stjames 0.0.40__tar.gz → 0.0.42__tar.gz

{stjames-0.0.40/stjames.egg-info → stjames-0.0.42}/PKG-INFO

@@ -1,11 +1,11 @@
 Metadata-Version: 2.1
 Name: stjames
-Version: 0.0.40
+Version: 0.0.42
 Summary: standardized JSON atom/molecule encoding scheme
 Author-email: Corin Wagen <corin@rowansci.com>
 Project-URL: Homepage, https://github.com/rowansci/stjames
 Project-URL: Bug Tracker, https://github.com/rowansci/stjames/issues
-Requires-Python: >=3.8
+Requires-Python: >=3.11
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: pydantic>=2.4
@@ -27,7 +27,7 @@ This is not intended to be run as a standalone library: it's basically just a bi
 
 ## Installation
 
-To install, ensure you have Python 3.8 or newer. Then run:
+To install, ensure you have Python 3.11 or newer. Then run:
 
 ```
 pip install stjames

{stjames-0.0.40 → stjames-0.0.42}/README.md

@@ -14,7 +14,7 @@ This is not intended to be run as a standalone library: it's basically just a bi
 
 ## Installation
 
-To install, ensure you have Python 3.8 or newer. Then run:
+To install, ensure you have Python 3.11 or newer. Then run:
 
 ```
 pip install stjames

{stjames-0.0.40 → stjames-0.0.42}/pyproject.toml

@@ -1,9 +1,9 @@
 [project]
 name = "stjames"
-version = "0.0.40"
+version = "0.0.42"
 description = "standardized JSON atom/molecule encoding scheme"
 readme = "README.md"
-requires-python = ">=3.8"
+requires-python = ">=3.11"
 authors = [
     { name = "Corin Wagen", email = "corin@rowansci.com" },
 ]
@@ -28,20 +28,33 @@ include = ["stjames", "stjames.*"]  # package names should match these glob patt
 exclude = []  # exclude packages matching these glob patterns (empty by default)
 namespaces = false  # to disable scanning PEP 420 namespaces (true by default)
 
+[tool.setuptools.package-data]
+"*" = ["*.json"]
+
 [tool.ruff]
 line-length = 160
 
 [tool.ruff.lint]
 select = [
-    "E",  # pycodestyle errors
-    "F",  # pyflakes
-    "I",  # isort
-    "W",  # pycodestyle warnings
+  "E",  # pycodestyle errors
+  "F",  # pyflakes
+  "I",  # isort
+  "W",  # pycodestyle warnings
 ]
 ignore = ["E741"]
 
 [tool.ruff.lint.per-file-ignores]
 "__init__.py" = ["F401", "F403"]
 
+[tool.pytest.ini_options]
+testpaths = ["stjames", "tests"]
+addopts = "--doctest-modules"
+doctest_optionflags = "NORMALIZE_WHITESPACE"
+markers = [
+  "smoke: sanity tests to reveal simple failures"
+]
+
 [tool.mypy]
 plugins = ["pydantic.mypy"]
+strict = true
+warn_unused_ignores = true

{stjames-0.0.40 → stjames-0.0.42}/stjames/__init__.py

@@ -1,6 +1,8 @@
 # ruff: noqa: I001
 
 from .calculation import *
+from .atom import *
+from .periodic_cell import *
 from .molecule import *
 from .workflows import *
 
@@ -21,3 +23,4 @@ from .mode import *
 from .status import *
 from .constraint import *
 from .message import *
+from .types import *

