stjames 0.0.47__py3-none-any.whl → 0.0.49__py3-none-any.whl

stjames/__init__.py

@@ -9,6 +9,7 @@ from .workflows import *
 from .scf_settings import *
 from .int_settings import *
 from .opt_settings import *
+from .compute_settings import *
 from .diis_settings import *
 from .thermochem_settings import *
 from .grid_settings import *

stjames/compute_settings.py

@@ -0,0 +1,10 @@
+from .base import Base, LowercaseStrEnum
+
+
+class ComputeType(LowercaseStrEnum):
+    CPU = "cpu"
+    GPU = "gpu"
+
+
+class ComputeSettings(Base):
+    compute_type: ComputeType = ComputeType.CPU

stjames/method.py

@@ -32,8 +32,10 @@ class Method(LowercaseStrEnum):
 
     AIMNET2_WB97MD3 = "aimnet2_wb97md3"
     MACE_MP_0 = "mace_mp_0"
+    MACE_MP_0B2_L = "mace_mp_0b2_l"
     OCP24_S = "ocp24_s"
     OCP24_L = "ocp24_l"
+    ORB_V2 = "orb_v2"
 
     GFN_FF = "gfn_ff"
     GFN0_XTB = "gfn0_xtb"
@@ -46,8 +48,14 @@ class Method(LowercaseStrEnum):
     OFF_SAGE_2_2_1 = "off_sage_2_2_1"
 
 
-NNPMethod = Literal[Method.AIMNET2_WB97MD3]
-NNP_METHODS = [Method.AIMNET2_WB97MD3]
+PrepackagedNNPMethod = Literal[Method.AIMNET2_WB97MD3, Method.OCP24_S, Method.OCP24_L]
+PREPACKAGED_NNP_METHODS = [Method.AIMNET2_WB97MD3, Method.OCP24_S, Method.OCP24_L]
+
+CorrectableNNPMethod = Literal[Method.MACE_MP_0B2_L, Method.ORB_V2]
+CORRECTABLE_NNP_METHODS = [Method.MACE_MP_0B2_L, Method.ORB_V2]
+
+NNPMethod = PrepackagedNNPMethod | CorrectableNNPMethod
+NNP_METHODS = [*PREPACKAGED_NNP_METHODS, *CORRECTABLE_NNP_METHODS]
 
 XTBMethod = Literal[Method.GFN_FF, Method.GFN0_XTB, Method.GFN1_XTB, Method.GFN2_XTB]
 XTB_METHODS = [Method.GFN_FF, Method.GFN0_XTB, Method.GFN1_XTB, Method.GFN2_XTB]
@@ -58,8 +66,8 @@ COMPOSITE_METHODS = [Method.HF3C, Method.B973C, Method.R2SCAN3C, Method.WB97X3C]
 FFMethod = Literal[Method.OFF_SAGE_2_2_1]
 FF_METHODS = [Method.OFF_SAGE_2_2_1]
 
-PrepackagedMethod = XTBMethod | CompositeMethod | NNPMethod | FFMethod
-PREPACKAGED_METHODS = [*XTB_METHODS, *COMPOSITE_METHODS, *NNP_METHODS, *FF_METHODS]
+PrepackagedMethod = XTBMethod | CompositeMethod | PrepackagedNNPMethod | FFMethod
+PREPACKAGED_METHODS = [*XTB_METHODS, *COMPOSITE_METHODS, *PREPACKAGED_NNP_METHODS, *FF_METHODS]
 
 MethodWithCorrection = Literal[Method.WB97XD3, Method.WB97XV, Method.WB97MV, Method.WB97MD3BJ, Method.DSDBLYPD3BJ]
 METHODS_WITH_CORRECTION = [Method.WB97XD3, Method.WB97XV, Method.WB97MV, Method.WB97MD3BJ, Method.DSDBLYPD3BJ, Method.B97D3BJ]

stjames/pdb.py

@@ -0,0 +1,197 @@
+from datetime import date
+from pathlib import Path
+from typing import Any, Literal
+
+import atomium  # type: ignore [import-untyped]
+from atomium.pdb import pdb_dict_to_data_dict, pdb_string_to_pdb_dict  # type: ignore [import-untyped]
+from pydantic import BaseModel, ConfigDict, Field
+
+from stjames.types import Matrix3x3, Vector3D
+
+# Mostly for testing purposes
+EXTRA: Literal["allow", "ignore", "forbid"] = "allow"
+
+
+class PDBAtom(BaseModel):
+    """An atom within a residue."""
+
+    model_config = ConfigDict(extra=EXTRA)
+
+    x: float
+    y: float
+    z: float
+    element: str
+    name: str
+    charge: float
+    occupancy: float
+    alt_loc: str | None
+    anisotropy: list[float]
+    bvalue: float
+    is_hetatm: bool
+
+
+class PDBWater(BaseModel):
+    """A water molecule."""
+
+    model_config = ConfigDict(extra=EXTRA)
+
+    name: str | None
+    full_name: str | None
+    atoms: dict[int, PDBAtom] = {}
+    internal_id: str | None
+    polymer: str
+
+
+class PDBResidue(BaseModel):
+    """A structure."""
+
+    model_config = ConfigDict(extra=EXTRA)
+
+    name: str | None
+    full_name: str | None = None
+    atoms: dict[int, PDBAtom] = {}
+    number: int
+
+
+class PDBPolymer(BaseModel):
+    """A polymer chain."""
+
+    model_config = ConfigDict(extra=EXTRA)
+
+    internal_id: str
+    helices: list[list[str]] = []
+    residues: dict[str, PDBResidue] = {}
+    sequence: str | None
+    strands: list[list[str]] = []
+
+
+class PDBNonPolymer(BaseModel):
+    """Non-polymeric molecules/atoms (e.g. ions and ligands)."""
+
+    model_config = ConfigDict(extra=EXTRA)
+
+    name: str
+    full_name: str | None = None
+    atoms: dict[int, PDBAtom]
+    internal_id: str
+    polymer: str
+
+
+class PDBModel(BaseModel):
+    """Structure data."""
+
+    model_config = ConfigDict(extra=EXTRA)
+
+    polymer: dict[str, PDBPolymer] = {}
+    non_polymer: dict[str, PDBNonPolymer] = Field(alias="non-polymer", default_factory=dict)
+    branched: dict[str, Any] = {}
+    water: dict[str, PDBWater] = {}
+
+
+class PDBTransformations(BaseModel):
+    """Transformations applied to the structure."""
+
+    model_config = ConfigDict(extra=EXTRA)
+
+    chains: list[str]
+    matrix: Matrix3x3
+    vector: Vector3D
+
+
+class PDBAssembly(BaseModel):
+    """How the structure was assembled."""
+
+    model_config = ConfigDict(extra=EXTRA)
+
+    transformations: list[PDBTransformations]
+    software: str | None
+    buried_surface_area: float | None
+    surface_area: float | None
+    delta_energy: float | None
+    id: int
+
+
+class PDBCrystallography(BaseModel):
+    """Crystallography related information."""
+
+    model_config = ConfigDict(extra=EXTRA)
+
+    space_group: str | None = None
+    unit_cell: list[float] | None = None
+
+
+class PDBGeometry(BaseModel):
+    """Details of the geometry."""
+
+    model_config = ConfigDict(extra=EXTRA)
+
+    assemblies: list[PDBAssembly] = []
+    crystallography: PDBCrystallography = Field(default_factory=PDBCrystallography)
+
+
+class PDBQuality(BaseModel):
+    """Quality metrics."""
+
+    model_config = ConfigDict(extra=EXTRA)
+
+    resolution: float | None = None
+    rfree: float | None = None
+    rvalue: float | None = None
+
+
+class PDBMissingResidue(BaseModel):
+    model_config = ConfigDict(extra=EXTRA)
+
+    name: str
+    id: str
+
+
+class PDBExperiment(BaseModel):
+    """Details of the experiment."""
+
+    model_config = ConfigDict(extra=EXTRA)
+
+    expression_system: str | None
+    missing_residues: list[PDBMissingResidue] = []
+    source_organism: str | None
+    technique: str | None
+
+
+class PDBDescription(BaseModel):
+    """A description of the molecule."""
+
+    model_config = ConfigDict(extra=EXTRA)
+
+    code: str | None
+    title: str | None
+    authors: list[str] = []
+    classification: str | None
+    deposition_date: date | None
+    keywords: list[str] = []
+
+
+class PDB(BaseModel):
+    """A PDB formatted file."""
+
+    model_config = ConfigDict(extra=EXTRA)
+
+    description: PDBDescription
+    experiment: PDBExperiment
+    geometry: PDBGeometry
+    models: list[PDBModel] = []
+    quality: PDBQuality = Field(default_factory=PDBQuality)
+
+
+def read_pdb(path: Path | str) -> PDB:
+    """Read a pdb located at path."""
+    return PDB.model_validate(atomium.open(str(path), data_dict=True))
+
+
+def fetch_pdb(code: str) -> PDB:
+    """Fetch a pdb from the Protein Data Bank."""
+    return PDB.model_validate(atomium.fetch(code, data_dict=True))
+
+
+def pdb_from_string(pdb: str) -> PDB:
+    """Read a PDB from a string."""
+    return PDB.model_validate(pdb_dict_to_data_dict(pdb_string_to_pdb_dict(pdb)))

