def GetCoordinates(file,atom_ref_ids, atom_name):
	"""
	This function returns the coordinates of a PDB file.

	PARAMETERS
	----------
	file : string
			PDB filename

	atom_ref_ids : list of strings
					the residue number of the reference atoms
	atom_name : string
					the PDB atom name of the reference PDB file

	RETURNS
	------
	res_coord: list of floats
	"""

	PDB = open(file)
	res_coord = []
	for line in PDB:
		if (line[0:4] == "ATOM") and (line[12:16].replace(" ","_") == atom_name) and (line[22:26].strip() in atom_ref_ids):
			x = float(line[30:38].strip())
			y = float(line[38:46].strip())
			z = float(line[46:54].strip())
			res_coord.append([x,y,z])

	return res_coord