diff --git a/Basis/Basis.ml b/Basis/Basis.ml
index 252b96b..e7e8eaf 100644
--- a/Basis/Basis.ml
+++ b/Basis/Basis.ml
@@ -1,41 +1,20 @@
-(** General basis set read from a file  *)
-type primitive = {
-    exponent: float ;
-    coefficient: float
-    }
+type t
 
-type element_name = string
-
-type general_contracted_shell = Angular_momentum.t * (primitive array)
-
-type basis_set = element_name * (general_contracted_shell array)
+let of_nuclei_and_general_basis n b =
+  Array.map (fun (e, center) ->
+    List.assoc e b
+    |> Array.map (fun (totAngMom, shell) ->
+      let expo = Array.map (fun General_basis.{exponent ; coefficient} ->
+        exponent) shell
+      and coef = Array.map (fun General_basis.{exponent ; coefficient} ->
+        coefficient) shell
+      in
+      Contracted_shell.create ~expo ~coef ~totAngMom ~center)
+  ) n
 
 
-let string_of_primitive ?id prim =
-  match id with
-  | None -> (string_of_float prim.exponent)^" "^(string_of_float prim.coefficient)
-  | Some i -> (string_of_int i)^" "^(string_of_float prim.exponent)^" "^(string_of_float prim.coefficient)
-
-
-let string_of_contracted_shell (angular_momentum, prim_array) =
-  let n = 
-    Array.length prim_array
-  in
-  Printf.sprintf "%s %d\n%s"
-    (Angular_momentum.to_string angular_momentum) n
-    (Array.init n (fun i -> string_of_primitive ~id:(i+1) prim_array.(i))
-     |> Array.to_list
-     |> String.concat "\n")
-
-
-let string_of_contracted_shell_array a =
-  Array.map string_of_contracted_shell a
+let to_string b =
+  Array.map (fun i -> Contracted_shell.to_string i) b
   |> Array.to_list
   |> String.concat "\n"
 
-
-let to_string (name, contracted_shell_array) =
-  Printf.sprintf "%s\n%s" name (string_of_contracted_shell_array contracted_shell_array)
-
-
-  
diff --git a/Basis/Contracted_shell.ml b/Basis/Contracted_shell.ml
index 5bc414c..2c4e195 100644
--- a/Basis/Contracted_shell.ml
+++ b/Basis/Contracted_shell.ml
@@ -17,6 +17,14 @@ let totAngMom a = a.totAngMom
 let norm_coef a i = a.norm_coef.(i)
 
 
+let to_string s =
+  let open Printf in
+  [ sprintf "center: %s" (Coordinate.to_string s.center) ; 
+    sprintf "angular momentum: %s" (Angular_momentum.to_string s.totAngMom) ]
+  @ (Array.map2 (fun e c -> sprintf "expo: %e  coeff: %e" e c) s.expo s.coef
+    |> Array.to_list) @ ["\n"]
+  |> String.concat "\n"
+
 (** Normalization coefficient of contracted function i, which depends on the
     exponent and the angular momentum. Two conventions can be chosen : a single
     normalisation factor for all functions of the class, or a coefficient which
diff --git a/Basis/ERI.ml b/Basis/ERI.ml
index d27432e..f88e5f0 100644
--- a/Basis/ERI.ml
+++ b/Basis/ERI.ml
@@ -210,8 +210,8 @@ let erint_contracted_class shell_a shell_b shell_c shell_d : float Zmap.t =
   let class_indices = 
     Angular_momentum.zkey_array
       (Angular_momentum.Kind_4 
-        (Contracted_shell.totAngMom shell_a, Contracted_shell.totAngMom shell_b,
-         Contracted_shell.totAngMom shell_c, Contracted_shell.totAngMom shell_d))
+        Contracted_shell.(totAngMom shell_a, totAngMom shell_b,
+                          totAngMom shell_c, totAngMom shell_d))
   in
 
   let contracted_class = 
diff --git a/Basis/Gamess_parser.mly b/Basis/Gamess_parser.mly
index ae84ac0..e15978a 100644
--- a/Basis/Gamess_parser.mly
+++ b/Basis/Gamess_parser.mly
@@ -13,7 +13,7 @@
 %token EOF
 
 %start input
-%type <Basis.basis_set> input
+%type <General_basis.t> input
 
 %% /* Grammar rules and actions follow */
 
@@ -43,7 +43,7 @@ primitive_list:
   | primitive_list primitive { $2 :: $1 }
 
 primitive: 
-  | INTEGER FLOAT FLOAT EOL { Basis.{exponent=$2 ; coefficient=$3 } }
+  | INTEGER FLOAT FLOAT EOL { General_basis.{exponent=$2 ; coefficient=$3 } }
 
