stjames 0.0.112__py3-none-any.whl → 0.0.115__py3-none-any.whl

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/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

@@ -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.dist-info → stjames-0.0.115.dist-info}/METADATA

@@ -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.dist-info → stjames-0.0.115.dist-info}/RECORD

@@ -9,7 +9,7 @@ stjames/constraint.py,sha256=B6oV0rYjmAWr8gpi5f03gRy_uuqjUURVDVwoez5Cfbg,2442
 stjames/correction.py,sha256=ZVErCcj4TPyZeKrdvXVjHa0tFynsCaoy96QZUVxWFM8,413
 stjames/engine.py,sha256=jaOHi3nhKZG85HAvKu-HuDl1Hh9nnJfhmOez2ghZXWA,293
 stjames/message.py,sha256=Rq6QqmHZKecWxYH8fVyXmuoCCPZv8YinvgykSeorXSU,216
-stjames/method.py,sha256=3HJ-dSK75HG-YPzgDVT8lQ0Ttld-TF984qDDTTAJk9A,4762
+stjames/method.py,sha256=rVIGevry4u6Zl9Bme5E7XxxzXD12aCvEdt-0oSiCFtI,4965
 stjames/mode.py,sha256=xw46Cc7f3eTS8i35qECi-8DocAlANhayK3w4akD4HBU,496
 stjames/molecule.py,sha256=4Tsa_gRC4C-qGPop24jRIs2q07r0LGbSRb-ApOaZa5c,20839
 stjames/opt_settings.py,sha256=HjKbyFWcxD10FZfbqLxx1RKT0rcXGBr8bmi4ms4U3Sw,684
@@ -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=ES0XlzaLpTjhLrNvcB0zFZa1b1ZHXekN72EbLsx0Skw,4723
+stjames/workflows/pka.py,sha256=i-jzl2lN0yRWc0tgrWSBCplITEByfRyEQrlUhjnzcBc,4580
+stjames/workflows/pose_analysis_md.py,sha256=KLxSSuM60UpVawDI2xTvsMXoLHFIlA2CtVbpD0uePF4,4803
 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-0.0.112.dist-info/licenses/LICENSE,sha256=i05z7xEhyrg6f8j0lR3XYjShnF-MJGFQ-DnpsZ8yiVI,1084
-stjames-0.0.112.dist-info/METADATA,sha256=uFnIQFjjqEHxaIKFXI-WxX5521fRNUfGQZiFqZfl6Fw,1725
-stjames-0.0.112.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-stjames-0.0.112.dist-info/top_level.txt,sha256=FYCwxl6quhYOAgG-mnPQcCK8vsVM7B8rIUrO-WrQ_PI,8
-stjames-0.0.112.dist-info/RECORD,,
+stjames-0.0.115.dist-info/licenses/LICENSE,sha256=i05z7xEhyrg6f8j0lR3XYjShnF-MJGFQ-DnpsZ8yiVI,1084
+stjames-0.0.115.dist-info/METADATA,sha256=SXjEZ5InRPFPo1QtWBhil1BqW-YIjY9b-xH8pt1F-3Y,1725
+stjames-0.0.115.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+stjames-0.0.115.dist-info/top_level.txt,sha256=FYCwxl6quhYOAgG-mnPQcCK8vsVM7B8rIUrO-WrQ_PI,8
+stjames-0.0.115.dist-info/RECORD,,