stjames/workflows/macropka.py
 stjames/workflows/molecular_dynamics.py
 stjames/workflows/multistage_opt.py
+stjames/workflows/nmr.py
 stjames/workflows/pka.py
 stjames/workflows/pose_analysis_md.py
 stjames/workflows/protein_cofolding.py

stjames-0.0.94/stjames/scf_settings.py

@@ -1,7 +0,0 @@
-from pydantic import BaseModel
-
-
-class SCFSettings(BaseModel):
-    max_iters: int = 250
-
-    soscf: bool = False