fixed fun little bug in which parsley ff C-Cl bonds weren't getting r…

…ecognized
ekwan · Jun 6, 2020 · 33d1cec · 33d1cec
1 parent 432d3bf
commit 33d1cec
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Showing 3 changed files with 350 additions and 2 deletions.
diff --git a/cctk/molecule.py b/cctk/molecule.py
@@ -108,9 +108,9 @@ def __str__(self):
         else:
             return f"Molecule ({len(self.atomic_numbers)} atoms)"
 
-    def assign_connectivity(self, cutoff=0.1, periodic_boundary_conditions=None):
+    def assign_connectivity(self, cutoff=0.2, periodic_boundary_conditions=None):
         """
-        Automatically recalculates bonds based on covalent radii. If two atoms are closer than the sum of their covalent radii + 0.5 Angstroms, then they are considered bonded.
+        Automatically recalculates bonds based on covalent radii. If two atoms are closer than the sum of their covalent radii + ``cutoff`` Angstroms, then they are considered bonded.
 
         Args:
             cutoff (float): the threshold (in Angstroms) for how close two covalent radii must be to be considered bonded