Fix dos files in qp_create

ocaml/Atom.ml

@@ -22,10 +22,15 @@ let of_string ~units s =
     }
   | [ name; x; y; z ] ->
     let e = Element.of_string name in
-    { element = e ;
-      charge  = Element.to_charge e;
-      coord   = Point3d.of_string ~units (String.concat " " [x; y; z])
-    }
+    begin
+      try
+      { element = e ;
+        charge  = Element.to_charge e;
+        coord   = Point3d.of_string ~units (String.concat " " [x; y; z])
+      }
+      with
+      | err -> (Printf.eprintf "name = \"%s\"\nxyz = (%s,%s,%s)\n%!" name x y z ; raise err)
+    end
   | _ -> raise (AtomError s)
 
 

ocaml/Molecule.ml

@@ -142,13 +142,21 @@ let of_xyz_string
   result
 
 
+let regexp_r = Str.regexp {|
|}
+let regexp_t = Str.regexp {|	|}
+
 
 let of_xyz_file
     ?(charge=(Charge.of_int 0)) ?(multiplicity=(Multiplicity.of_int 1))
     ?(units=Units.Angstrom)
     filename =
   let lines =
-    match Io_ext.input_lines filename with
+    Io_ext.input_lines filename
+    |> List.map (fun s -> Str.global_replace regexp_r "" s)
+    |> List.map (fun s -> Str.global_replace regexp_t " " s)
+  in
+  let lines =
+    match lines with
     | natoms :: title :: rest ->
           let natoms = 
             try
@@ -173,6 +181,8 @@ let of_zmt_file
     ?(units=Units.Angstrom)
     filename =
   Io_ext.read_all filename
+  |> Str.global_replace regexp_r ""
+  |> Str.global_replace regexp_t " "
   |> Zmatrix.of_string
   |> Zmatrix.to_xyz_string
   |> of_xyz_string ~charge ~multiplicity ~units

ocaml/Point3d.ml

@@ -24,7 +24,9 @@ let of_string ~units s =
   let l = s
           |> String_ext.split ~on:' '
           |> List.filter (fun x -> x <> "")
-          |> list_map float_of_string
+          |> list_map (fun x ->
+                 try float_of_string x with
+                 | Failure msg -> (Printf.eprintf "Bad string: \"%s\"\n%!" x ; failwith msg) )
           |> Array.of_list
   in
   { x = l.(0) *. f ;