Fix missed fialed embedding check bug

pnnl · Feb 23, 2024 · 26bf720 · 26bf720
1 parent 8233598
commit 26bf720
Showing 1 changed file with 9 additions and 9 deletions.
diff --git a/isicle/geometry.py b/isicle/geometry.py
@@ -299,7 +299,7 @@ def __init__(self, **kwargs):
         self.__dict__.update(dict.fromkeys(self._defaults, self._default_value))
         self.__dict__.update(kwargs)
 
-    def _is_embedded(self):
+    def _is_embedded(self, mol):
         """
         Check if molecule has embedded 3D coordinates.
 
@@ -311,7 +311,7 @@ def _is_embedded(self):
         """
 
         try:
-            self.mol.GetConformers()
+            mol.GetConformer().Is3D()
             return True
         except:
             return False
@@ -386,17 +386,17 @@ def _forcefield_selector(forcefield, mw):
         # Embed molecule 3D coordinates
         if embed is True:
             # Attempt embedding
-            try:
-                Chem.AllChem.EmbedMolecule(mol)
-
-            # Use random coordinates
-            except:
-                Chem.AllChem.EmbedMolecule(mol, useRandomCoords=True)
+            res = Chem.AllChem.EmbedMolecule(mol)
+            if res == -1:
+                # Use random coordinates
+                res = Chem.AllChem.EmbedMolecule(mol, useRandomCoords=True)
+                if res == -1:
+                    raise ValueError("Embedding failure.")
 
         # Optimize according to supplied forcefield
         if forcefield is not None:
             # Check if embedded
-            if self._is_embedded():
+            if self._is_embedded(mol):
                 # Forcefield selection
                 if "mmff94s" in forcefield.lower():
                     _forcefield_selector(forcefield, mol)(