stjames 0.0.94__py3-none-any.whl → 0.0.96__py3-none-any.whl

stjames/scf_settings.py

@@ -1,7 +1,19 @@
-from pydantic import BaseModel
+from .base import Base, LowercaseStrEnum
 
 
-class SCFSettings(BaseModel):
-    max_iters: int = 250
+class UseSOSCF(LowercaseStrEnum):
+    ALWAYS = "always"
+    UPON_FAILURE = "upon_failure"
+    NEVER = "never"
+
+
+class SCFSettings(Base):
+    """
+    Settings for SCF convergence.
 
-    soscf: bool = False
+    :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/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/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/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_chemical_shifts: the per-atom shifts for each conformer
+    :param chemical_shifts: the per-atom shifts
+    """
+
+    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_chemical_shifts: list[Annotated[list[float], AfterValidator(round_list(3))]] = []
+    chemical_shifts: Annotated[list[float], AfterValidator(round_list(3))] = []

{stjames-0.0.94.dist-info → stjames-0.0.96.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: stjames
-Version: 0.0.94
+Version: 0.0.96
 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.dist-info → stjames-0.0.96.dist-info}/RECORD

@@ -16,7 +16,7 @@ stjames/opt_settings.py,sha256=LEwGXUEKq5TfU5rr60Z4QQBhCqiw1Ch5w0M_lXawWo8,642
 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
-stjames/scf_settings.py,sha256=Wx_Op5k4renAd-kUV1Utstb7iLxc5OHMQpOHJaAMAHA,113
+stjames/scf_settings.py,sha256=ecEVP3aKArNorpbP0mapnbc-EMjjzx4jeVW6q9tvqsw,436
 stjames/settings.py,sha256=qZ3yhuMIQNiLs8Z-uEyVReSg2IQAjnDzQ6euHHqE6xI,6128
 stjames/solvent.py,sha256=u037tmu-9oa21s-WEDZ7VC7nuNVjkqR2ML4JWjWSME4,1158
 stjames/status.py,sha256=KQHDqWSd4kBLow23YLcfOkFdtqN61RFZI-jf2zANWRY,501
@@ -35,7 +35,7 @@ stjames/data/isotopes.json,sha256=5ba8QnLrHD_Ypv2xekv2cIRwYrX3MQ19-1FOFtt0RuU,83
 stjames/data/nist_isotopes.json,sha256=d5DNk1dX0iB1waEYIRR6JMHuA7AuYwSBEgBvb4EKyhM,14300
 stjames/data/read_nist_isotopes.py,sha256=y10FNjW43QpC45qib7VHsIghEwT7GG5rsNwHdc9osRI,3309
 stjames/data/symbol_element.json,sha256=vl_buFusTqBd-muYQtMLtTDLy2OtBI6KkBeqkaWRQrg,1186
-stjames/workflows/__init__.py,sha256=S5Z8bOWvvh9-TYV2VgfSpfvvfN1ceShTo5Dro5tmlP0,2796
+stjames/workflows/__init__.py,sha256=wGTCSEvGmLVG-dnkylVsKq7_27n8gQlFfsJiX9RN33w,2890
 stjames/workflows/admet.py,sha256=h8ph6oeRCxU3-_jqRRWPg3RZcheu9JzCHiWqSC9VYKY,1296
 stjames/workflows/basic_calculation.py,sha256=ZX3KwhfyyCTjc2ougQIL4If7gtwZP9WjqpL45mBquW0,573
 stjames/workflows/bde.py,sha256=g_In-caftXiimrhfdptHjpfrYQUs3vF58qYmRnaTN8g,10825
@@ -46,11 +46,12 @@ stjames/workflows/docking.py,sha256=CgpLjMfpPka1fcg0VJPeyJCOnZjnJTrgfNeMAKiX4zM,
 stjames/workflows/electronic_properties.py,sha256=GT3-NC7w-dbcOJ-3AzJ7LgzH6frTbiH2Iyb9BCa-SvY,4112
 stjames/workflows/fukui.py,sha256=T6TDg-lcE-sfTDVpa3KFBenLe7PGUO2QrQ2jNuw_iiU,1756
 stjames/workflows/hydrogen_bond_basicity.py,sha256=q9eXty68ZyCmrB6G_8bfeOT8Ui_IQquRPu6z-3rNreQ,1589
-stjames/workflows/ion_mobility.py,sha256=HbO_222pjiG4YeJ70kYtQJvXQJieDSMAU5y26vIx1vI,1316
+stjames/workflows/ion_mobility.py,sha256=rvvAt4ZD-Npl0tHL7TEuaS3XKjHiMkSZVzyJoivdyps,1665
 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=fDtP94oKErPvRlR1x4kSYSycICizTNROEdwnLsxP72c,1997
 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
@@ -60,8 +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-0.0.94.dist-info/licenses/LICENSE,sha256=i7ehYBS-6gGmbTcgU4mgk28pyOx2kScJ0kcx8n7bWLM,1084
-stjames-0.0.94.dist-info/METADATA,sha256=WjfSeqw_fW_J-9vstRKCwTHyJ5TVi0ZYO2BujRC2ucw,1724
-stjames-0.0.94.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-stjames-0.0.94.dist-info/top_level.txt,sha256=FYCwxl6quhYOAgG-mnPQcCK8vsVM7B8rIUrO-WrQ_PI,8
-stjames-0.0.94.dist-info/RECORD,,
+stjames-0.0.96.dist-info/licenses/LICENSE,sha256=i7ehYBS-6gGmbTcgU4mgk28pyOx2kScJ0kcx8n7bWLM,1084
+stjames-0.0.96.dist-info/METADATA,sha256=kZzb-iwZIsgUHNbeGR9CyRD1zoBqwAntUFyIQ2LBJNI,1724
+stjames-0.0.96.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+stjames-0.0.96.dist-info/top_level.txt,sha256=FYCwxl6quhYOAgG-mnPQcCK8vsVM7B8rIUrO-WrQ_PI,8
+stjames-0.0.96.dist-info/RECORD,,