feat: added atom size as parameter to protein and removed magic number

Author: HarrisonTCodes

src/ursina_proteins/protein.py

@@ -92,6 +92,7 @@ class Protein:
     def __init__(
         self,
         pdb_filepath: str,
+        atoms_size: float = 0.1,
         helices_thickness: float = 4,
         coils_thickness: float = 1,
         chains_smoothness: float = 3,
@@ -105,6 +106,7 @@ def __init__(
 
         Args:
             pdb_filepath: Path to the PDB file.
+            atoms_size: Size of individual atoms in the atoms mesh (default: 0.1).
             helices_thickness: Thickness of helix meshes (default: 4).
             coils_thickness: Thickness of coil meshes (default: 1).
             chains_smoothness: Smoothness factor for chain rendering (default: 3).
@@ -120,7 +122,7 @@ def __init__(
         structure_center_of_mass = self.structure.center_of_mass()
 
         self.atoms_entity = Entity(
-            model=self.compute_atoms_mesh(atom_element_color_map),
+            model=self.compute_atoms_mesh(atoms_size, atom_element_color_map),
             origin=structure_center_of_mass,
             *args,
             **kwargs,
@@ -144,14 +146,17 @@ def __init__(
 
         self.entities = [self.atoms_entity, self.helices_entity, self.coils_entity]
 
-    def compute_atoms_mesh(self, element_color_map: dict[str, Color]) -> Mesh:
+    def compute_atoms_mesh(
+        self, atoms_size: float, element_color_map: dict[str, Color]
+    ) -> Mesh:
         """
         Compute the mesh of atoms in the protein structure.
 
         This method creates an icosahedron for each atom in the protein structure
         and assigns colors based on the element type, combining them into one mesh.
 
         Args:
+            atoms_size: Size of individual atoms.
             element_color_map: Color mapping for atom elements.
 
         Returns:
@@ -166,7 +171,7 @@ def compute_atoms_mesh(self, element_color_map: dict[str, Color]) -> Mesh:
         for index, atom in enumerate(self.structure.get_atoms()):
             # Vertices
             verts.extend(
-                [(vert * 0.1) + atom.get_coord() for vert in ICOSAHEDRON_VERTS]
+                [(vert * atoms_size) + atom.get_coord() for vert in ICOSAHEDRON_VERTS]
             )
 
             # Faces (triangles)