stjames/settings.py

@@ -4,8 +4,9 @@ from pydantic import computed_field, field_validator, model_validator
 
 from .base import Base, UniqueList
 from .basis_set import BasisSet
+from .compute_settings import ComputeSettings
 from .correction import Correction
-from .method import METHODS_WITH_CORRECTION, PREPACKAGED_METHODS, Method
+from .method import CORRECTABLE_NNP_METHODS, METHODS_WITH_CORRECTION, PREPACKAGED_METHODS, Method
 from .mode import Mode
 from .opt_settings import OptimizationSettings
 from .scf_settings import SCFSettings
@@ -30,6 +31,7 @@ class Settings(Base):
     scf_settings: SCFSettings = SCFSettings()
     opt_settings: OptimizationSettings = OptimizationSettings()
     thermochem_settings: ThermochemistrySettings = ThermochemistrySettings()
+    compute_settings: ComputeSettings = ComputeSettings()
 
     # mypy has this dead wrong (https://docs.pydantic.dev/2.0/usage/computed_fields/)
     # Python 3.12 narrows the reason for the ignore to prop-decorator
@@ -38,12 +40,14 @@ class Settings(Base):
     def level_of_theory(self) -> str:
         corrections = list(filter(lambda x: x not in (None, ""), self.corrections))
 
-        if self.method in PREPACKAGED_METHODS or self.basis_set is None:
+        if self.method in CORRECTABLE_NNP_METHODS:
+            method = self.method.value if not corrections else f"{self.method.value}-{'-'.join(c.value for c in corrections)}"
+        elif self.method in PREPACKAGED_METHODS or self.basis_set is None:
             method = self.method.value
-        elif self.method in METHODS_WITH_CORRECTION or len(corrections) == 0:
+        elif self.method in METHODS_WITH_CORRECTION or not corrections:
             method = f"{self.method.value}/{self.basis_set.name.lower()}"
         else:
-            method = f"{self.method.value}-{'-'.join([c.value for c in corrections])}/{self.basis_set.name.lower()}"
+            method = f"{self.method.value}-{'-'.join(c.value for c in corrections)}/{self.basis_set.name.lower()}"
 
         if self.solvent_settings is not None:
             method += f"/{self.solvent_settings.model.value}({self.solvent_settings.solvent.value})"

stjames/workflows/hydrogen_bond_basicity.py

@@ -11,6 +11,9 @@ class HydrogenBondAcceptorSite(Base):
 
 
 class HydrogenBondBasicityWorkflow(Workflow):
+    do_csearch: bool = True
+    do_optimization: bool = True
+
     # UUID of optimization
     optimization: UUID | None = None
 

