Source Code for Module dx.opendx

 1  ############################################################################### 
 2  #                                                                             # 
 3  # Copyright (C) 2003-2005 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 system 
24  from re import search 
25   
26  from isosurface_3D import Iso3D 
27   
28   
29 -class OpenDX: 
30 -    def __init__(self, relax): 
31          """Class containting the function for OpenDX.""" 
32   
33          # Place the program class structure under self.relax 
34          self.relax = relax 
35   
36          # Set up all the classes. 
37          self.iso3d = Iso3D(relax) 
38   
39   
40 -    def map(self, run=None, params=None, map_type='Iso3D', res_num=None, inc=20, lower=None, upper=None, axis_incs=10, file="map", dir="dx", point=None, point_file="point", remap=None): 
41          """Function for mapping the given space and creating OpenDX files.""" 
42   
43          # Residue index. 
44          index = None 
45          if res_num: 
46              for i in xrange(len(self.relax.data.res[run])): 
47                  if self.relax.data.res[run][i].num == res_num: 
48                      index = i 
49                      break 
50              if index == None: 
51                  raise RelaxNoResError, res_num 
52   
53          # Space type. 
54          if search("^[Ii]so3[Dd]", map_type): 
55              if len(params) != 3: 
56                  raise RelaxError, "The 3D isosurface map requires a 3 parameter model." 
57   
58              # Create the map. 
59              self.iso3d.map_space(run, params, res_num, index, inc, lower, upper, axis_incs, file, dir, point, point_file, remap) 
60          else: 
61              raise RelaxError, "The map type '" + map_type + "' is not supported." 
62   
63   
64 -    def run(self, file="map", dir="dx", dx_exe="dx", vp_exec=1): 
65          """Function for running OpenDX.""" 
66   
67          # Text for changing to the directory dir. 
68          dir_text = "" 
69          if dir != None: 
70              dir_text = " -directory " + dir 
71   
72          # Text for executing OpenDX. 
73          execute_text = "" 
74          if vp_exec: 
75              execute_text = " -execute" 
76   
77          # Run OpenDX. 
78          system(dx_exe + dir_text + " -program " + file + ".net" + execute_text + " &") 
79