stjames 0.0.114__py3-none-any.whl → 0.0.116__py3-none-any.whl

stjames/workflows/conformer_search.py

@@ -9,9 +9,10 @@ from ..base import LowercaseStrEnum
 from ..constraint import Constraint
 from ..method import Method, XTBMethod
 from ..mode import Mode
+from ..molecule import Molecule
 from ..types import UUID, FloatPerAtom, round_float_per_atom
 from .multistage_opt import MultiStageOptMixin
-from .workflow import MoleculeWorkflow
+from .workflow import MoleculeWorkflow, SMILESWorkflow
 
 _sentinel = object()
 
@@ -377,12 +378,16 @@ class ConformerSearchMixin(ConformerGenMixin, MultiStageOptMixin):
         return self
 
 
-class ConformerSearchWorkflow(ConformerSearchMixin, MoleculeWorkflow):
+class ConformerSearchWorkflow(ConformerSearchMixin, SMILESWorkflow, MoleculeWorkflow):
     """
     ConformerSearch Workflow.
 
+    This workflow supports both SMILES and 3D molecular input. Some conformer generation settings
+    support both methods; others (like CREST) require 3D information. Only one should be supplied.
+
     Inherited:
     :param initial_molecule: Molecule of interest
+    :param initial_smiles: SMILES of the molecule of interest
     :param conf_gen_mode: Mode for calculations
     :param conf_gen_settings: settings for conformer generation
     :param mso_mode: Mode for MultiStageOptSettings
@@ -401,6 +406,21 @@ class ConformerSearchWorkflow(ConformerSearchMixin, MoleculeWorkflow):
     :param energies: energies of the molecules
     """
 
+    initial_smiles: str = ""
+    initial_molecule: Molecule | None = None  # type: ignore [assignment]
+
     # Results
     conformer_uuids: list[list[UUID | None]] = Field(default_factory=list)
     energies: Annotated[FloatPerAtom, AfterValidator(round_float_per_atom(6))] = Field(default_factory=list)
+
+    @model_validator(mode="after")
+    def validate_mol_input(self) -> Self:
+        """Ensure that only one of initial_molecule or initial_smiles is set."""
+
+        if not (bool(self.initial_smiles) ^ bool(self.initial_molecule)):
+            raise ValueError("Can only set one of initial_molecule and initial_smiles")
+
+        if isinstance(self.conf_gen_settings, iMTDSettings) and (self.initial_molecule is None):
+            raise ValueError("iMTDSettings requires `initial_molecule` to be set")
+
+        return self

stjames/workflows/docking.py

@@ -1,6 +1,6 @@
 """Docking workflow."""
 
-from typing import Annotated, Self, TypeAlias
+from typing import Annotated, Literal, Self, TypeAlias
 
 from pydantic import AfterValidator, ConfigDict, field_validator, model_validator
 
@@ -46,12 +46,23 @@ class VinaSettings(DockingSettings):
     """
     Controls how AutoDock Vina is run.
 
+    :param executable: which Vina implementation is run.
+    :param scoring_function: which scoring function is employed.
     :param exhaustiveness: how many times Vina attempts to find a pose.
         8 is typical, 32 is considered relatively careful.
     """
 
+    executable: Literal["qvina2", "vina"] = "vina"
+    scoring_function: Literal["vinardo", "vina"] = "vinardo"
     exhaustiveness: int = 8
 
+    @model_validator(mode="after")
+    def check_executable_scoring_function(self) -> Self:
+        """Check if the combination of exectuable and scoring function is supported."""
+        if (self.executable == "qvina2") and (self.scoring_function == "vinardo"):
+            raise ValueError("qvina2 does not implement the vinardo scoring function!")
+        return self
+
 
 class DockingWorkflow(MoleculeWorkflow):
     """

stjames/workflows/pka.py

@@ -10,7 +10,7 @@ from ..molecule import Molecule
 from ..solvent import Solvent
 from .workflow import DBCalculation, MoleculeWorkflow, SMILESWorkflow
 
