extract_pymol_commands

#!/usr/bin/env python
import sys, os
from optparse import OptionParser

parser = OptionParser()
parser.add_option("-o", "--pmlfile", dest="pmlfile", help="write report to FILE.pml",
                  metavar="FILE.pml", default="~/tmp/rosetta.pml")
parser.add_option("-t", "--tag", dest="tag", help="tag to print, default all", default="")
parser.add_option("-k", "--killpymol", dest="kill", help="kill pymol when run",
                  action="store_true", default=False)
parser.add_option("-r", "--removeold", dest="rm", help="", action="store_true", default=False)
opt, args = parser.parse_args()
outfile = os.path.expanduser(opt.pmlfile)

if len(args) is 0:
   inputstream = sys.stdin
   print "pymolcmd: extract lines from STDIN starting with 'PYMOL_CMD %s' and put them in file: %s" % (
      opt.tag, outfile)
elif len(args) is 1:
   infname = os.path.expanduser(args[0])
   inputstream = open(infname)
   print "pymolcmd: extract lines from file '%s' starting with 'PYMOL_CMD %s' and put them in file: %s" % (
      infname, opt.tag, outfile)
else:
   sys.exit("don't know what do to with extra args: " + str(args))

if opt.kill:
   print "KILLING MacPyMOL!!!!!"
   os.system("killall MacPyMOL")
if opt.rm:
   print "REMOVING (if exists)", outfile
   if os.path.exists(outfile):
      os.remove(outfile)

with open(outfile, 'w') as out:
   for l in inputstream.readlines():
      if l.startswith("PYMOL_CMD"):
         tmp, tag = l.split()[:2]
         if not opt.tag or opt.tag == tag:
            out.write(l[len(tmp) + len(tag) + 2:])
      else:
         print l,

if inputstream is not sys.stdin:
   inputstream.close()