#!/usr/bin/env python
# -*- coding: utf-8 -*-

import sys
import os

if __name__ == "__main__":
  # Make sure we can import stuff from this file's directory
  sys.path.append(os.path.join(os.path.abspath(os.path.dirname(sys.argv[0])), "..", "lib-python"))
  sys.path.append(os.path.abspath(os.path.dirname(sys.argv[0])))

from prosci import shell
from prosci.util.pdb import Pdb

params = shell.Params(usage="USAGE: %s [-i] [--renumber] [pdbfile...]", helpoption="help", allowed=['i'])

if not params.args:
  a = Pdb("", sys.stdin)
  if params.isOpt("--renumber"):
    a.renumber()
  sys.stdout.write(str(a))

if params.isOpt('i'):
  for filename in params.args:
    a = Pdb(filename)
    if params.isOpt("--renumber"):
      a.renumber()
    f = open(filename, 'w')
    f.write(str(a))
    f.close()
else:
  for filename in params.args:
    a = Pdb(filename)
    if params.isOpt("--renumber"):
      a.renumber()
    sys.stdout.write(str(a))
