new znframe versionn

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "znframe"
-version = "0.1.4"
+version = "0.1.5"
 description = "ZnFrame - ASE-like Interface based on dataclasses"
 authors = ["zincwarecode <[email protected]>"]
 readme = "README.md"

znframe/frame.py

@@ -7,10 +7,17 @@
 from copy import deepcopy
 import json
 import typing as t
+import enum
 
 from znframe.bonds import ASEComputeBonds
 
 
+class ComputeProperties(enum.Enum):
+    bonds = "bonds"
+    radii = "radii"
+    colors = "colors"
+
+
 def _cell_to_array(cell: t.Union[np.ndarray, ase.cell.Cell]) -> np.ndarray:
     if isinstance(cell, np.ndarray):
         return cell
@@ -79,21 +86,40 @@ class Frame:
         converter=_cell_to_array, eq=cmp_using(np.array_equal), default=np.zeros(3)
     )
 
+    recompute: t.List[ComputeProperties] = field(
+        factory=lambda: [
+            ComputeProperties.bonds,
+            ComputeProperties.radii,
+            ComputeProperties.colors,
+        ]
+    )
+
     def __attrs_post_init__(self):
+        if ComputeProperties.bonds in self.recompute:
+            self.connectivity = None
+        if ComputeProperties.radii in self.recompute:
+            self.arrays.pop("radii", None)
+        if ComputeProperties.colors in self.recompute:
+            self.arrays.pop("colors", None)
         if self.connectivity is None:
             ase_bond_calculator = ASEComputeBonds()
             self.connectivity = ase_bond_calculator.build_graph(self.to_atoms())
             self.connectivity = ase_bond_calculator.get_bonds(self.connectivity)
 
         if "colors" not in self.arrays:
-            self.arrays["colors"] = [
-                rgb2hex(jmol_colors[number]) for number in self.numbers
-            ]
+            self.arrays["colors"] = np.array(
+                [rgb2hex(jmol_colors[number]) for number in self.numbers]
+            )
         if "radii" not in self.arrays:
-            self.arrays["radii"] = [get_radius(number) for number in self.numbers]
+            self.arrays["radii"] = np.array(
+                [get_radius(number) for number in self.numbers]
+            )
 
     @classmethod
-    def from_atoms(cls, atoms: ase.Atoms):
+    def from_atoms(
+        cls,
+        atoms: ase.Atoms,
+    ):
         arrays = deepcopy(atoms.arrays)
         info = deepcopy(atoms.info)
 
@@ -158,7 +184,7 @@ def to_atoms(self) -> ase.Atoms:
         return atoms
 
     def to_dict(self, built_in_types: bool = True) -> dict:
-        data = attrs.asdict(self)
+        data = attrs.asdict(self, filter=lambda attr, _: attr.name != "recompute")
         if built_in_types:
             return data
         else: