source: util/src/ShiftPeriodic.py.in@ 48cd93

#!@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) < 9):
  print "Usage: "+sys.argv[0]+" <file> <offset> <box x> <box y> <box z> <shift x> <shift y> <shift z>"
  print "Output goes to STDOUT."
  sys.exit(1)

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

# parse the file and obtain maxid
print "Parsing the PDB file "+sys.argv[1]+"."
file = open(sys.argv[1], "r")
atoms = {}
maxid=-1
for line in file:
  # simpy print everything else
  if "END" in line or "CONECT" in line or "MASTER" in line or "#" in line:
    print line
  else:
    fields=line.split()
    for i in range(3):
      value=float(fields[i+offset])+shift[i]
      while value > box[i]:
        value = value - box[i]
      while value < 0:
        value = value + box[i]
      fields[i+offset] = str(value)
    for j in range(len(fields)):
      wrout("%s " % (fields[j]))
    wrout("\n")

sys.exit(0)