stjames-0.0.42/stjames/atom.py

@@ -0,0 +1,66 @@
+from typing import Self, Sequence
+
+from pydantic import NonNegativeInt
+
+from .base import Base
+from .data import ELEMENT_SYMBOL, SYMBOL_ELEMENT
+from .types import Vector3D
+
+
+class Atom(Base):
+    atomic_number: NonNegativeInt
+    position: Vector3D  # in Å
+
+    def __repr__(self) -> str:
+        """
+        >>> Atom(atomic_number=2, position=[0, 1, 2])
+        Atom(2, [0.00000, 1.00000, 2.00000])
+        """
+        x, y, z = self.position
+        return f"Atom({self.atomic_number}, [{x:.5f}, {y:.5f}, {z:.5f}])"
+
+    def __str__(self) -> str:
+        """
+        >>> str(Atom(atomic_number=2, position=[0, 1, 2]))
+        'He    0.0000000000    1.0000000000    2.0000000000'
+        """
+        x, y, z = self.position
+        return f"{self.atomic_symbol:2} {x:15.10f} {y:15.10f} {z:15.10f}"
+
+    @property
+    def atomic_symbol(self) -> str:
+        """
+        >>> Atom(atomic_number=2, position=[0, 1, 2]).atomic_symbol
+        'He'
+        """
+        return ELEMENT_SYMBOL[self.atomic_number]
+
+    def edited(self, atomic_number: int | None = None, position: Sequence[float] | None = None) -> Self:
+        """
+        Create a new Atom with the specified changes.
+
+        >>> a = Atom(atomic_number=2, position=[0, 1, 2])
+        >>> a2 = a.edited(3)
+        >>> a is a2
+        False
+        >>> a2
+        Atom(3, [0.00000, 1.00000, 2.00000])
+        """
+        if atomic_number is None:
+            atomic_number = self.atomic_number
+        if position is None:
+            position = list(self.position)
+
+        return self.__class__(atomic_number=atomic_number, position=position)
+
+    @classmethod
+    def from_xyz(cls: type[Self], xyz_line: str) -> Self:
+        """
+        >>> Atom.from_xyz("H 0 0 0")
+        Atom(1, [0.00000, 0.00000, 0.00000])
+        """
+        name, *xyz = xyz_line.split()
+        symbol = int(name) if name.isdigit() else SYMBOL_ELEMENT[name]
+        if not len(xyz) == 3:
+            raise ValueError("XYZ file should have 3 coordinates per atom")
+        return cls(atomic_number=symbol, position=xyz)

stjames-0.0.42/stjames/base.py

@@ -0,0 +1,42 @@
+from enum import Enum
+from typing import Annotated, Any, Hashable, TypeVar
+
+import numpy as np
+import pydantic
+
+_T = TypeVar("_T")
+
+
+class Base(pydantic.BaseModel):
+    @pydantic.field_validator("*", mode="before")
+    @classmethod
+    def coerce_numpy(cls, val: _T) -> _T | list[Any]:
+        if isinstance(val, np.ndarray):
+            return val.tolist()  # type: ignore [no-any-return, unused-ignore]
+
+        return val
+
+
+class LowercaseStrEnum(str, Enum):
+    """Enum where hyphens, underscores, and case are ignored."""
+
+    @classmethod
+    def _missing_(cls, value: object) -> str | None:
+        for member in cls:
+            if isinstance(value, str):
+                if member.lower().replace("-", "").replace("_", "") == value.lower().replace("-", "").replace("_", ""):
+                    return member
+        return None
+
+
+# cf. https://github.com/pydantic/pydantic-core/pull/820#issuecomment-1670475909
+_H = TypeVar("_H", bound=Hashable)
+
+
+def _validate_unique_list(v: list[_H]) -> list[_H]:
+    if len(v) != len(set(v)):
+        raise ValueError("this list must be unique, and isn't!")
+    return v
+
+
+UniqueList = Annotated[list[_H], pydantic.AfterValidator(_validate_unique_list)]

{stjames-0.0.40 → stjames-0.0.42}/stjames/basis_set.py

@@ -1,10 +1,6 @@
-import pydantic
-from pydantic import PositiveFloat, PositiveInt
+from typing import Optional, Self
 
-try:
-    from typing import Optional, Self
-except ImportError:
-    from typing_extensions import Optional, Self
+from pydantic import PositiveFloat, PositiveInt, model_validator
 
 from .base import Base
 
@@ -14,7 +10,7 @@ class BasisSetOverride(Base):
     atomic_numbers: Optional[list[PositiveInt]] = None
     atoms: Optional[list[PositiveInt]] = None  # 1-indexed
 
-    @pydantic.model_validator(mode="after")
+    @model_validator(mode="after")
     def check_override(self) -> Self:
         # ^ is xor
         assert (self.atomic_numbers is not None) ^ (self.atoms is not None), "Exactly one of ``atomic_numbers`` or ``atoms`` must be specified!"