{stjames-0.0.47.dist-info → stjames-0.0.49.dist-info}/METADATA

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: stjames
-Version: 0.0.47
+Version: 0.0.49
 Summary: standardized JSON atom/molecule encoding scheme
 Author-email: Corin Wagen <corin@rowansci.com>
 Project-URL: Homepage, https://github.com/rowansci/stjames
@@ -8,6 +8,7 @@ Project-URL: Bug Tracker, https://github.com/rowansci/stjames/issues
 Requires-Python: >=3.11
 Description-Content-Type: text/markdown
 License-File: LICENSE
+Requires-Dist: atomium<2,>=1
 Requires-Dist: pydantic>=2.4
 Requires-Dist: numpy
 

{stjames-0.0.47.dist-info → stjames-0.0.49.dist-info}/RECORD

@@ -1,23 +1,25 @@
-stjames/__init__.py,sha256=LkWCylP4VeXyQL0iu5w6yeYK1UHjcUH55hwWXTy4mQQ,576
+stjames/__init__.py,sha256=8kqGRUcrOQY07DHp6VJN7GEttPPTHw49QpieMeQqkwE,608
 stjames/_deprecated_solvent_settings.py,sha256=gj5j9p3zakIwSTK5_ndqBXJx--IzjZNxZ75z-wipLOo,450
 stjames/atom.py,sha256=w7q-x9xpBw4sJ1WGrWt65WAaStxhz-m7dugXCYEOpq4,2064
 stjames/base.py,sha256=hroQjvC8G88UiK520i1TDqnOlgw_ihmzevQGTO5yeUY,1215
 stjames/basis_set.py,sha256=wI3M2q9uPf9jhKpAi4E2DrsyKzloDGLRjAlk7krdYgc,949
 stjames/calculation.py,sha256=O2LwwQ_cOLmDOGXTHA9J71YbUZXigUSbvbLA-fSVm3w,915
+stjames/compute_settings.py,sha256=N312PevuI4V2EswJSimitLB_JC92thTCGoZJjXFccxo,191
 stjames/constraint.py,sha256=B6oV0rYjmAWr8gpi5f03gRy_uuqjUURVDVwoez5Cfbg,2442
 stjames/correction.py,sha256=ZVErCcj4TPyZeKrdvXVjHa0tFynsCaoy96QZUVxWFM8,413
 stjames/diis_settings.py,sha256=4m1EQQWBlpHhMnWopix8qOqJv7QCluvdnV9jSKJDFtE,552
 stjames/grid_settings.py,sha256=WrSNGc-8_f87YBZYt9Hh7RbhM4MweADoVzwBMcSqcsE,640
 stjames/int_settings.py,sha256=5HXp8opt5ZyY1UpmfaK7NVloWVLM5jkG0elEEqpVLUo,896
 stjames/message.py,sha256=Rq6QqmHZKecWxYH8fVyXmuoCCPZv8YinvgykSeorXSU,216
-stjames/method.py,sha256=teV0nQZTu8gRSZdFpMhjHtvLPf-XeTIMy330rYWDeZ8,1855
+stjames/method.py,sha256=dWlDoB5xxWqPg6pdQyEeLG7aPsg4cux9ckfaA6GVsD0,2280
 stjames/mode.py,sha256=xw46Cc7f3eTS8i35qECi-8DocAlANhayK3w4akD4HBU,496
 stjames/molecule.py,sha256=v8NikFHfwOahXSo4VKGSqeHKI2HIoRdNjGE0GkZgNS4,10554
 stjames/opt_settings.py,sha256=gxXGtjy9l-Q5Wen9eO6T6HHRCuS8rfOofdVQIJj0JcI,550
+stjames/pdb.py,sha256=goigN-UO72y-nnHmNF4HWp8K_ZYfJorg6TCqWpsNQIU,4519
 stjames/periodic_cell.py,sha256=JDCyynpamggTNi_HnTnnotRbeSMBfYc-srhD-IwUnrg,996
 stjames/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 stjames/scf_settings.py,sha256=WotVgVrayQ_8PUHP39zVtG7iLT9PV41lpzruttFACP8,2356
-stjames/settings.py,sha256=tfgEYns6WdsheQ6wpR6uyI8O4s2iTqyH7YWtNQ36k74,8666
