stjames 0.0.112__tar.gz → 0.0.115__tar.gz

{stjames-0.0.112/stjames.egg-info → stjames-0.0.115}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: stjames
-Version: 0.0.112
+Version: 0.0.115
 Summary: standardized JSON atom/molecule encoding scheme
 Author-email: Corin Wagen <corin@rowansci.com>
 Project-URL: Homepage, https://github.com/rowansci/stjames

{stjames-0.0.112 → stjames-0.0.115}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "stjames"
-version = "0.0.112"
+version = "0.0.115"
 description = "standardized JSON atom/molecule encoding scheme"
 readme = "README.md"
 requires-python = ">=3.11"

{stjames-0.0.112 → stjames-0.0.115}/stjames/method.py

@@ -8,7 +8,10 @@ class Method(LowercaseStrEnum):
     HARTREE_FOCK = "hf"
     HF3C = "hf_3c"
 
+    # DFT methods
+    ## Pure functionals
     PBE = "pbe"
+    BP86 = "bp86"
     B973C = "b97_3c"
     B97D3BJ = "b97_d3bj"
     R2SCAN = "r2scan"
@@ -16,45 +19,53 @@ class Method(LowercaseStrEnum):
     TPSS = "tpss"
     M06L = "m06l"
 
+    ## Hybrid functionals
     PBE0 = "pbe0"
     B3LYP = "b3lyp"
     TPSSH = "tpssh"
     M06 = "m06"
     M062X = "m062x"
 
+    ## Range-separated hybrid functionals
     CAMB3LYP = "camb3lyp"
     WB97XD3 = "wb97x_d3"
     WB97XV = "wb97x_v"
+    WB97X3C = "wb97x_3c"
     WB97MV = "wb97m_v"
     WB97MD3BJ = "wb97m_d3bj"
-    WB97X3C = "wb97x_3c"
 
+    ## Double hybrid functionals
     DSDBLYPD3BJ = "dsd_blyp_d3bj"
 
+    ## ML functionals
+    SKALA = "skala"
+
+    # NNPs
     AIMNET2_WB97MD3 = "aimnet2_wb97md3"
+
     MACE_MP_0 = "mace_mp_0"
     MACE_MP_0B2_L = "mace_mp_0b2_l"
+
     OMOL25_CONSERVING_S = "omol25_conserving_s"
     UMA_M_OMOL = "uma_m_omol"
     UMA_S_OMOL = "uma_s_omol"
     ORB_V3_CONSERVATIVE_INF_OMAT = "orb_v3_conservative_inf_omat"
     ORB_V3_CONSERVATIVE_OMOL = "orb_v3_conservative_omol"
 
+    EGRET_1 = "egret_1"
+    EGRET_1E = "egret_1e"
+    EGRET_1T = "egret_1t"
+
+    # Semiempirical methods
     GFN_FF = "gfn_ff"
     GFN0_XTB = "gfn0_xtb"
     GFN1_XTB = "gfn1_xtb"
     GFN2_XTB = "gfn2_xtb"
     G_XTB = "g_xtb"
 
-    # this was going to be removed, but Jonathon wrote such a nice basis set test... it's off the front end.
-    BP86 = "bp86"
-
+    # Force fields
     OFF_SAGE_2_2_1 = "off_sage_2_2_1"
 
-    EGRET_1 = "egret_1"
-    EGRET_1E = "egret_1e"
-    EGRET_1T = "egret_1t"
-
     def default_engine(self, *, is_periodic: bool = False) -> Engine:
         """
         Return the canonical Engine for this quantum-chemistry method.
@@ -86,6 +97,8 @@ class Method(LowercaseStrEnum):
                 return Engine.OPENFF
             case Method.EGRET_1 | Method.EGRET_1E | Method.EGRET_1T:
                 return Engine.EGRET
+            case Method.SKALA:
+                return Engine.PYSCF
             case _:
                 # All remaining methods (HF, DFT, composite, etc.) fall back to Psi4
                 return Engine.PSI4

{stjames-0.0.112 → stjames-0.0.115}/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-0.0.112 → stjames-0.0.115}/stjames/workflows/pose_analysis_md.py

@@ -5,7 +5,7 @@ from pydantic import AfterValidator, PositiveFloat, PositiveInt, model_validator
 from ..base import Base, round_float
 from ..pdb import PDB
 from ..types import UUID, round_list
-from .workflow import MoleculeWorkflow
+from .workflow import SMILESWorkflow
 
 
 class BindingPoseContact(Base):
@@ -36,7 +36,7 @@ class BindingPoseTrajectory(Base):
     contacts: list[BindingPoseContact] = []
 
 
-class PoseAnalysisMolecularDynamicsWorkflow(MoleculeWorkflow):
+class PoseAnalysisMolecularDynamicsWorkflow(SMILESWorkflow):
     """
     Pose analysis molecular dynamics workflow.
 
@@ -45,12 +45,13 @@ class PoseAnalysisMolecularDynamicsWorkflow(MoleculeWorkflow):
     If, for whatever reason, the workflow is initialized with both a `target_uuid` and a `target`, the UUID will be ignored.
 
     Inherited:
-    :param initial_molecule: Molecule of interest
+    :param initial_smiles: ligand's SMILES
     :param mode: Mode for workflow (currently unused)
 
     New:
     :param protein: PDB of the protein.
     :param protein_uuid: UUID of the protein.
+    :param ligand_residue_name: ligand's residue name
     :param num_trajectories: how many trajectories to run
     :param equilibration_time_ns: how long to equilibrate trajectories for, in nanoseconds
     :param simulation_time_ns: how long to run trajectories for, in nanoseconds
@@ -73,6 +74,7 @@ class PoseAnalysisMolecularDynamicsWorkflow(MoleculeWorkflow):
 
     protein: PDB | None = None
     protein_uuid: UUID | None = None
+    ligand_residue_name: str = "LIG"
 
     num_trajectories: PositiveInt = 4
     equilibration_time_ns: Annotated[PositiveFloat, AfterValidator(round_float(3))] = 5

{stjames-0.0.112 → stjames-0.0.115/stjames.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: stjames
-Version: 0.0.112
+Version: 0.0.115
 Summary: standardized JSON atom/molecule encoding scheme
 Author-email: Corin Wagen <corin@rowansci.com>
 Project-URL: Homepage, https://github.com/rowansci/stjames