fragmentation bug fix

Author: Oliver Scott

scaffoldgraph/core/fragment.py

@@ -145,7 +145,7 @@ def fragment(self, scaffold):
             # Collect all removable atoms in the molecule
             remove_atoms = set()
             for index, atom in zip(ring.aix, ring.atoms):
-                if rings.info.NumAtomRings(index) == 1:
+                if rings.info.NumAtomRings(index) == 1 or any([not b.IsInRing() for b in atom.GetBonds()]):
                     if atom.GetDegree() > 2:  # Evoke linker collection
                         collect_linker_atoms(edit.GetAtomWithIdx(index), remove_atoms)
                     else:  # Add ring atom to removable set
@@ -236,7 +236,7 @@ def fragment(self, scaffold):
             edit = RWMol(scaffold.mol)
             remove_atoms = set()
             for index, atom in zip(ring.aix, ring.atoms):
-                if info.NumAtomRings(index) == 1:
+                if info.NumAtomRings(index) == 1 or any([not b.IsInRing() for b in atom.GetBonds()]):
                     if atom.GetDegree() > 2:  # Evoke linker collection
                         collect_linker_atoms(edit.GetAtomWithIdx(index), remove_atoms)
                     else:

scaffoldgraph/core/scaffold.py

@@ -353,7 +353,10 @@ def get_attachment_points(self, include_exocyclic=False):
         ri = self.owner.rings.info
         for atom in self.atoms:
             index = atom.GetIdx()
-            if ri.NumAtomRings(index) == 1:
+            if (
+                    ri.NumAtomRings(index) == 1 or
+                    any([not b.IsInRing() for b in atom.GetBonds()])
+            ):
                 if atom.GetDegree() > 2:
                     if (
                         include_exocyclic is False
@@ -615,10 +618,9 @@ def get_attachment_points(self, include_exocyclic=False):
 
         """
         attachments = set()
-        ri = self.owner.rings.info
         for atom in self.atoms:
             index = atom.GetIdx()
-            if ri.NumAtomRings(index) == 1:
+            if any([not b.IsInRing() for b in atom.GetBonds()]):
                 if atom.GetDegree() > 2:
                     if (
                         include_exocyclic is False