#!/usr/bin/env __XPLOR_DIR__/bin/pyXplor

import sys
argv = sys.argv
dele =0
usage = '''usage: %s <pdbFile>

    generates a psf file from the given pdb file.
    the psf file is written in a filename derived the input filename.
options are-:
      -delUnknown     - to delete the unknown atoms from
                        the PDB file before the psf file is been written.
                        The option is off if not specified.
      -help-script    - prints out the usage of the script
         
    this is a work in progress. Please report problems to
    xplor-nih@nmr.cit.nih.gov
''' % argv[0]
(opts,pdbfile)=xplor.parseArguments(["delUnknown:0","help-script:0"])
for op in opts:
   if(op[0]=='help-script'):
      print usage
      sys.exit(0)
   if(op[0]=='delUnknown'):
      dele=1
   pass
infile=pdbfile[0]

if not open(infile):
    print "file not found or not readable: %s" % infile
    sys.exit(1)
    pass

from string import join
try:
    if len(infile.split('.')) == 1:
       outfile=infile
    else:
       outfile=join(infile.split('.')[:-1],'.')
except:
    outfile=infile
    pass

outfile += '.psf'

from psfGen import pdbToPSF
pdbToPSF(open(infile).read())

if (dele==1):
    import protocol
    protocol.initCoords(files=infile)
    xplor.simulation.deleteAtoms("not known")
psfFilename=outfile
xplor.command("write psf output=%s end" % psfFilename)