stjames 0.0.87__tar.gz → 0.0.89__tar.gz

{stjames-0.0.87/stjames.egg-info → stjames-0.0.89}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: stjames
-Version: 0.0.87
+Version: 0.0.89
 Summary: standardized JSON atom/molecule encoding scheme
 Author-email: Corin Wagen <corin@rowansci.com>
 Project-URL: Homepage, https://github.com/rowansci/stjames

{stjames-0.0.87 → stjames-0.0.89}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "stjames"
-version = "0.0.87"
+version = "0.0.89"
 description = "standardized JSON atom/molecule encoding scheme"
 readme = "README.md"
 requires-python = ">=3.11"

{stjames-0.0.87 → stjames-0.0.89}/stjames/method.py

@@ -36,6 +36,7 @@ class Method(LowercaseStrEnum):
     OCP24_S = "ocp24_s"
     OCP24_L = "ocp24_l"
     OMOL25_CONSERVING_S = "omol25_conserving_s"
+    UMA_M_OMOL = "uma_m_omol"
     ORB_V2 = "orb_v2"
     ORB_V3_CONSERVATIVE_INF_OMAT = "orb_v3_conservative_inf_omat"
 
@@ -62,6 +63,7 @@ PrepackagedNNPMethod = Literal[
     Method.OCP24_S,
     Method.OCP24_L,
     Method.OMOL25_CONSERVING_S,
+    Method.UMA_M_OMOL,
     Method.RM1,
     Method.ORB_V3_CONSERVATIVE_INF_OMAT,
     Method.EGRET_1,
@@ -74,6 +76,7 @@ PREPACKAGED_NNP_METHODS = [
     Method.OCP24_S,
     Method.OCP24_L,
     Method.OMOL25_CONSERVING_S,
+    Method.UMA_M_OMOL,
     Method.RM1,
     Method.ORB_V3_CONSERVATIVE_INF_OMAT,
     Method.EGRET_1,

{stjames-0.0.87 → stjames-0.0.89}/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-0.0.87 → stjames-0.0.89}/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-0.0.87 → stjames-0.0.89}/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-0.0.87 → stjames-0.0.89/stjames.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: stjames
-Version: 0.0.87
+Version: 0.0.89
 Summary: standardized JSON atom/molecule encoding scheme
 Author-email: Corin Wagen <corin@rowansci.com>
 Project-URL: Homepage, https://github.com/rowansci/stjames