{stjames-0.0.40 → stjames-0.0.42}/stjames/calculation.py

@@ -5,6 +5,7 @@ from .message import Message
 from .molecule import Molecule
 from .settings import Settings
 from .status import Status
+from .types import UUID
 
 
 class StJamesVersion(LowercaseStrEnum):
@@ -29,6 +30,7 @@ class Calculation(Base):
     messages: list[Message] = []
 
     engine: Optional[str] = "peregrine"
+    uuids: list[UUID | None] | None = None
 
     # not to be changed by end users, diff. versions will have diff. defaults
     json_format: str = StJamesVersion.V0

stjames-0.0.42/stjames/constraint.py

@@ -0,0 +1,36 @@
+from pydantic import PositiveFloat, PositiveInt
+
+from .base import Base, LowercaseStrEnum
+
+
+class ConstraintType(LowercaseStrEnum):
+    """Different sorts of constraints."""
+
+    BOND = "bond"
+    ANGLE = "angle"
+    DIHEDRAL = "dihedral"
+
+
+class Constraint(Base):
+    """Represents a single (absolute) constraint."""
+
+    constraint_type: ConstraintType
+    atoms: list[PositiveInt]  # 1-indexed
+
+
+class PairwiseHarmonicConstraint(Base):
+    """
+    Represents a harmonic constraint, with a characteristic spring constant.
+    """
+
+    atoms: tuple[PositiveInt, PositiveInt]  # 1-indexed
+    spring_constant: PositiveFloat  # kcal/mol / Å**2
+
+
+class SphericalHarmonicConstraint(Base):
+    """
+    Represents a spherical harmonic constraint to keep a system near the origin.
+    """
+
+    confining_radius: PositiveFloat
+    confining_force_constant: PositiveFloat = 10  # kcal/mol / Å**2

stjames-0.0.42/stjames/data/__init__.py

@@ -0,0 +1 @@
+from .elements import *

stjames-0.0.42/stjames/data/bragg_radii.json

@@ -0,0 +1 @@
+{"1": 0.661, "2": 0.661, "3": 2.74, "4": 1.984, "5": 1.606, "6": 1.323, "7": 1.228, "8": 1.134, "9": 0.945, "10": 0.9, "11": 3.402, "12": 2.835, "13": 2.362, "14": 2.079, "15": 1.89, "16": 1.89, "17": 1.89, "18": 1.89, "19": 4.157, "20": 3.402, "21": 3.024, "22": 2.656, "23": 2.551, "24": 2.656, "25": 2.656, "26": 2.656, "27": 2.551, "28": 2.551, "29": 2.551, "30": 2.551, "31": 2.457, "32": 2.362, "33": 2.173, "34": 2.173, "35": 2.173, "36": 2.173, "37": 4.441, "38": 3.78, "39": 3.402, "40": 2.929, "41": 2.74, "42": 2.74, "43": 2.551, "44": 2.457, "45": 2.551, "46": 2.646, "47": 3.024, "48": 2.929, "49": 2.929, "50": 2.74, "51": 2.74, "52": 2.646, "53": 2.646, "54": 2.646, "55": 4.913, "56": 4.063, "57": 3.685, "58": 3.496, "59": 3.496, "60": 3.496, "61": 3.496, "62": 3.496, "63": 3.496, "64": 3.402, "65": 3.307, "66": 3.307, "67": 3.307, "68": 3.307, "69": 3.307, "70": 3.307, "71": 3.307, "72": 3.307, "73": 2.929, "74": 2.74, "75": 2.551, "76": 2.551, "77": 2.457, "78": 2.551, "79": 2.551, "80": 2.551, "81": 2.835, "82": 3.591, "83": 3.024, "84": 3.024, "85": 3.591, "86": 3.591, "87": 3.591, "88": 4.063, "89": 4.063, "90": 3.685, "91": 3.401, "92": 3.401, "93": 3.307, "94": 3.307, "95": 3.307, "96": 3.307, "97": 3.307, "98": 3.307, "99": 3.307, "100": 3.307, "101": 3.307, "102": 3.307, "103": 3.307, "104": 3.307, "105": 3.307}

stjames-0.0.42/stjames/data/elements.py

@@ -0,0 +1,27 @@
+"""Read elemental data from files."""
+
+import json
+from collections import namedtuple
+from importlib import resources
+
+data_dir = resources.files("stjames").joinpath("data")
+
+with data_dir.joinpath("symbol_element.json").open() as f:
+    SYMBOL_ELEMENT: dict[str, int] = json.loads(f.read())
+
+ELEMENT_SYMBOL = {v: k for k, v in SYMBOL_ELEMENT.items()}
+
+Isotope = namedtuple("Isotope", ["relative_atomic_mass", "isotopic_composition", "standard_atomic_weight"])
+with data_dir.joinpath("nist_isotopes.json").open() as f:
+    d = json.loads(f.read())
+
+    ISOTOPES: dict[int, dict[int, Isotope]] = {
+        int(k): {
+            int(kk): Isotope(*vv)
+            for kk, vv in v.items()  # stay open
+        }
+        for k, v in d.items()
+    }
+
+with data_dir.joinpath("bragg_radii.json").open() as f:
+    BRAGG_RADII: dict[int, float] = json.loads(f.read())

