stjames 0.0.88__py3-none-any.whl → 0.0.90__py3-none-any.whl

stjames/workflows/bde.py

@@ -6,10 +6,11 @@ from typing import Annotated, Any, Iterable, Self, TypeVar
 from pydantic import AfterValidator, BaseModel, Field, PositiveInt, ValidationInfo, field_validator, model_validator
 
 from ..base import round_optional_float
+from ..method import Method
 from ..mode import Mode
 from ..molecule import Molecule
 from ..types import UUID
-from .multistage_opt import MultiStageOptMixin
+from .multistage_opt import MultiStageOptMixin, mso_settings_from_method_string
 from .workflow import MoleculeWorkflow
 
 # the id of a mutable object may change, thus using object()
@@ -57,13 +58,13 @@ class BDEWorkflow(MoleculeWorkflow, MultiStageOptMixin):
 
     Inherited:
     :param initial_molecule: Molecule of interest
-    :param mode: Mode for workflow
     :param multistage_opt_settings: set by mode unless mode=MANUAL (ignores additional settings if set)
     :param solvent: solvent to use for singlepoint
     :param xtb_preopt: pre-optimize with xtb (sets based on mode when None)
     :param frequencies: whether to calculate frequencies
 
     Overridden:
+    :param mode: Mode for workflow or method string from BDE_METHODS
     :param mso_mode: Mode for MultiStageOptSettings
 
     Turned off:
@@ -81,6 +82,7 @@ class BDEWorkflow(MoleculeWorkflow, MultiStageOptMixin):
     :param bdes: BDE results
     """
 
+    mode: Mode | str  # type: ignore [assignment]
     mso_mode: Mode = _sentinel_mso_mode  # type: ignore [assignment]
     optimize_fragments: bool = None  # type: ignore [assignment]
 
@@ -95,6 +97,13 @@ class BDEWorkflow(MoleculeWorkflow, MultiStageOptMixin):
     optimization_energy: float | None = None
     bdes: list[BDE] = Field(default_factory=list)
 
+    def __repr__(self) -> str:
+        if self.mode != Mode.MANUAL:
+            name = self.mode.name if isinstance(self.mode, Mode) else self.mode
+            return f"<{type(self).__name__} {name}>"
+
+        return f"<{type(self).__name__} {self.level_of_theory}>"
+
     def __str__(self) -> str:
         r"""
         Return a string representation of the BDE workflow.
@@ -104,7 +113,8 @@ class BDEWorkflow(MoleculeWorkflow, MultiStageOptMixin):
         (1,)
         (2,)
         """
-        return f"{type(self).__name__} {self.mode.name}\n" + "\n".join(map(str, self.fragment_indices))
+        name = self.mode.name if isinstance(self.mode, Mode) else self.mode
+        return f"{type(self).__name__} {name}\n" + "\n".join(map(str, self.fragment_indices))
 
     @property
     def level_of_theory(self) -> str:
@@ -142,7 +152,14 @@ class BDEWorkflow(MoleculeWorkflow, MultiStageOptMixin):
     @classmethod
     def set_mso_mode(cls, values: dict[str, Any]) -> dict[str, Any]:
         """Set the MultiStageOptSettings mode to match current BDE mode."""
-        values["mso_mode"] = values["mode"]
+        mode = values["mode"].upper()
+        if mode in BDE_METHODS:
+            values["mso_mode"] = Mode.MANUAL
+            values["multistage_opt_settings"] = mso_settings_from_method_string(mode)
+        else:
+            values["mode"] = Mode(mode)
+            values["mso_mode"] = values["mode"]
+
         return values
 
     @model_validator(mode="after")
@@ -158,6 +175,8 @@ class BDEWorkflow(MoleculeWorkflow, MultiStageOptMixin):
             case Mode.RAPID | Mode.CAREFUL | Mode.METICULOUS:
                 # Default on
                 self.optimize_fragments = self.optimize_fragments or self.optimize_fragments is None
+            case m if m in BDE_METHODS:
+                self.optimize_fragments = True
             case _:
                 raise NotImplementedError(f"{self.mode} not implemented.")
 
@@ -260,3 +279,11 @@ def find_AB_bonds(molecule: Molecule, a: int, b: int, distance_max: float) -> It
             atomic_number_indices(molecule, b),
         ),
     )
+
+
+BDE_METHODS = {
+    f"{Method.G_XTB.name}",
+    f"{Method.G_XTB.name}//{Method.GFN2_XTB.name}",
+    f"{Method.R2SCAN3C.name}//{Method.GFN2_XTB.name}",
+    f"{Method.OMOL25_CONSERVING_S.name}",
+}

stjames/workflows/ion_mobility.py

@@ -13,10 +13,13 @@ class IonMobilityWorkflow(MoleculeWorkflow):
     :param mode: Mode for workflow (currently unused)
 
     New:
+    :param protonate: automatically protonate the molecule
+    :param temperature: the temperature, in Kelvin
     :param do_csearch: whether to perform a conformational search
     :param do_optimization: whether to perform an optimization
 
     Results:
+    :param conformers: the UUIDs of the conformers
     :param conformer_ccs: the collision cross section (Å**2) per conformer
     :param conformer_ccs_stdev: the uncertainty in the same
     :param conformer_weights: the Boltzmann weights at RT
@@ -24,8 +27,11 @@ class IonMobilityWorkflow(MoleculeWorkflow):
     :param average_ccs_stdev: the uncertainty in the same
     """
 
+    protonate: bool = False
+    temperature: float = 300
     do_csearch: bool = True
     do_optimization: bool = True
+
     conformers: list[UUID] = []
 
     conformer_ccs: list[float] = []

stjames/workflows/multistage_opt.py

@@ -271,7 +271,6 @@ class MultiStageOptMixin(BaseModel):
 def mso_settings_from_method_string(
     methods: str,
     solvent: Solvent | None = None,
-    use_solvent_for_opt: bool = False,
     constraints: list[Constraint] | None = None,
     transition_state: bool = False,
     frequencies: bool = False,

stjames/workflows/pose_analysis_md.py

@@ -86,7 +86,7 @@ class PoseAnalysisMolecularDynamicsWorkflow(MoleculeWorkflow):
     constrain_hydrogens: bool = True
     nonbonded_cutoff: Annotated[PositiveFloat, AfterValidator(round_float(3))] = 8.0
 
-    protein_prune_cutoff: Annotated[PositiveFloat, AfterValidator(round_float(3))] = 9.0
+    protein_prune_cutoff: Annotated[PositiveFloat, AfterValidator(round_float(3))] | None = None
     protein_restraint_cutoff: Annotated[PositiveFloat, AfterValidator(round_float(3))] = 7.0
     protein_restraint_constant: Annotated[PositiveFloat, AfterValidator(round_float(3))] = 100
 
@@ -100,6 +100,7 @@ class PoseAnalysisMolecularDynamicsWorkflow(MoleculeWorkflow):
     @model_validator(mode="after")
     def check_cutoff_sanity(self) -> Self:
         """Check if protein is provided."""
-        if self.protein_prune_cutoff < self.protein_restraint_cutoff:
-            raise ValueError("Pruning cutoff must be larger than restraint cutoff")
+        if self.protein_prune_cutoff is not None:
+            if self.protein_prune_cutoff < self.protein_restraint_cutoff:
+                raise ValueError("Pruning cutoff must be larger than restraint cutoff")
         return self

{stjames-0.0.88.dist-info → stjames-0.0.90.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: stjames
-Version: 0.0.88
+Version: 0.0.90
 Summary: standardized JSON atom/molecule encoding scheme
 Author-email: Corin Wagen <corin@rowansci.com>
 Project-URL: Homepage, https://github.com/rowansci/stjames

