Molecule.fragmented: maintain atom numbers in fragments

do not renumber atoms for fragments

src/topology.rs

@@ -89,9 +89,13 @@ impl Molecule {
 
     /// Break molecule into multiple fragments based on its bonding
     /// connectivity. Return molecules whole connected by bonds
-    /// without periodic lattice
+    /// without periodic lattice. The atom numbers in fragments will
+    /// be the same as in their parent.
     pub fn fragmented(&self) -> impl Iterator<Item = Self> + '_ {
-        self.graph().connected_components().map(|g| Molecule::from_graph(g))
+        self.graph().connected_components().map(|g| {
+            let numbers: Vec<_> = g.node_indices().map(|n| self.atom_sn(n)).collect();
+            Molecule::from_graph_raw(g, numbers)
+        })
     }
 
     /// Return the number of fragments based on bonding connectivity.