-CHEMPROP_NEVOLIANUS2025_ALLOWED_SOLVENTS = {
+CHEMPROP_NEVOLIANIS2025_ALLOWED_SOLVENTS = {
     Solvent.WATER,
     Solvent.DIMETHYLSULFOXIDE,
     Solvent.DIMETHYLFORMAMIDE,
@@ -24,7 +24,7 @@ CHEMPROP_NEVOLIANUS2025_ALLOWED_SOLVENTS = {
 
 class MicroscopicpKaMethod(LowercaseStrEnum):
     AIMNET2_WAGEN2024 = "aimnet2_wagen2024"
-    CHEMPROP_NEVOLIANUS2025 = "chemprop_nevolianus2025"
+    CHEMPROP_NEVOLIANIS2025 = "chemprop_nevolianis2025"
 
 
 class pKaMicrostate(Base):
@@ -102,8 +102,8 @@ class pKaWorkflow(SMILESWorkflow, MoleculeWorkflow):
             case MicroscopicpKaMethod.AIMNET2_WAGEN2024:
                 if self.solvent is not Solvent.WATER:
                     raise ValueError(f"{self.microscopic_pka_method} only supports water")
-            case MicroscopicpKaMethod.CHEMPROP_NEVOLIANUS2025:
-                if self.solvent not in CHEMPROP_NEVOLIANUS2025_ALLOWED_SOLVENTS:
+            case MicroscopicpKaMethod.CHEMPROP_NEVOLIANIS2025:
+                if self.solvent not in CHEMPROP_NEVOLIANIS2025_ALLOWED_SOLVENTS:
                     raise ValueError(f"Solvent `{self.solvent}` is not supported by method `{self.microscopic_pka_method}`.")
                 if len(self.protonate_atoms) or len(self.deprotonate_atoms):
                     raise ValueError(f"Method `{self.microscopic_pka_method}` does not support selecting atoms by number.")

stjames/workflows/pose_analysis_md.py

@@ -76,8 +76,8 @@ class PoseAnalysisMolecularDynamicsWorkflow(SMILESWorkflow):
     protein_uuid: UUID | None = None
     ligand_residue_name: str = "LIG"
 
-    num_trajectories: PositiveInt = 4
-    equilibration_time_ns: Annotated[PositiveFloat, AfterValidator(round_float(3))] = 5
+    num_trajectories: PositiveInt = 1
+    equilibration_time_ns: Annotated[PositiveFloat, AfterValidator(round_float(3))] = 1
     simulation_time_ns: Annotated[PositiveFloat, AfterValidator(round_float(3))] = 10
 
     temperature: Annotated[PositiveFloat, AfterValidator(round_float(3))] = 300

{stjames-0.0.114.dist-info → stjames-0.0.116.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: stjames
-Version: 0.0.114
+Version: 0.0.116
 Summary: standardized JSON atom/molecule encoding scheme
 Author-email: Corin Wagen <corin@rowansci.com>
 Project-URL: Homepage, https://github.com/rowansci/stjames