stjames-0.0.42/stjames/data/isotopes.json

@@ -0,0 +1 @@
+{"H": {"1.007825": 0.999885, "2.014102": 0.000115, "3.016049": 0.0}, "He": {"3.016029": 1e-06, "4.002603": 0.999999}, "Li": {"6.015123": 0.0759, "7.016003": 0.9241}, "Be": {"9.012183": 1.0}, "B": {"10.012937": 0.199, "11.009305": 0.801}, "C": {"12.0": 0.9893, "13.003355": 0.0107, "14.003242": 0.0}, "N": {"14.003074": 0.99636, "15.000109": 0.00364}, "O": {"15.994915": 0.99757, "16.999132": 0.00038, "17.99916": 0.00205}, "F": {"18.998403": 1.0}, "Ne": {"19.99244": 0.9048, "20.993847": 0.0027, "21.991385": 0.0925}, "Na": {"22.989769": 1.0}, "Mg": {"23.985042": 0.7899, "24.985837": 0.1, "25.982593": 0.1101}, "Al": {"26.981539": 1.0}, "Si": {"27.976927": 0.92223, "28.976495": 0.04685, "29.97377": 0.03092}, "P": {"30.973762": 1.0}, "S": {"31.972071": 0.9499, "32.971459": 0.0075, "33.967867": 0.0425, "35.967081": 0.0001}, "Cl": {"34.968853": 0.7576, "36.965903": 0.2424}, "Ar": {"35.967545": 0.003336, "37.962732": 0.000629, "39.962383": 0.996035}, "K": {"38.963706": 0.932581, "39.963998": 0.000117, "40.961825": 0.067302}, "Ca": {"39.962591": 0.96941, "41.958618": 0.00647, "42.958766": 0.00135, "43.955482": 0.02086, "45.953689": 4e-05, "47.952523": 0.00187}, "Sc": {"44.955908": 1.0}, "Ti": {"45.952628": 0.0825, "46.951759": 0.0744, "47.947942": 0.7372, "48.947866": 0.0541, "49.944787": 0.0518}, "V": {"49.947156": 0.0025, "50.943957": 0.9975}, "Cr": {"49.946042": 0.04345, "51.940506": 0.83789, "52.940648": 0.09501, "53.938879": 0.02365}, "Mn": {"54.938044": 1.0}, "Fe": {"53.939609": 0.05845, "55.934936": 0.91754, "56.935393": 0.02119, "57.933274": 0.00282}, "Co": {"58.933194": 1.0}, "Ni": {"57.935342": 0.68077, "59.930786": 0.26223, "60.931056": 0.011399, "61.928345": 0.036346, "63.927967": 0.009255}, "Cu": {"62.929598": 0.6915, "64.92779": 0.3085}, "Zn": {"63.929142": 0.4917, "65.926034": 0.2773, "66.927128": 0.0404, "67.924845": 0.1845, "69.925319": 0.0061}, "Ga": {"68.925573": 0.60108, "70.924703": 0.39892}, "Ge": {"69.924249": 0.2057, "71.922076": 0.2745, "72.923459": 0.0775, "73.921178": 0.365, "75.921403": 0.0773}, "As": {"74.921595": 1.0}, "Se": {"73.922476": 0.0089, "75.919214": 0.0937, "76.919914": 0.0763, "77.917309": 0.2377, "79.916522": 0.4961, "81.916699": 0.0873}, "Br": {"78.918338": 0.5069, "80.91629": 0.4931}, "Kr": {"77.920365": 0.00355, "79.916378": 0.02286, "81.913483": 0.11593, "82.914127": 0.115, "83.911498": 0.56987, "85.910611": 0.17279}, "Rb": {"84.91179": 0.7217, "86.909181": 0.2783}, "Sr": {"83.913419": 0.0056, "85.909261": 0.0986, "86.908878": 0.07, "87.905613": 0.8258}, "Y": {"88.90584": 1.0}, "Zr": {"89.904698": 0.5145, "90.90564": 0.1122, "91.905035": 0.1715, "93.906311": 0.1738, "95.908271": 0.028}, "Nb": {"92.906373": 1.0}, "Mo": {"91.906808": 0.1453, "93.905085": 0.0915, "94.905839": 0.1584, "95.904676": 0.1667, "96.906018": 0.096, "97.905405": 0.2439, "99.907472": 0.0982}, "Tc": {"96.906367": 0.0, "97.907212": 0.0, "98.906251": 0.0}, "Ru": {"95.90759": 0.0554, "97.905287": 0.0187, "98.905934": 0.1276, "99.904214": 0.126, "100.905577": 0.1706, "101.904344": 0.3155, "103.905428": 0.1862}, "Rh": {"102.905498": 