Logo Search packages:      
Sourcecode: pymol version File versions  Download package

remote_pdb_load.py

# Copyright Notice
# ================
# 
# The PyMOL Plugin source code in this file is copyrighted, but you can
# freely use and copy it as long as you don't change or remove any of
# the copyright notices.
# 
# ----------------------------------------------------------------------
# This PyMOL Plugin is Copyright (C) 2004 by Charles Moad <cmoad@indiana.edu>
# 
#                        All Rights Reserved
# 
# Permission to use, copy, modify, distribute, and distribute modified
# versions of this software and its documentation for any purpose and
# without fee is hereby granted, provided that the above copyright
# notice appear in all copies and that both the copyright notice and
# this permission notice appear in supporting documentation, and that
# the name(s) of the author(s) not be used in advertising or publicity
# pertaining to distribution of the software without specific, written
# prior permission.
# 
# THE AUTHOR(S) DISCLAIM ALL WARRANTIES WITH REGARD TO THIS SOFTWARE,
# INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS.  IN
# NO EVENT SHALL THE AUTHOR(S) BE LIABLE FOR ANY SPECIAL, INDIRECT OR
# CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF
# USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR
# OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR
# PERFORMANCE OF THIS SOFTWARE.
# ----------------------------------------------------------------------

from Tkinter import *
from pymol import cmd

def __init__(self):
   # Simply add the menu entry and callback
   self.menuBar.addmenuitem('Plugin', 'command',
                            'PDB Loader Service',
                            label = 'PDB Loader Service',
                            command = lambda s=self : FetchPDB(s))

# Class that simply takes the pdbcode from a dialog and retrieves the file
class FetchPDB:
   def __init__(self, app):
      import tkSimpleDialog
      import tkMessageBox
      import urllib
      import gzip
      import os
      import string

      pdbCode = tkSimpleDialog.askstring('PDB Loader Service',
                                         'Please enter a 4-digit pdb code:',
                                         parent=app.root)
      
      if pdbCode: # None is returned for user cancel
         pdbCode = string.upper(pdbCode)
         filename = urllib.urlretrieve('http://www.rcsb.org/pdb/cgi/export.cgi/' +
                                       pdbCode + '.pdb.gz?format=PDB&pdbId=' +
                                       pdbCode + '&compression=gz')[0]
         if (os.path.getsize(filename) > 0): # If 0, then pdb code was invalid
            # Uncompress the file while reading
            fpin = gzip.open(filename)

            # Form the pdb output name
            outputname = os.path.dirname(filename) + os.sep + pdbCode + '.pdb'
            fpout = open(outputname, 'w')
            fpout.write(fpin.read()) # Write pdb file
            
            fpin.close()
            fpout.close()
            
            cmd.load(outputname) # Load the fresh pdb

         else:
            tkMessageBox.showerror('Invalid Code',
                                   'You entered an invalid pdb code:' + pdbCode,
                                   parent=app.root)

         os.remove(filename) # Remove tmp file (leave the pdb)


Generated by  Doxygen 1.6.0   Back to index