#!@PYTHON@
#
# Shifts atoms in a given coordination file periodically

import sys, string, re, math
wrerr = sys.stderr.write
wrout = sys.stdout.write

if (len(sys.argv) < 10):
  print "Usage: "+sys.argv[0]+" <xyzfile> <element offset> <xyzoffset> <box x> <box y> <box z> <shift x> <shift y> <shift z>"
  print "Output goes to STDOUT."
  sys.exit(1)

# get parameters
elementoffset=int(sys.argv[2])
xyzoffset=int(sys.argv[3])
box=[float(sys.argv[4]), float(sys.argv[5]),float(sys.argv[6])]
shift=[float(sys.argv[7]),float(sys.argv[8]),float(sys.argv[9])]

# parse the file and obtain maxid
wrerr("Parsing the coordinate file "+sys.argv[1]+".\n")
file = open(sys.argv[1], "r")
#wrout(file.readline())
#wrout(file.readline())
atoms = {}
maxid=-1
nr=0
for line in file:
  # simpy print everything else
  if not ("END" in line or "CONECT" in line or "MASTER" in line or "#" in line):
    nr+=1
file.close()
file = open(sys.argv[1], "r")
wrout("%d\n\tShifted by $shift from PDB file.\n" % (nr))
for line in file:
  # simpy print everything else
  if not ("END" in line or "CONECT" in line or "MASTER" in line or "#" in line):
    fields=line.split()
    for i in range(3):
      value=float(fields[i+xyzoffset])+shift[i]
      while value > box[i]:
        value = value - box[i]
      while value < 0:
        value = value + box[i]
      fields[i+xyzoffset] = str(value)
    wrout("%s\t%lg\t%lg\t%lg" % (fields[elementoffset], float(fields[0+xyzoffset]), float(fields[1+xyzoffset]), float(fields[2+xyzoffset])))
    wrout("\n")

sys.exit(0)