1.0}, "Pd": {"101.905602": 0.0102, "103.904031": 0.1114, "104.90508": 0.2233, "105.90348": 0.2733, "107.903892": 0.2646, "109.905172": 0.1172}, "Ag": {"106.905092": 0.51839, "108.904755": 0.48161}, "Cd": {"105.90646": 0.0125, "107.904183": 0.0089, "109.903007": 0.1249, "110.904183": 0.128, "111.902763": 0.2413, "112.904408": 0.1222, "113.903365": 0.2873, "115.904763": 0.0749}, "In": {"112.904062": 0.0429, "114.903879": 0.9571}, "Sn": {"111.904824": 0.0097, "113.902783": 0.0066, "114.903345": 0.0034, "115.901743": 0.1454, "116.902954": 0.0768, "117.901607": 0.2422, "118.903311": 0.0859, "119.902202": 0.3258, "121.903444": 0.0463, "123.905277": 0.0579}, "Sb": {"120.903812": 0.5721, "122.904213": 0.4279}, "Te": {"119.904059": 0.0009, "121.903043": 0.0255, "122.90427": 0.0089, "123.902817": 0.0474, "124.90443": 0.0707, "125.903311": 0.1884, "127.904461": 0.3174, "129.906223": 0.3408}, "I": {"126.904472": 1.0}, "Xe": {"123.905892": 0.000952, "125.904298": 0.00089, "127.903531": 0.019102, "128.904781": 0.264006, "129.903509": 0.04071, "130.905084": 0.212324, "131.904155": 0.269086, "133.905395": 0.104357, "135.907214": 0.088573}, "Cs": {"132.905452": 1.0}, "Ba": {"129.906321": 0.00106, "131.905061": 0.00101, "133.904508": 0.02417, "134.905688": 0.06592, "135.904576": 0.07854, "136.905827": 0.11232, "137.905247": 0.71698}, "La": {"137.907115": 0.000888, "138.906356": 0.999112}, "Ce": {"135.907129": 0.00185, "137.905991": 0.00251, "139.905443": 0.8845, "141.90925": 0.11114}, "Pr": {"140.907658": 1.0}, "Nd": {"141.907729": 0.27152, "142.90982": 0.12174, "143.910093": 0.23798, "144.912579": 0.08293, "145.913123": 0.17189, "147.916899": 0.05756, "149.920902": 0.05638}, "Pm": {"144.912756": 0.0, "146.915145": 0.0}, "Sm": {"143.912006": 0.0307, "146.914904": 0.1499, "147.914829": 0.1124, "148.917192": 0.1382, "149.917283": 0.0738, "151.91974": 0.2675, "153.922217": 0.2275}, "Eu": {"150.919858": 0.4781, "152.921238": 0.5219}, "Gd": {"151.9198": 0.002, "153.920874": 0.0218, "154.92263": 0.148, "155.922131": 0.2047, "156.923969": 0.1565, "157.924112": 0.2484, "159.927062": 0.2186}, "Tb": {"158.925355": 1.0}, "Dy": {"155.924285": 0.00056, "157.924416": 0.00095, "159.925205": 0.02329, "160.926941": 0.18889, "161.926806": 0.25475, "162.928738": 0.24896, "163.929182": 0.2826}, "Ho": {"164.930329": 1.0}, "Er": {"161.928788": 0.00139, "163.929209": 0.01601, "165.930299": 0.33503, "166.932055": 0.22869, "167.932377": 0.26978, "169.93547": 0.1491}, "Tm": {"168.934218": 1.0}, "Yb": {"167.93389": 0.00123, "169.934766": 0.02982, "170.93633": 0.1409, "171.936386": 0.2168, "172.938215": 0.16103, "173.938866": 0.32026, "175.942576": 0.12996}, "Lu": {"174.940775": 0.97401, "175.94269": 0.02599}, "Hf": {"173.940046": 0.0016, "175.941408": 0.0526, "176.943228": 0.186, "177.943706": 0.2728, "178.945823": 0.1362, "179.946557": 0.3508}, "Ta": {"179.947465": 0.00012, "180.947996": 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195.084], "192": [191.9610387, 0.00782, 195.084], "194": [193.9626809, 0.3286, 195.084], "195": [194.9647917, 0.3378, 195.084], "196": [195.96495209, 0.2521, 195.084], "198": [197.9678949, 0.07356, 