import giepy as gp
import giechem as gc

def read_xyz_file(filename):
	#
	# Reads an .xyz file with the format:
	# #_atoms
	# ignored line
	# a1	X	Y	Z
	# a2	X	Y	Z
	# a3	X	Y	Z
	# ...
	# an	X	Y	Z
	#
	# where #_atoms = an integer indicating the number of atoms in the molecule
	# a1...an are element symbols or atomic numbers
	# X Y Z are the XYZ coordinates of the atom
	#
	input = gp.RichFile(filename)
	input_lines = input.next_split_line(splitter=None)
	tokens = input_lines.next()
	try:
		numatms = int(tokens[0])
	except ValueError:
		print "Error reading line 1 of .xyz file"
		return False
	tokens = input_lines.next()
	molecule = gc.Molecule(name=tokens[0])
	try:
		while True:
			tokens = input_lines.next()
			molecule.add_atom(id=tokens[0], coords=[ x for x in tokens[1:]])
	except StopIteration:
		pass
	if numatms != molecule.num_atoms():
		print "Incorrect number of atoms in .xyz file"
		return False
	return molecule

if __name__ == '__main__':
	import sys
	molecule = read_xyz_file(sys.argv[1])