+stjames/settings.py,sha256=NrNtHq-78BNp4RMP0tsABv4BjS5EscANakCyRdImI-A,8967
 stjames/solvent.py,sha256=u037tmu-9oa21s-WEDZ7VC7nuNVjkqR2ML4JWjWSME4,1158
 stjames/status.py,sha256=wTKNcNxStoEHrxxgr_zTyN90NITa3rxMQZzOgrCifEw,332
 stjames/task.py,sha256=OLINRqe66o7t8arffilwmggrF_7TH0L79u6DhGruxV8,329
@@ -39,7 +41,7 @@ stjames/workflows/conformer_search.py,sha256=y64WpdVZcrUit9ub-yWwJ0zNK8ofPlcjOG4
 stjames/workflows/descriptors.py,sha256=lRRCsGzad3nIg0wI1090ffaXB0FVh0nRRb2lNxCY0kI,281
 stjames/workflows/electronic_properties.py,sha256=0PqS04CfLM4pzx67Ph3JJTrzc1LCwDTT5E8x4_wW-g8,3888
 stjames/workflows/fukui.py,sha256=CsJ3_gvzqEqcxwYN7bnNIa37F3KlLm7obsU77TGmDgo,348
-stjames/workflows/hydrogen_bond_basicity.py,sha256=xn4AP_PbCUluzrj05ufw3LaN-xBMsAmt2mFsVy1bf-8,455
+stjames/workflows/hydrogen_bond_basicity.py,sha256=Luvov2DlDvZN06W-mU6YaN7wcIrTLwzdoWww-jNE3x4,517
 stjames/workflows/molecular_dynamics.py,sha256=4HmYETU1VT2BA4-PqAayRZLjnj1WuYxd5bqpIyH9g5k,2465
 stjames/workflows/multistage_opt.py,sha256=0ou-UYMGIrewZIg3QZIgwS_eweYdsh2pRplxgRCqLcE,13572
 stjames/workflows/pka.py,sha256=zpR90Yv2L-D56o2mGArM8027DWpnFFnay31UR9Xh5Nc,774
@@ -48,8 +50,8 @@ stjames/workflows/scan.py,sha256=cQ29DKlLCH7_6_1TFATnaM3ac9G1asUoRoDDlQYAfG0,860
 stjames/workflows/spin_states.py,sha256=TXHqB7ClTkkCy1Yfcsv99v2woAhT8oG1-uaF20-oMbQ,4592
 stjames/workflows/tautomer.py,sha256=owZOOfGlohxlaOG1pGpx7dVPvas8ZEnl_9Ms5F0Kpms,421
 stjames/workflows/workflow.py,sha256=tIu5naADYgYS7kdW8quvGEWHWosBcrIdcD7L86v-uMQ,976
-stjames-0.0.47.dist-info/LICENSE,sha256=i7ehYBS-6gGmbTcgU4mgk28pyOx2kScJ0kcx8n7bWLM,1084
-stjames-0.0.47.dist-info/METADATA,sha256=jJX69FHFW3VDQtIwM7lR7tIZgM_CDeIvbC8qeERRhMU,1627
-stjames-0.0.47.dist-info/WHEEL,sha256=A3WOREP4zgxI0fKrHUG8DC8013e3dK3n7a6HDbcEIwE,91
-stjames-0.0.47.dist-info/top_level.txt,sha256=FYCwxl6quhYOAgG-mnPQcCK8vsVM7B8rIUrO-WrQ_PI,8
-stjames-0.0.47.dist-info/RECORD,,
+stjames-0.0.49.dist-info/LICENSE,sha256=i7ehYBS-6gGmbTcgU4mgk28pyOx2kScJ0kcx8n7bWLM,1084
+stjames-0.0.49.dist-info/METADATA,sha256=NFSiP9l2CXcYhOCEGaOQ95nXTxRxwQHSewRZit1FW88,1656
+stjames-0.0.49.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
+stjames-0.0.49.dist-info/top_level.txt,sha256=FYCwxl6quhYOAgG-mnPQcCK8vsVM7B8rIUrO-WrQ_PI,8
+stjames-0.0.49.dist-info/RECORD,,

{stjames-0.0.47.dist-info → stjames-0.0.49.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (75.7.0)
+Generator: setuptools (75.8.0)
 Root-Is-Purelib: true
 Tag: py3-none-any