195.084]}, "79": {"197": [196.96656879, 1.0, 196.966569]}, "80": {"196": [195.9658326, 0.0015, 200.592], "198": [197.9667686, 0.0997, 200.592], "199": [198.96828064, 0.1687, 200.592], "200": [199.96832659, 0.231, 200.592], "201": [200.97030284, 0.1318, 200.592], "202": [201.9706434, 0.2986, 200.592], "204": [203.97349398, 0.0687, 200.592]}, "81": {"203": [202.9723446, 0.2952, 204.382], "205": [204.9744278, 0.7048, 204.382]}, "82": {"204": [203.973044, 0.014, 207.2], "206": [205.9744657, 0.241, 207.2], "207": [206.9758973, 0.221, 207.2], "208": [207.9766525, 0.524, 207.2]}, "83": {"209": [208.9803991, 1.0, 208.9804]}, "84": {"209": [208.9824308, 0, 209.0], "210": [209.9828741, 0, 209.0]}, "85": {"210": [209.9871479, 0, 210.0], "211": [210.9874966, 0, 210.0]}, "86": {"211": [210.9906011, 0, 222.0], "220": [220.0113941, 0, 222.0], "222": [222.0175782, 0, 222.0]}, "87": {"223": [223.019736, 0, 223.0]}, "88": {"223": [223.0185023, 0, 226.0], "224": [224.020212, 0, 226.0], "226": [226.0254103, 0, 226.0], "228": [228.0310707, 0, 226.0]}, "89": {"227": [227.0277523, 0, 227.0]}, "90": {"230": [230.0331341, 0, 232.0377], "232": [232.0380558, 1.0, 232.0377]}, "91": {"231": [231.0358842, 1.0, 231.03588]}, "92": {"233": [233.0396355, 0, 238.02891], "234": [234.0409523, 5.4e-05, 238.02891], "235": [235.0439301, 0.007204, 238.02891], "236": [236.0455682, 0, 238.02891], "238": [238.0507884, 0.992742, 238.02891]}, "93": {"236": [236.04657, 0, 237.0], "237": [237.0481736, 0, 237.0]}, "94": {"238": [238.0495601, 0, 244.0], "239": [239.0521636, 0, 244.0], "240": [240.0538138, 0, 244.0], "241": [241.0568517, 0, 244.0], "242": [242.0587428, 0, 244.0], "244": [244.0642053, 0, 244.0]}, "95": {"241": [241.0568293, 0, 241.0568293], "243": [243.0613813, 0, 243.0613813]}, "96": {"243": [243.0613893, 0, 243.0613893], "244": [244.0627528, 0, 244.0627528], "245": [245.0654915, 0, 245.0654915], "246": [246.0672238, 0, 246.0672238], "247": [247.0703541, 0, 247.0703541], "248": [248.0723499, 0, 248.0723499]}, "97": {"247": [247.0703073, 0, 247.0703073], "249": [249.0749877, 0, 249.0749877]}, "98": {"249": [249.0748539, 0, 249.0748539], "250": [250.0764062, 0, 250.0764062], "251": [251.0795886, 0, 251.0795886], "252": [252.0816272, 0, 252.0816272]}, "99": {"252": [252.08298, 0, 252.08298]}, "100": {"257": [257.0951061, 0, 257.0951061]}, "101": {"258": [258.0984315, 0, 258.0984315], "260": [260.10365, 0, 260.10365]}, "102": {"259": [259.10103, 0, 259.10103]}, "103": {"262": [262.10961, 0, 262.10961]}, "104": {"267": [267.12179, 0, 267.12179]}, "105": {"268": [268.12567, 0, 268.12567]}, "106": {"271": [271.13393, 0, 271.13393]}, "107": {"272": [272.13826, 0, 272.13826]}, "108": {"270": [270.13429, 0, 270.13429]}, "109": {"276": [276.15159, 0, 276.15159]}, "110": {"281": [281.16451, 0, 281.16451]}, "111": {"280": [280.16514, 0, 280.16514]}, "112": {"285": [285.17712, 0, 285.17712]}, "113": {"284": [284.17873, 0, 284.17873]}, "114": {"289": [289.19042, 0, 289.19042]}, "115": {"288": [288.19274, 0, 288.19274]}, "116": {"293": [293.20449, 0, 293.20449]}, "117": {"292": [292.20746, 0, 292.20746]}, "118": {"294": [294.21392, 0, 294.21392]}}

stjames-0.0.42/stjames/data/read_nist_isotopes.py

@@ -0,0 +1,116 @@
+"""
+Read the NIST isotopes data file and write it to a JSON file.
+
+NIST Isotopes data from:
+https://physics.nist.gov/cgi-bin/Compositions/stand_alone.pl?ele=&all=all&ascii=ascii2
+"""
+
+import json
+from collections import defaultdict
+from importlib import resources
+from typing import Callable, TypeVar
+
+data_dir = resources.files("stjames").joinpath("data")
+
+_T = TypeVar("_T")
+
+
+def process_line(line: str, fmt: Callable[[str], _T] = str) -> _T:  # type: ignore[assignment]
+    """
+    Process a line from the NIST data file.
+
+    :param line: line to process
+    :param fmt: function to format the value
+    >>> process_line("Atomic Number = 1", int)
+    1
+    """
+    return fmt(line.split("=")[-1].strip())
+
+
+def fmt_float(val: str) -> float:
+    """
+    Format a float from the NIST data file.
+
+    >>> fmt_float(" 1.00784(7)")
+    1.00784
+    """
+    return float(val.strip().split("(")[0])
+
+
+def fmt_maybe_list(val: str) -> float:
+    """
+    Format a float or list of floats from the NIST data file.
+
+    Only the first value is returned.
+
+    >>> fmt_maybe_list("1.00784(7)")
+    1.00784
+    >>> fmt_maybe_list(" [1.00784,1.00811]")
+    1.00784
+    >>> fmt_maybe_list(" [98]")
+    98.0
+    """
+    val = val.strip()
+    if val.startswith("["):
+        val = val[1:-1].split(",")[0]
+    return fmt_float(val)
+
+
+def process_chunk(chunk: str) -> tuple[int, int, tuple[float, float, float]]:
+    r"""
+    Atomic Number, Mass Number, (Relative Atomic Mass, Isotopic Composition, Standard Atomic Weight)
+
+    >>> process_chunk('''\
+    ... Atomic Number = 1
+    ... Atomic Symbol = H
+    ... Mass Number = 1
+    ... Relative Atomic Mass = 1.00784(7)
+    ... Isotopic Composition = 0.999885(70)
+    ... Standard Atomic Weight = [1.00784,1.00811]
+    ... Notes = m
+    ... ''')
+    (1, 1, (1.00784, 0.999885, 1.00784))
+    """
+    lines = chunk.splitlines()
+
+    atomic_number = process_line(lines[0], int)
+    _atomic_symbol = process_line(lines[1], str)
+    mass_number = process_line(lines[2], int)
+    relative_atomic_mass = process_line(lines[3], fmt_float)
+    try:
+        isotopic_composition = process_line(lines[4], fmt_float)
+    except ValueError:
+        isotopic_composition = 0
+    try:
+        standard_atomic_weight = process_line(lines[5], fmt_maybe_list)
+    except ValueError:
+        standard_atomic_weight = relative_atomic_mass
+
+    return atomic_number, mass_number, (relative_atomic_mass, isotopic_composition, standard_atomic_weight)
+
+
+def read_nist_isotopes() -> dict[int, dict[int, tuple[float, float, float]]]:
+    """
+    Read the NIST data file and write it to a JSON file.
+
+    {Atomic Number: {Mass Number, (Relative Atomic Mass, Isotopic Composition, Standard Atomic Weight)}}
+    """
+    with data_dir.joinpath("nist_isotopes.txt").open() as f:
+        next(f), next(f)  # Skip the first two lines
+        nist_isotopes = f.read()
+
+    isotopes: dict[int, dict[int, tuple[float, float, float]]] = defaultdict(dict)
+    for chunk in nist_isotopes.split("\n\n"):
+        atomic_number, mass_number, values = process_chunk(chunk)
+        isotopes[atomic_number][mass_number] = values
+
+    with open("nist_isotopes.json", "w") as f:
+        json.dump(isotopes, f)
+
+    return isotopes
+
+
+if __name__ == "__main__":
+    from pprint import pprint
+
+    pprint(read_nist_isotopes())

stjames-0.0.42/stjames/data/symbol_element.json

@@ -0,0 +1 @@
+{"Bq": 0, "H": 1, "He": 2, "Li": 3, "Be": 4, "B": 5, "C": 6, "N": 7, "O": 8, "F": 9, "Ne": 10, "Na": 11, "Mg": 12, "Al": 13, "Si": 14, "P": 15, "S": 16, "Cl": 17, "Ar": 18, "K": 19, "Ca": 20, "Sc": 21, "Ti": 22, "V": 23, "Cr": 24, "Mn": 25, "Fe": 26, "Co": 27, "Ni": 28, "Cu": 29, "Zn": 30, "Ga": 31, "Ge": 32, "As": 33, "Se": 34, "Br": 35, "Kr": 36, "Rb": 37, "Sr": 38, "Y": 39, "Zr": 40, "Nb": 41, "Mo": 42, "Tc": 43, "Ru": 44, "Rh": 45, "Pd": 46, "Ag": 47, "Cd": 48, "In": 49, "Sn": 50, "Sb": 51, "Te": 52, "I": 53, "Xe": 54, "Cs": 55, "Ba": 56, "La": 57, "Ce": 58, "Pr": 59, "Nd": 60, "Pm": 61, "Sm": 62, "Eu": 63, "Gd": 64, "Tb": 65, "Dy": 66, "Ho": 67, "Er": 68, "Tm": 69, "Yb": 70, "Lu": 71, "Hf": 72, "Ta": 73, "W": 74, "Re": 75, "Os": 76, "Ir": 77, "Pt": 78, "Au": 79, "Hg": 80, "Tl": 81, "Pb": 82, "Bi": 83, "Po": 84, "At": 85, "Rn": 86, "Fr": 87, "Ra": 88, "Ac": 89, "Th": 90, "Pa": 91, "U": 92, "Np": 93, "Pu": 94, "Am": 95, "Cm": 96, "Bk": 97, "Cf": 98, "Es": 99, "Fm": 100, "Md": 101, "No": 102, "Lr": 103, "Rf": 104, "Db": 105, "Sg": 106, "Bh": 107, "Hs": 108, "Mt": 109, "Ds": 110, "Rg": 111, "Cn": 112, "Nh": 113, "Fl": 114, "Mc": 115, "Lv": 116, "Ts": 117, "Og": 118}

{stjames-0.0.40 → stjames-0.0.42}/stjames/method.py

@@ -29,10 +29,43 @@ class Method(LowercaseStrEnum):
 
     AIMNET2_WB97MD3 = "aimnet2_wb97md3"
 
+    GFN_FF = "gfn_ff"
     GFN0_XTB = "gfn0_xtb"
     GFN1_XTB = "gfn1_xtb"
     GFN2_XTB = "gfn2_xtb"
-    GFN_FF = "gfn_ff"
 
     # this was going to be removed, but Jonathon wrote such a nice basis set test... it's off the front end.
     BP86 = "bp86"
+
+
+MLFF = [
+    Method.AIMNET2_WB97MD3,
+]
+
+XTB_METHODS = [
+    Method.GFN_FF,
+    Method.GFN0_XTB,
+    Method.GFN1_XTB,
+    Method.GFN2_XTB,
+]
+
+COMPOSITE_METHODS = [
+    Method.HF3C,
+    Method.B973C,
+    Method.R2SCAN3C,
+    Method.WB97X3C,
+]
+
+PREPACKAGED_METHODS = [
+    *MLFF,
+    *XTB_METHODS,
+    *COMPOSITE_METHODS,
+]
+
+METHODS_WITH_CORRECTION = [
+    Method.WB97XD3,
+    Method.WB97XV,
+    Method.WB97MV,
+    Method.WB97MD3BJ,
+    Method.DSDBLYPD3BJ,
+]