#
#
#

__author__ = "Magdalena A. Jonikas"
__version__ = "1.0"
__date__ = " 5/20/09 "
__doc__ = """ Fixes pdb files generated by vmd for use with c2a 
              Requires two arguments:
              1. The name of the existing pdb file
              2. The desired name for the output pdb file"""


import sys

if __name__=='__main__':
    pdbIn = open(sys.argv[1]).readlines()
    pdbOut = open(sys.argv[2], 'w')
    for line in pdbIn:
        if line[0:4]=='ATOM':
            res= line[17:20]
            if res=='G  ': res='  G'
            if res=='U  ': res='  U'
            if res=='A  ': res='  A'
            if res=='C  ': res='  C'
            newline = line[:17]+res+line[20:]
            pdbOut.write(newline)
        else: pdbOut.write(line)
    pdbOut.close()