dropped periodictable dependency

Author: ntampellini

pixi.lock

@@ -4,17 +4,17 @@
 
 import numpy as np
 from networkx import Graph, all_simple_paths, from_numpy_array, set_node_attributes
-from periodictable import elements
 from scipy.spatial.distance import cdist
 
 from prism_pruner.algebra import dihedral
+from prism_pruner.periodic_table import RADII_TABLE
 from prism_pruner.typing import Array1D_bool, Array1D_str, Array2D_float
 
 
 @lru_cache()
 def d_min_bond(a1: str, a2: str, factor: float = 1.2) -> float:
     """Return the bond distance between two atoms."""
-    return factor * (elements.symbol(a1).covalent_radius + elements.symbol(a2).covalent_radius)  # type: ignore [no-any-return]
+    return factor * (RADII_TABLE[a1] + RADII_TABLE[a2])
 
 
 def graphize(

prism_pruner/graph_manipulations.py

@@ -0,0 +1,221 @@
+"""Atomic Masses and Covalent Radii."""
+
+MASSES_TABLE = {
+    "H": 1.00800,
+    "He": 4.00260,
+    "Li": 6.94000,
+    "Be": 9.01218,
+    "B": 10.81000,
+    "C": 12.01100,
+    "N": 14.00700,
+    "O": 15.99900,
+    "F": 18.99840,
+    "Ne": 20.17970,
+    "Na": 22.98977,
+    "Mg": 24.30500,
+    "Al": 26.98154,
+    "Si": 28.08500,
+    "P": 30.97376,
+    "S": 32.06000,
+    "Cl": 35.45000,
+    "Ar": 39.95000,
+    "K": 39.09830,
+    "Ca": 40.07800,
+    "Sc": 44.95591,
+    "Ti": 47.86700,
+    "V": 50.94150,
+    "Cr": 51.99610,
+    "Mn": 54.93804,
+    "Fe": 55.84500,
+    "Co": 58.93319,
+    "Ni": 58.69340,
+    "Cu": 63.54600,
+    "Zn": 65.38000,
+    "Ga": 69.72300,
+    "Ge": 72.63000,
+    "As": 74.92159,
+    "Se": 78.97100,
+    "Br": 79.90400,
+    "Kr": 83.79800,
+    "Rb": 85.46780,
+    "Sr": 87.62000,
+    "Y": 88.90584,
+    "Zr": 91.22400,
+    "Nb": 92.90637,
+    "Mo": 95.95000,
+    "Tc": 98.00000,
+    "Ru": 101.07000,
+    "Rh": 102.90549,
+    "Pd": 106.42000,
+    "Ag": 107.86820,
+    "Cd": 112.41400,
+    "In": 114.81800,
+    "Sn": 118.71000,
+    "Sb": 121.76000,
+    "Te": 127.60000,
+    "I": 126.90447,
+    "Xe": 131.29300,
+    "Cs": 132.90545,
+    "Ba": 137.32700,
+    "La": 138.90547,
+    "Ce": 140.11600,
+    "Pr": 140.90766,
+    "Nd": 144.24200,
+    "Pm": 145.00000,
+    "Sm": 150.36000,
+    "Eu": 151.96400,
+    "Gd": 157.25000,
+    "Tb": 158.92535,
+    "Dy": 162.50000,
+    "Ho": 164.93033,
+    "Er": 167.25900,
+    "Tm": 168.93422,
+    "Yb": 173.04500,
+    "Lu": 174.96680,
+    "Hf": 178.48600,
+    "Ta": 180.94788,
+    "W": 183.84000,
+    "Re": 186.20700,
+    "Os": 190.23000,
+    "Ir": 192.21700,
+    "Pt": 195.08400,
+    "Au": 196.96657,
+    "Hg": 200.59200,
+    "Tl": 204.38000,
+    "Pb": 207.20000,
+    "Bi": 208.98040,
+    "Po": 209.00000,
+    "At": 210.00000,
+    "Rn": 222.00000,
+    "Fr": 223.00000,
+    "Ra": 226.00000,
+    "Ac": 227.00000,
+    "Th": 232.03770,
+    "Pa": 231.03588,
+    "U": 238.02891,
+    "Np": 237.00000,
+    "Pu": 244.00000,
+    "Am": 243.00000,
+    "Cm": 247.00000,
+    "Bk": 247.00000,
+    "Cf": 251.00000,
+    "Es": 252.00000,
+    "Fm": 257.00000,
+    "Md": 258.00000,
+    "No": 259.00000,
+    "Lr": 262.00000,
+    "Rf": 261.00000,
+    "Db": 262.00000,
+    "Sg": 266.00000,
+    "Bh": 264.00000,
+    "Hs": 277.00000,
+    "Mt": 268.00000,
+    "Ds": 281.00000,
+    "Rg": 272.00000,
+    "Cn": 285.00000,
+    "Nh": 286.00000,
+    "Fl": 289.00000,
+    "Mc": 289.00000,
+    "Lv": 293.00000,
+    "Ts": 294.00000,
+    "Og": 294.00000,
+}
+
+RADII_TABLE = {
+    "H": 0.31,
+    "He": 0.28,
+    "Li": 1.28,
+    "Be": 0.96,
+    "B": 0.84,
+    "C": 0.76,
+    "N": 0.71,
+    "O": 0.66,
+    "F": 0.57,
+    "Ne": 0.58,
+    "Na": 1.66,
+    "Mg": 1.41,
+    "Al": 1.21,
+    "Si": 1.11,
+    "P": 1.07,
+    "S": 1.05,
+    "Cl": 1.02,
+    "Ar": 1.06,
+    "K": 2.03,
+    "Ca": 1.76,
+    "Sc": 1.70,
+    "Ti": 1.60,
+    "V": 1.53,
+    "Cr": 1.39,
+    "Mn": 1.39,
+    "Fe": 1.32,
+    "Co": 1.26,
+    "Ni": 1.24,
+    "Cu": 1.32,
+    "Zn": 1.22,
+    "Ga": 1.22,
+    "Ge": 1.20,
+    "As": 1.19,
+    "Se": 1.20,
+    "Br": 1.20,
+    "Kr": 1.16,
+    "Rb": 2.20,
+    "Sr": 1.95,
+    "Y": 1.90,
+    "Zr": 1.75,
+    "Nb": 1.64,
+    "Mo": 1.54,
+    "Tc": 1.47,
+    "Ru": 1.46,
+    "Rh": 1.42,
+    "Pd": 1.39,
+    "Ag": 1.45,
+    "Cd": 1.44,
+    "In": 1.42,
+    "Sn": 1.39,
+    "Sb": 1.39,
+    "Te": 1.38,
+    "I": 1.39,
+    "Xe": 1.40,
+    "Cs": 2.44,
+    "Ba": 2.15,
+    "La": 2.07,
+    "Ce": 2.04,
+    "Pr": 2.03,
+    "Nd": 2.01,
+    "Pm": 1.99,
+    "Sm": 1.98,
+    "Eu": 1.98,
+    "Gd": 1.96,
+    "Tb": 1.94,
+    "Dy": 1.92,
+    "Ho": 1.92,
+    "Er": 1.89,
+    "Tm": 1.90,
+    "Yb": 1.87,
+    "Lu": 1.87,
+    "Hf": 1.75,
+    "Ta": 1.70,
+    "W": 1.62,
+    "Re": 1.51,
+    "Os": 1.44,
+    "Ir": 1.41,
+    "Pt": 1.36,
+    "Au": 1.36,
+    "Hg": 1.32,
+    "Tl": 1.45,
+    "Pb": 1.46,
+    "Bi": 1.48,
+    "Po": 1.40,
+    "At": 1.50,
+    "Rn": 1.50,
+    "Fr": 2.60,
+    "Ra": 2.21,
+    "Ac": 2.15,
+    "Th": 2.06,
+    "Pa": 2.00,
+    "U": 1.96,
+    "Np": 1.90,
+    "Pu": 1.87,
+    "Am": 1.80,
+    "Cm": 1.69,
+}

prism_pruner/periodic_table.py

@@ -6,11 +6,11 @@
 
 import numpy as np
 from networkx import Graph, connected_components
-from periodictable import elements
 from scipy.spatial.distance import cdist
 
 from prism_pruner.algebra import get_inertia_moments
 from prism_pruner.graph_manipulations import graphize
+from prism_pruner.periodic_table import MASSES_TABLE
 from prism_pruner.rmsd import rmsd_and_max
 from prism_pruner.torsion_module import (
     get_angles,
@@ -647,7 +647,7 @@ def prune_by_moment_of_inertia(
         max_dE=max_dE,
         debugfunction=debugfunction,
         max_dev=max_deviation,
-        masses=np.array([elements.symbol(a).mass for a in atoms]),
+        masses=np.array([MASSES_TABLE[a] for a in atoms]),
     )
 
     return _run(prunerconfig)

prism_pruner/pruner.py

@@ -10,7 +10,6 @@ requires-python = ">=3.12"
 dependencies = [
     "networkx>=3.0",
     "numpy>=2.0",
-    "periodictable",
     "scipy>=1.10",
     "tqdm>=4"
 ]
@@ -104,10 +103,6 @@ ignore_missing_imports = true
 module = "networkx.*"
 ignore_missing_imports = true
 
-[[tool.mypy.overrides]]
-module = "periodictable.*"
-ignore_missing_imports = true
-
 [tool.pytest.ini_options]
 testpaths = ["tests", "prism_pruner"]
 addopts = "--doctest-modules"