stjames 0.0.99__py3-none-any.whl → 0.0.101__py3-none-any.whl

stjames/molecule.py

@@ -157,12 +157,20 @@ class Molecule(Base):
             return None
         return self.energy + self.thermal_enthalpy_corr
 
+    @property
+    def enthalpy(self) -> Optional[float]:
+        return self.sum_energy_enthalpy
+
     @property
     def sum_energy_free_energy(self) -> Optional[float]:
         if (self.energy is None) or (self.thermal_free_energy_corr is None):
             return None
         return self.energy + self.thermal_free_energy_corr
 
+    @property
+    def gibbs_free_energy(self) -> Optional[float]:
+        return self.sum_energy_free_energy
+
     @pydantic.model_validator(mode="after")
     def check_electron_sanity(self) -> Self:
         num_electrons = sum(self.atomic_numbers) - self.charge

stjames/workflows/__init__.py

@@ -9,6 +9,7 @@ from .conformer import *
 from .conformer_search import *
 from .descriptors import *
 from .docking import *
+from .double_ended_ts_search import DoubleEndedTSSearchWorkflow
 from .electronic_properties import *
 from .fukui import *
 from .hydrogen_bond_basicity import *
@@ -36,6 +37,7 @@ WORKFLOW_NAME = Literal[
     "conformer_search",
     "descriptors",
     "docking",
+    "double_ended_ts_search",
     "electronic_properties",
     "fukui",
     "hydrogen_bond_basicity",
@@ -63,6 +65,7 @@ WORKFLOW_MAPPING: dict[WORKFLOW_NAME, Workflow] = {
     "conformer_search": ConformerSearchWorkflow,  # type: ignore [dict-item]
     "descriptors": DescriptorsWorkflow,  # type: ignore [dict-item]
     "docking": DockingWorkflow,  # type: ignore [dict-item]
+    "double_ended_ts_search": DoubleEndedTSSearchWorkflow,  # type: ignore [dict-item]
     "electronic_properties": ElectronicPropertiesWorkflow,  # type: ignore [dict-item]
     "fukui": FukuiIndexWorkflow,  # type: ignore [dict-item]
     "hydrogen_bond_basicity": HydrogenBondBasicityWorkflow,  # type: ignore [dict-item]

stjames/workflows/basic_calculation.py

@@ -1,5 +1,10 @@
 """Basic calculation workflow."""
 
+from typing import Self
+
+from pydantic import model_validator
+
+from ..engine import Engine
 from ..settings import Settings
 from ..types import UUID
 from .workflow import MoleculeWorkflow
@@ -20,5 +25,12 @@ class BasicCalculationWorkflow(MoleculeWorkflow):
     """
 
     settings: Settings
-    engine: str
+    engine: Engine = None  # type: ignore [assignment]
     calculation_uuid: UUID | None = None
+
+    @model_validator(mode="after")
+    def set_engine(self) -> Self:
+        """Set the calculation engine."""
+        self.engine = self.engine or self.settings.method.default_engine()
+
+        return self

stjames/workflows/nmr.py

@@ -29,7 +29,7 @@ class NMRPeak(Base):
 
     nucleus: int
     shift: Annotated[float, AfterValidator(round_float(3))]
-    atom_indices: set[int]
+    atom_indices: list[int]
 
 
 class NMRSpectroscopyWorkflow(MoleculeWorkflow):
@@ -68,6 +68,6 @@ class NMRSpectroscopyWorkflow(MoleculeWorkflow):
     boltzmann_weights: 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: list[set[int]] = []
+    symmetry_equivalent_nuclei: list[list[int]] = []
 
     predicted_peaks: dict[int, list[NMRPeak]] = {}

{stjames-0.0.99.dist-info → stjames-0.0.101.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: stjames
-Version: 0.0.99
+Version: 0.0.101
 Summary: standardized JSON atom/molecule encoding scheme
 Author-email: Corin Wagen <corin@rowansci.com>
 Project-URL: Homepage, https://github.com/rowansci/stjames