{stjames-0.0.114.dist-info → stjames-0.0.116.dist-info}/RECORD

@@ -42,9 +42,9 @@ stjames/workflows/admet.py,sha256=qFUpCFiLW-3gzuEjCMNBJ6DEG_vquJcPAsN4SVZRfdE,12
 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=sQayHL5aGY8WssQOGW4lPh1aXLfcPJewG9WUiC8il6A,14744
+stjames/workflows/conformer_search.py,sha256=1kBUT0yCcTPTCtxg1tlTKHRRXkfNYNqzla_89lDEL9k,15696
 stjames/workflows/descriptors.py,sha256=T4tc7xdtBdxESGO86KR323jPQ2pgwxBqgV0khA6MEgQ,584
-stjames/workflows/docking.py,sha256=sJFSGyIve-q55UEir2rV9Pk7L09_pPuSy2K00JLvA68,4138
+stjames/workflows/docking.py,sha256=t30kqeFXQ0yrlqvN6Jdwt0SdfnJLDsfK-7yFi0gwNbY,4753
 stjames/workflows/double_ended_ts_search.py,sha256=ovJgEVFc6c3mijCE3TKAY70YvqNmAZ5Y4XgV4-tIxBI,3127
 stjames/workflows/electronic_properties.py,sha256=GT3-NC7w-dbcOJ-3AzJ7LgzH6frTbiH2Iyb9BCa-SvY,4112
 stjames/workflows/fukui.py,sha256=095GDGSSEc5PDD1aoKM8J7icgR5tfwS5Bs9XxFQHge4,2387
@@ -55,8 +55,8 @@ stjames/workflows/macropka.py,sha256=Krj0xXuB-u57Kqlf4bbRiHDUWCpliFr6YPiYqPmYaWk
 stjames/workflows/molecular_dynamics.py,sha256=HqWNxxPSAphfI0DdbTERFkq8UeBjEvhnA_ETv0xw_RY,3522
 stjames/workflows/multistage_opt.py,sha256=UN-4WLsT2WEjO5KqDPrcCkb708Co-ZScHx3g2bto768,16597
 stjames/workflows/nmr.py,sha256=1QEF4SB6dWIr-jzLEZ7V972UnRUOTufOJSHwIGyV3dM,2681
-stjames/workflows/pka.py,sha256=EaeC61dIiG_-ymA_BY0Be-pATpI2sHhYVRu4DXKRYzA,4580
-stjames/workflows/pose_analysis_md.py,sha256=KLxSSuM60UpVawDI2xTvsMXoLHFIlA2CtVbpD0uePF4,4803
+stjames/workflows/pka.py,sha256=i-jzl2lN0yRWc0tgrWSBCplITEByfRyEQrlUhjnzcBc,4580
+stjames/workflows/pose_analysis_md.py,sha256=dpWVKC-8fPdw6ExIXk9xbeVBDUMUYQECpixb-oFa23I,4803
 stjames/workflows/protein_cofolding.py,sha256=cN0WUh8trrWwzNvoU75hB-VectIer-g5sMKgibQJcfE,4293
 stjames/workflows/redox_potential.py,sha256=7S18t9Y3eynSnA3lZbRlvLfdbgeBopdiigLzt1zxg5c,3871
 stjames/workflows/scan.py,sha256=DXQBpa2t2PowAtOwmdgpxaSLq--fEShljzAGSb8Nf5U,2993
@@ -65,8 +65,8 @@ stjames/workflows/spin_states.py,sha256=0degmE-frovgoXweshZyjfjqL7nkbaFoO9YoJhvQ
 stjames/workflows/strain.py,sha256=paYxDDQTB1eYP_c2kLVz1-QX7Vpw0LLb3ujnFin_SOM,1834
 stjames/workflows/tautomer.py,sha256=7eYKziGPg8Km6lfowTzSkgJfJ4SHUPrAmnTf8Bi-SB0,1164
 stjames/workflows/workflow.py,sha256=OE05pt2ZOd8TzTOlBngXCVg9wv_553ZR60VNRPlq0f8,1953
-stjames-0.0.114.dist-info/licenses/LICENSE,sha256=i05z7xEhyrg6f8j0lR3XYjShnF-MJGFQ-DnpsZ8yiVI,1084
-stjames-0.0.114.dist-info/METADATA,sha256=g-8yhWenZ6ulvAFzbqp-TFYi9u6FWUsGfus8qw0WMKk,1725
-stjames-0.0.114.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-stjames-0.0.114.dist-info/top_level.txt,sha256=FYCwxl6quhYOAgG-mnPQcCK8vsVM7B8rIUrO-WrQ_PI,8
-stjames-0.0.114.dist-info/RECORD,,
+stjames-0.0.116.dist-info/licenses/LICENSE,sha256=i05z7xEhyrg6f8j0lR3XYjShnF-MJGFQ-DnpsZ8yiVI,1084
+stjames-0.0.116.dist-info/METADATA,sha256=IbTEKrb49Z5vD7QdSV412MBQQH4Yv2uSftLO2IoObzY,1725
+stjames-0.0.116.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+stjames-0.0.116.dist-info/top_level.txt,sha256=FYCwxl6quhYOAgG-mnPQcCK8vsVM7B8rIUrO-WrQ_PI,8
+stjames-0.0.116.dist-info/RECORD,,