{stjames-0.0.88.dist-info → stjames-0.0.90.dist-info}/RECORD

@@ -40,7 +40,7 @@ stjames/data/symbol_element.json,sha256=vl_buFusTqBd-muYQtMLtTDLy2OtBI6KkBeqkaWR
 stjames/workflows/__init__.py,sha256=S5Z8bOWvvh9-TYV2VgfSpfvvfN1ceShTo5Dro5tmlP0,2796
 stjames/workflows/admet.py,sha256=h8ph6oeRCxU3-_jqRRWPg3RZcheu9JzCHiWqSC9VYKY,1296
 stjames/workflows/basic_calculation.py,sha256=ZX3KwhfyyCTjc2ougQIL4If7gtwZP9WjqpL45mBquW0,573
-stjames/workflows/bde.py,sha256=hdTjwma5L9SrU5F5r6dB1ruB_B6buBUtZHf2sanNW2k,9802
+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
 stjames/workflows/descriptors.py,sha256=T4tc7xdtBdxESGO86KR323jPQ2pgwxBqgV0khA6MEgQ,584
@@ -48,13 +48,13 @@ stjames/workflows/docking.py,sha256=GCW_-JeEZcMXKZ9EQFOxWUYRo0jsbzwIv10aSz8KuaQ,
 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=e6XSidrud5qSkrAcjzOzgHaf-G09JoP09V76myjdyjc,1097
+stjames/workflows/ion_mobility.py,sha256=HbO_222pjiG4YeJ70kYtQJvXQJieDSMAU5y26vIx1vI,1316
 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=P8rxMUhKXMmDi7Id95IOTEmM0xN1ErsKcDJfgY08vjc,16538
+stjames/workflows/multistage_opt.py,sha256=SpbA8hNvktnlLS7C-9mBNGluBSrdVS8ygHl1C4TzWcI,16499
 stjames/workflows/pka.py,sha256=j3vBh2YM3nJzJ1XJKPsmYahRCeaU9n3P-G-u9_moaFw,2065
-stjames/workflows/pose_analysis_md.py,sha256=hRObMVt4VlL3TMo9yb6SxcpVhjiuPX0tUyaQwbe7qxc,4657
+stjames/workflows/pose_analysis_md.py,sha256=ES0XlzaLpTjhLrNvcB0zFZa1b1ZHXekN72EbLsx0Skw,4723
 stjames/workflows/protein_cofolding.py,sha256=_05DCzzKGZFtns9HARAMjcWxVrJU9DPb3VNVWSgwWR8,2173
 stjames/workflows/redox_potential.py,sha256=7S18t9Y3eynSnA3lZbRlvLfdbgeBopdiigLzt1zxg5c,3871
 stjames/workflows/scan.py,sha256=DXQBpa2t2PowAtOwmdgpxaSLq--fEShljzAGSb8Nf5U,2993
@@ -62,8 +62,8 @@ 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-0.0.88.dist-info/licenses/LICENSE,sha256=i7ehYBS-6gGmbTcgU4mgk28pyOx2kScJ0kcx8n7bWLM,1084
-stjames-0.0.88.dist-info/METADATA,sha256=lRcyR0nsmJ-Kag_9Zw2qzKNE2-h9FXe6cCXkaScrseU,1724
-stjames-0.0.88.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-stjames-0.0.88.dist-info/top_level.txt,sha256=FYCwxl6quhYOAgG-mnPQcCK8vsVM7B8rIUrO-WrQ_PI,8
-stjames-0.0.88.dist-info/RECORD,,
+stjames-0.0.90.dist-info/licenses/LICENSE,sha256=i7ehYBS-6gGmbTcgU4mgk28pyOx2kScJ0kcx8n7bWLM,1084
+stjames-0.0.90.dist-info/METADATA,sha256=IbwiPJaGd1rkTp0eSNDf5yTAHqnJ21wTIgI18ObeaHA,1724
+stjames-0.0.90.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+stjames-0.0.90.dist-info/top_level.txt,sha256=FYCwxl6quhYOAgG-mnPQcCK8vsVM7B8rIUrO-WrQ_PI,8
+stjames-0.0.90.dist-info/RECORD,,