diff --git a/ocaml/Atom.ml b/ocaml/Atom.ml index d02b20d8..49e788e8 100644 --- a/ocaml/Atom.ml +++ b/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) diff --git a/ocaml/Molecule.ml b/ocaml/Molecule.ml index 603244c8..3771b6f9 100644 --- a/ocaml/Molecule.ml +++ b/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 diff --git a/ocaml/Point3d.ml b/ocaml/Point3d.ml index 57b02bfe..4df375e4 100644 --- a/ocaml/Point3d.ml +++ b/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 ;