{stjames-0.0.99.dist-info → stjames-0.0.101.dist-info}/RECORD

@@ -11,7 +11,7 @@ stjames/engine.py,sha256=4Vt1uF1jNGPj-06F2I73oU5RoH1MlNOlDRSNkWN91NE,315
 stjames/message.py,sha256=Rq6QqmHZKecWxYH8fVyXmuoCCPZv8YinvgykSeorXSU,216
 stjames/method.py,sha256=gZbrHAivm2OXCbF3_6swei1LG6YQ7Uo1EY7aN0x3XHs,4501
 stjames/mode.py,sha256=xw46Cc7f3eTS8i35qECi-8DocAlANhayK3w4akD4HBU,496
-stjames/molecule.py,sha256=l4S6prH1xflnZtbwidSF2THsiHaSJtRiy1rmUbH366Q,20631
+stjames/molecule.py,sha256=4Tsa_gRC4C-qGPop24jRIs2q07r0LGbSRb-ApOaZa5c,20839
 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
@@ -37,9 +37,9 @@ stjames/data/read_nist_isotopes.py,sha256=y10FNjW43QpC45qib7VHsIghEwT7GG5rsNwHdc
 stjames/data/symbol_element.json,sha256=vl_buFusTqBd-muYQtMLtTDLy2OtBI6KkBeqkaWRQrg,1186
 stjames/optimization/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 stjames/optimization/freezing_string_method.py,sha256=eEQBqbYHgJH9gVRLDIFtGuPcsHHMLAAt1hF3jtq70lo,2285
-stjames/workflows/__init__.py,sha256=wGTCSEvGmLVG-dnkylVsKq7_27n8gQlFfsJiX9RN33w,2890
+stjames/workflows/__init__.py,sha256=-HhT_DJeYCzTO-FeM-wabFyxwLreTE8bXHuaSx3Ylzg,3071
 stjames/workflows/admet.py,sha256=h8ph6oeRCxU3-_jqRRWPg3RZcheu9JzCHiWqSC9VYKY,1296
-stjames/workflows/basic_calculation.py,sha256=ZX3KwhfyyCTjc2ougQIL4If7gtwZP9WjqpL45mBquW0,573
+stjames/workflows/basic_calculation.py,sha256=sAgHBcNHE72ZbZPB9vyZShALRC4zOVw6It6cpJlbX2A,911
 stjames/workflows/bde.py,sha256=g_In-caftXiimrhfdptHjpfrYQUs3vF58qYmRnaTN8g,10825
 stjames/workflows/conformer.py,sha256=18aO6ngMBeGAmQkBdLGCCHr398RIYr1v2hD2IT1u4cc,3005
 stjames/workflows/conformer_search.py,sha256=4yPEKIIedeaVvaAwgjwC1FxiHqM6n2zOF6c9Yk_q1oA,13513
@@ -54,7 +54,7 @@ stjames/workflows/irc.py,sha256=ZP7icylW8rgo_Uh7h3bmyumn0ru1IyF-61nP5Jnmq3M,3402
 stjames/workflows/macropka.py,sha256=KRIyk4gsSYL3eqyzCDndStGLwjWSo60cgCAzvAoD1Nk,3754
 stjames/workflows/molecular_dynamics.py,sha256=HqWNxxPSAphfI0DdbTERFkq8UeBjEvhnA_ETv0xw_RY,3522
 stjames/workflows/multistage_opt.py,sha256=SpbA8hNvktnlLS7C-9mBNGluBSrdVS8ygHl1C4TzWcI,16499
-stjames/workflows/nmr.py,sha256=LKIOJHenzPTALv2ov5cImMknZ4JiYjxnpVSctbIRKvA,2708
+stjames/workflows/nmr.py,sha256=Fw7k_ZvIaxpAxkdgW2xMORhaI5s5BY_v7_VEPG1Ylgc,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
@@ -64,8 +64,8 @@ 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-0.0.99.dist-info/licenses/LICENSE,sha256=i7ehYBS-6gGmbTcgU4mgk28pyOx2kScJ0kcx8n7bWLM,1084
-stjames-0.0.99.dist-info/METADATA,sha256=TA09ljwdu02vJTrymmWrQjit0bjQ5Md7h-_92kST6dw,1724
-stjames-0.0.99.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-stjames-0.0.99.dist-info/top_level.txt,sha256=FYCwxl6quhYOAgG-mnPQcCK8vsVM7B8rIUrO-WrQ_PI,8
-stjames-0.0.99.dist-info/RECORD,,
+stjames-0.0.101.dist-info/licenses/LICENSE,sha256=i05z7xEhyrg6f8j0lR3XYjShnF-MJGFQ-DnpsZ8yiVI,1084
+stjames-0.0.101.dist-info/METADATA,sha256=TNvGMRniR9D4VJTlQygqa0ZuEtgVLsqeN9jfkNRLdxQ,1725
+stjames-0.0.101.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+stjames-0.0.101.dist-info/top_level.txt,sha256=FYCwxl6quhYOAgG-mnPQcCK8vsVM7B8rIUrO-WrQ_PI,8
+stjames-0.0.101.dist-info/RECORD,,

{stjames-0.0.99.dist-info → stjames-0.0.101.dist-info}/licenses/LICENSE

@@ -1,6 +1,6 @@
 The MIT License
 
-Copyright (c) Rowan (https://rowansci.com)
+Copyright (c) Rowan Scientific Corporation
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal