chore: add constants + cleanups

Author: timurbazhirov

.pre-commit-config.yaml

@@ -7,6 +7,7 @@ repos:
       - id: isort
       - id: mypy
       - id: check-yaml
+        exclude: ^tests/js
       - id: end-of-file-fixer
       - id: trailing-whitespace
   - repo: local

src/py/mat3ra/code/__init__.py

@@ -1,4 +1,4 @@
-from typing import Any, Dict, Optional
+from typing import Any, Dict
 
 from mat3ra.utils import object as object_utils
 
@@ -26,7 +26,7 @@ def set_prop(self, name: str, value: Any) -> None:
     def unset_prop(self, name: str) -> None:
         del self._json[name]
 
-    def set_props(self, json: Dict[str, Any] = {}) -> "BaseUnderscoreJsonPropsHandler":
+    def set_props(self, json: Dict[str, Any] = {}) -> Any:
         for key, value in json.items():
             self.set_prop(key, value)
         return self

src/py/mat3ra/code/constants.py

@@ -1,9 +1,43 @@
+from math import pi
+
+
 class Coefficients:
+    # Same as used in: JS/TS
     EV_TO_RY = 0.0734986176
     BOHR_TO_ANGSTROM = 0.52917721092
     ANGSTROM_TO_BOHR = 1 / 0.52917721092
     EV_A_TO_RY_BOHR = 1 / 25.71104309541616
 
+    # The below is migrated from:
+    # https://github.com/Exabyte-io/express/blob/22614e549cdc3b0c344718b72ee2000383d77922/express/parsers/settings.py
+    # and originally taken from https://github.com/hplgit/physical-quantities/blob/master/PhysicalQuantities.py
+
+    # Internal, for convenience purposes
+    _c = 299792458.0  # speed of light, m/s
+    _mu0 = 4.0e-7 * pi  # permeability of vacuum
+    _eps0 = 1 / _mu0 / _c**2  # permittivity of vacuum
+    _Grav = 6.67259e-11  # gravitational constant
+    _hplanck = 6.6260755e-34  # Planck constant, J s
+    _hbar = _hplanck / (2 * pi)  # Planck constant / 2pi, J s
+    _e = 1.60217733e-19  # elementary charge
+    _me = 9.1093897e-31  # electron mass
+    _mp = 1.6726231e-27  # proton mass
+    _Nav = 6.0221367e23  # Avogadro number
+    _k = 1.380658e-23  # Boltzmann constant, J/K
+    _amu = 1.6605402e-27  # atomic mass unit, kg
+
+    # External
+    BOHR = 4e10 * pi * _eps0 * _hbar**2 / _me / _e**2  # Bohr radius in angstrom
+    eV = 1.0
+    HARTREE = _me * _e**3 / 16 / pi**2 / _eps0**2 / _hbar**2  # in eV
+    RYDBERG = 0.5 * HARTREE  # in eV
+    Ry = RYDBERG
+    Ha = HARTREE
+    kJ = 1000.0 / _e
+    kcal = 4.184 * kJ
+    cm_inv_to_ev = 0.00012398  # cm^-1 to eV
+    ry_bohr_to_eV_A = 25.71104309541616  # or RYDBERG / BOHR
+
 
 class Tolerance:
     # in crystal coordinates

src/py/mat3ra/code/entity.py

@@ -47,7 +47,12 @@ def to_json(self, exclude: List[str] = []) -> Dict[str, Any]:
         return self.clean(object_utils.clone_deep(object_utils.omit(self._json, exclude)))
 
     def clone(self, extra_context: Dict[str, Any] = {}) -> Any:
-        return self.__class__.__init__({**self.to_json(), **extra_context})
+        config = self.to_json()
+        config.update(extra_context)
+        # To avoid:
+        #   Argument 1 to "__init__" of "BaseUnderscoreJsonPropsHandler" has incompatible type "Dict[str, Any]";
+        #   expected "BaseUnderscoreJsonPropsHandler"
+        return self.__class__.__init__(config)  # type: ignore[arg-type]
 
     @staticmethod
     def validate_data(data: Dict[str, Any], clean: bool = False):