Source Code for Module generic_fns.molmol

  1  ############################################################################### 
  2  #                                                                             # 
  3  # Copyright (C) 2004 Edward d'Auvergne                                        # 
  4  #                                                                             # 
  5  # This file is part of the program relax.                                     # 
  6  #                                                                             # 
  7  # relax is free software; you can redistribute it and/or modify               # 
  8  # it under the terms of the GNU General Public License as published by        # 
  9  # the Free Software Foundation; either version 2 of the License, or           # 
 10  # (at your option) any later version.                                         # 
 11  #                                                                             # 
 12  # relax is distributed in the hope that it will be useful,                    # 
 13  # but WITHOUT ANY WARRANTY; without even the implied warranty of              # 
 14  # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the               # 
 15  # GNU General Public License for more details.                                # 
 16  #                                                                             # 
 17  # You should have received a copy of the GNU General Public License           # 
 18  # along with relax; if not, write to the Free Software                        # 
 19  # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA   # 
 20  #                                                                             # 
 21  ############################################################################### 
 22   
 23  from os import popen 
 24   
 25   
 26 -class Molmol: 
 27 -    def __init__(self, relax): 
 28          """Class containing the functions for viewing molecules.""" 
 29   
 30          self.relax = relax 
 31   
 32          # Initialise the command history (for reopening Molmol pipes). 
 33          self.clear_history() 
 34   
 35   
 36 -    def clear_history(self): 
 37          """Function for clearing the Molmol command history.""" 
 38   
 39          self.command_history = "" 
 40   
 41   
 42 -    def open_pipe(self): 
 43          """Function for opening a Molmol pipe.""" 
 44   
 45          # Open the Molmol pipe. 
 46          self.relax.data.molmol = popen("molmol -f -", 'w', 0) 
 47   
 48          # Execute the command history. 
 49          if len(self.command_history) > 0: 
 50              self.write(self.command_history, store_command=0) 
 51              return 
 52   
 53          # Test if the PDB file has been loaded. 
 54          if hasattr(self.relax.data, 'pdb'): 
 55              self.open_pdb() 
 56   
 57          # Run InitAll to remove everything from molmol. 
 58          else: 
 59              self.write("InitAll yes") 
 60   
 61   
 62 -    def open_pdb(self, run=None): 
 63          """Function for opening the PDB file in Molmol.""" 
 64   
 65          # Argument. 
 66          if run: 
 67              self.run = run 
 68   
 69          # Test if the pipe is open. 
 70          if not self.pipe_open(): 
 71              return 
 72   
 73          # Run InitAll to remove everything from molmol. 
 74          self.write("InitAll yes") 
 75   
 76          # Open the PDB. 
 77          self.write("ReadPdb " + self.relax.data.pdb[self.run].file_name) 
 78   
 79   
 80 -    def pipe_open(self): 
 81          """Function for testing if the Molmol pipe is open.""" 
 82   
 83          # Test if a pipe has been opened. 
 84          if not hasattr(self.relax.data, 'molmol'): 
 85              return 0 
 86   
 87          # Test if the pipe has been broken. 
 88          try: 
 89              self.relax.data.molmol.write('\n') 
 90          except IOError: 
 91              return 0 
 92   
 93          # The pipe is open. 
 94          return 1 
 95   
 96   
 97 -    def view(self, run=None): 
 98          """Function for running Molmol.""" 
 99   
100          # Arguments. 
101          self.run = run 
102   
103          # Open a Molmol pipe. 
104          if self.pipe_open(): 
105              raise RelaxError, "The Molmol pipe already exists." 
106          else: 
107              self.open_pipe() 
108   
109   
110 -    def write(self, command=None, store_command=1): 
111          """Function for writing to the Molmol pipe. 
112   
113          This function is also used to execute a user supplied Molmol command. 
114          """ 
115   
116          # Reopen the pipe if needed. 
117          if not self.pipe_open(): 
118              self.open_pipe() 
119   
120          # Write the command to the pipe. 
121          self.relax.data.molmol.write(command + '\n') 
122   
123          # Place the command in the command history. 
124          if store_command: 
125              self.command_history = self.command_history + command + "\n" 
126