Merge pull request #23 from talagayev/gyration

Radius of gyration implementation
talagayev · Dec 12, 2024 · 54ed4be · 54ed4be
2 parents 3b16951 + 1259152
commit 54ed4be
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Showing 2 changed files with 36 additions and 3 deletions.
diff --git a/mdonatello/mdonatello.py b/mdonatello/mdonatello.py
@@ -33,6 +33,7 @@
     Stereocenters,
     HeavyAtoms,
     AllAtoms,
+    RadiusOfGyration,
     HeavyAtomsWeight,
 )
 
@@ -289,6 +290,7 @@ def update_display(self, _=None):
                 HeavyAtoms(self.current_mol),
                 AllAtoms(self.current_mol),
                 HeavyAtomsWeight(self.current_mol),
+                RadiusOfGyration(self.current_mol),
             ]
             physiochem_html = [
                 HTML(str(prop)) for prop in physiochem_properties

diff --git a/mdonatello/properties.py b/mdonatello/properties.py
@@ -292,22 +292,22 @@ class AllAtoms(Property):
     Parameters:
     -----------
     mol : Chem.Mol
-        The RDKit Mol object of the molecule for which the heavy atom count is being calculated.
+        The RDKit Mol object of the molecule for which the atom count is being calculated.
 
     Returns:
     --------
     float
         The atom count of the molecule.
     """
 
-    name = "Heavy Atoms"
+    name = "All Atoms"
     values_format = False
     unit = ""
 
     @cached_property
     def property_value(self) -> float:
         """
-        Calculates the heavy atoms of the molecule.
+        Calculates the atoms of the molecule.
 
         Returns:
         --------
@@ -348,6 +348,37 @@ def property_value(self) -> float:
         return rdMolDescriptors.CalcNumHeavyAtoms(self.mol)
 
 
+class RadiusOfGyration(Property):
+    """A class for calculating the radius of gyration of a molecule.
+
+    Parameters:
+    -----------
+    mol : Chem.Mol
+        The RDKit Mol object of the molecule for which the radius of gyration is being calculated.
+
+    Returns:
+    --------
+    float
+        The radius of gyration of the molecule.
+    """
+
+    name = "Gyration Radius"
+    values_format = True
+    unit = ""
+
+    @cached_property
+    def property_value(self) -> float:
+        """
+        Calculates the heavy atoms of the molecule.
+
+        Returns:
+        --------
+        float
+            The heavy atom count of the molecule.
+        """
+        return rdMolDescriptors.CalcRadiusOfGyration(self.mol)
+
+
 class HeavyAtomsWeight(Property):
     """A class for calculating the molecular weight of heavy atoms of a molecule.