#!/usr/bin/env ruby

raise "$0 inppdb outpdb" unless ARGV.size == 2

File.open(ARGV.last, "w") do |aFile|
    File.open(ARGV.first).each_line do |line|
        if line =~ /^ATOM  /
            line.sub!(/ O1P/, " OP1")
            line.sub!(/ O2P/, " OP2")
            line.sub!(/ C5M/, " C7 ")
            line.sub!(/  A (\w)/, ' DA \1')
            line.sub!(/  C (\w)/, ' DC \1')
            line.sub!(/  G (\w)/, ' DG \1')
            line.sub!(/  T (\w)/, ' DT \1')
            line.sub!(/1\.00  0\.00/, "1.00  1.00")
        end
        aFile.puts line
    end
end