 
 
diff --git a/Basis/General_basis.ml b/Basis/General_basis.ml
new file mode 100644
index 0000000..7ea7642
--- /dev/null
+++ b/Basis/General_basis.ml
@@ -0,0 +1,40 @@
+(** General basis set read from a file  *)
+type primitive = {
+    exponent: float ;
+    coefficient: float
+    }
+
+type element_name = string
+
+type general_contracted_shell = Angular_momentum.t * (primitive array)
+
+type t = element_name * (general_contracted_shell array)
+
+
+let string_of_primitive ?id prim =
+  match id with
+  | None -> (string_of_float prim.exponent)^" "^(string_of_float prim.coefficient)
+  | Some i -> (string_of_int i)^" "^(string_of_float prim.exponent)^" "^(string_of_float prim.coefficient)
+
+
+let string_of_contracted_shell (angular_momentum, prim_array) =
+  let n = 
+    Array.length prim_array
+  in
+  Printf.sprintf "%s %d\n%s"
+    (Angular_momentum.to_string angular_momentum) n
+    (Array.init n (fun i -> string_of_primitive ~id:(i+1) prim_array.(i))
+     |> Array.to_list
+     |> String.concat "\n")
+
+
+let string_of_contracted_shell_array a =
+  Array.map string_of_contracted_shell a
+  |> Array.to_list
+  |> String.concat "\n"
+
+
+let to_string (name, contracted_shell_array) =
+  Printf.sprintf "%s\n%s" name (string_of_contracted_shell_array contracted_shell_array)
+
+
diff --git a/Basis/Shell_pair.ml b/Basis/Shell_pair.ml
index 87d97c6..af46c61 100644
--- a/Basis/Shell_pair.ml
+++ b/Basis/Shell_pair.ml
@@ -21,15 +21,15 @@ let create_array ?(cutoff=0.) p_a p_b =
     else -. (log cutoff)
   in
 
-  let center_ab =
-    Coordinate.(Contracted_shell.center p_a |- Contracted_shell.center p_b)
+  let center_ab = Coordinate.(
+    Contracted_shell.center p_a |- Contracted_shell.center p_b )
   in
   let norm_sq =
     Coordinate.dot center_ab center_ab
   in
   Array.init (Contracted_shell.size p_a) (fun i ->
-      let p_a_expo_center =
-        Coordinate.(Contracted_shell.expo p_a i |. Contracted_shell.center p_a)
+      let p_a_expo_center = Coordinate.(
+        Contracted_shell.expo p_a i |. Contracted_shell.center p_a )
       in
       let f1 = 
         Contracted_shell.norm_coef p_a i
@@ -50,13 +50,13 @@ let create_array ?(cutoff=0.) p_a p_b =
             in
             if (norm < cutoff) then
               raise Null_contribution;
-            let p_b_expo_center =
-              Coordinate.(Contracted_shell.expo p_b j |. Contracted_shell.center p_b)
+            let p_b_expo_center = Coordinate.(
+              Contracted_shell.expo p_b j |. Contracted_shell.center p_b )
             in
             let expo = Contracted_shell.(expo p_a i +. expo p_b j) in
             let expo_inv = 1. /. expo in
-            let center =
-              Coordinate.( expo_inv |. (p_a_expo_center |+ p_b_expo_center ) )
+            let center = Coordinate.(
+              expo_inv |. (p_a_expo_center |+ p_b_expo_center ) )
             in
             let argexpo =
               Contracted_shell.(expo p_a i *. expo p_b j) *. norm_sq *. expo_inv
diff --git a/Makefile b/Makefile
index e06bb59..7b5d1c0 100644
--- a/Makefile
+++ b/Makefile
@@ -9,12 +9,11 @@ MLLFILES=$(wildcard */*.mll) $(wildcard *.mll)
 MLYFILES=$(wildcard */*.mly) $(wildcard *.mly) 
 MLFILES= $(wildcard */*.ml)  $(wildcard *.ml) 
 MLIFILES=$(wildcard */*.mli) $(wildcard *.mli) 
-ALL_EXE=$(patsubst %.ml,%.native,$(wildcard qp_*.ml)) 
+ALL_EXE=$(patsubst %.ml,%.native,$(wildcard run_*.ml)) 
 
