Added subdirectories for each model and modified README.md.

Author: jrfaeder

AB/AB.bngl

@@ -0,0 +1,26 @@
+begin model
+  begin parameters
+    A0 100  # Initial number of A molecules
+    B0 100  # Initial number of B molecules
+    ka 0.01 # A-B association rate constant (1/molecule 1/s)
+    kd 1    # A-B dissociation rate constant (1/s)
+  end parameters
+  begin molecule types
+    A(b)
+    B(a)
+  end molecule types
+  begin seed species
+    A(b) A0
+    B(a) B0
+  end seed species
+  begin observables
+    Molecules A A(b)
+    Molecules B B(a)
+    Molecules C A(b!1).B(a!1)
+  end observables
+  begin reaction rules
+    A(b) + B(a) <-> A(b!1).B(a!1) ka, kd
+  end reaction rules
+end model
+
+simulate({method=>"ode",t_end=>10,n_steps=>200})

ABC.bngl renamed to ABC/ABC.bngl

@@ -4,11 +4,13 @@ The files presented here are meant to provide a moderately paced but comprehensi
 
 **Click on the link to see the BNGL code.**
 
-[`ABC.bngl`](ABC.bngl)
+[`ABC.bngl`](ABC/ABC.bngl)
 : Simple binding model in BNGL using unstructured molecules to represent each species. Demonstrates basic syntax of `simulate` command.
 
-[`ABC_scan.bngl`](ABC_scan.bngl)
+[`ABC_scan.bngl`](ABC/ABC_scan.bngl)
 : Simple binding model modified to use`parameters` block, which enables `parameter_scan`. Also demonstrates use of `#` for comments and `\` for line continuation.
 
+[`AB.bngl`](AB/AB.bngl)
+: Simple binding model re-factored to used structured molecules with binding sites and a binding rule that adds or deletes a bond.
 
 ![Flagman](images/Flagman.gif)