 .PHONY: default 
 
-#default: $(ALL_EXE) 
-default: test.byte
+default: $(ALL_EXE) 
 
 tests: $(ALL_TESTS) 
 
diff --git a/Nuclei/Nuclei.ml b/Nuclei/Nuclei.ml
index a4b528c..f0834c1 100644
--- a/Nuclei/Nuclei.ml
+++ b/Nuclei/Nuclei.ml
@@ -1,4 +1,4 @@
-type coordinates = ( (Element.t * (float array)) array)
+type coordinates = ( (Element.t * Coordinate.t) array)
 
 let of_xyz_file ~filename =
   let lexbuf =
@@ -21,5 +21,5 @@ let of_zmt_file ~filename =
   in aux []
   |> Zmatrix.of_string
   |> Zmatrix.to_xyz
-  |> Array.map (fun (e,x,y,z) -> (e, [|x;y;z|]))
+  |> Array.map (fun (e,x,y,z) -> (e, Coordinate.of_3_floats x y z ))
     
diff --git a/Nuclei/Xyz_parser.mly b/Nuclei/Xyz_parser.mly
index 19c9c4b..4785570 100644
--- a/Nuclei/Xyz_parser.mly
+++ b/Nuclei/Xyz_parser.mly
@@ -12,7 +12,7 @@ exception InputError of string
 %token EOF
 
 %start input
-%type <(Element.t * (float array)) array> input
+%type <(Element.t * Coordinate.t) array> input
 
 %% /* Grammar rules and actions follow */
 
@@ -49,10 +49,10 @@ atoms_xyz:
 
 atoms_list:
   | { [] }
-  | atoms_list WORD SPACE FLOAT SPACE FLOAT SPACE FLOAT EOL { (Element.of_string $2, [| $4;$6;$8 |]) :: $1 }
-  | atoms_list WORD SPACE FLOAT SPACE FLOAT SPACE FLOAT SPACE EOL { (Element.of_string $2, [| $4;$6;$8 |]) :: $1 }
-  | atoms_list INTEGER SPACE FLOAT SPACE FLOAT SPACE FLOAT EOL { (Element.of_int $2, [| $4;$6;$8 |]) :: $1 }
-  | atoms_list INTEGER SPACE FLOAT SPACE FLOAT SPACE FLOAT SPACE EOL { (Element.of_int $2, [| $4;$6;$8 |]) :: $1 }
+  | atoms_list WORD SPACE FLOAT SPACE FLOAT SPACE FLOAT          EOL { (Element.of_string $2, Coordinate.of_3_floats $4 $6 $8 ) :: $1 }
+  | atoms_list WORD SPACE FLOAT SPACE FLOAT SPACE FLOAT SPACE    EOL { (Element.of_string $2, Coordinate.of_3_floats $4 $6 $8 ) :: $1 }
+  | atoms_list INTEGER SPACE FLOAT SPACE FLOAT SPACE FLOAT       EOL { (Element.of_int $2, Coordinate.of_3_floats $4 $6 $8 ) :: $1 }
+  | atoms_list INTEGER SPACE FLOAT SPACE FLOAT SPACE FLOAT SPACE EOL { (Element.of_int $2, Coordinate.of_3_floats $4 $6 $8 ) :: $1 }
 
 
 
diff --git a/run_integrals.ml b/run_integrals.ml
new file mode 100644
index 0000000..7328191
--- /dev/null
+++ b/run_integrals.ml
@@ -0,0 +1,37 @@
+let basis_file : string option ref = ref None
+let coord_file : string option ref = ref None
+
+
+let speclist = [
+( "-b" , Arg.String (fun x -> basis_file := Some x) ,
+  "File containing the atomic basis set.") ;
+( "-c" , Arg.String (fun x -> coord_file := Some x) ,
+  "File containing the nuclear coordinates.") ;
+]
+
+let run ~coord ~basis =
+  let coord_file = 
+    match coord with 
+    | None -> raise (Invalid_argument "Coordinate file should be specified")
+    | Some x -> x
+  and basis_file = 
+    match basis with 
+    | None -> raise (Invalid_argument "Basis set file should be specified")
+    | Some x -> x
+  in
+  let nuclei = 
+    Nuclei.of_xyz_file ~filename:coord_file
+  and general_basis =
+    Gamess_reader.read ~filename:basis_file
+  in
+  let basis =
+    Basis.of_nuclei_and_general_basis nuclei general_basis
+  in
+  Array.map Basis.to_string basis
+  |> Array.iter print_endline 
+
+
+let () =
+  let usage_msg = "Quantum Chemistry Package. Options available:" in
+  Arg.parse speclist (fun _ -> ()) usage_msg;
+  run ~coord:!coord_file ~basis:!basis_file