Source Code for Module dx.opendx

  1  ############################################################################### 
  2  #                                                                             # 
  3  # Copyright (C) 2003 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 Numeric import zeros 
 24  from os import system 
 25  from re import match 
 26   
 27  from isosurface_3D import Iso3D 
 28   
 29   
 30 -class OpenDX: 
 31 -    def __init__(self, relax): 
 32          """Class containting the function for OpenDX.""" 
 33   
 34          # Place the program class structure under self.relax 
 35          self.relax = relax 
 36   
 37          # Set up all the classes. 
 38          self.iso3d = Iso3D(relax) 
 39   
 40   
 41 -    def map(self, run=None, res_num=None, map_type='Iso3D', inc=20, lower=None, upper=None, swap=None, file="map", dir="dx", point=None, point_file="point", remap=None, labels=None): 
 42          """Function for mapping the given space and creating OpenDX files.""" 
 43   
 44          # Residue index. 
 45          index = None 
 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          # The number of parameters. 
 54          n = len(self.relax.data.res[run][index].params) 
 55   
 56          # Lower bounds. 
 57          if lower != None: 
 58              if len(lower) != n: 
 59                  raise RelaxLenError, ('lower bounds', n) 
 60   
 61          # Upper bounds. 
 62          if upper != None: 
 63              if len(upper) != n: 
 64                  raise RelaxLenError, ('upper bounds', n) 
 65   
 66          # Axes swapping. 
 67          if swap != None: 
 68              if len(swap) != n: 
 69                  raise RelaxLenError, ('axes swapping', n) 
 70              test = zeros(n) 
 71              for i in xrange(n): 
 72                  if swap[i] >= n: 
 73                      raise RelaxError, "The integer " + `swap[i]` + " is greater than the final array element." 
 74                  elif swap[i] < 0: 
 75                      raise RelaxError, "All integers of the swap argument must be positive." 
 76                  test[swap[i]] = 1 
 77              for i in xrange(n): 
 78                  if test[i] != 1: 
 79                      raise RelaxError, "The swap argument is invalid (possibly duplicated integer values)." 
 80   
 81          # Point. 
 82          if point != None: 
 83              if len(point) != n: 
 84                  raise RelaxLenError, ('point', n) 
 85   
 86          # Axis labels. 
 87          if labels != None: 
 88              if len(labels) != n: 
 89                  raise RelaxLenError, ('axis labels', n) 
 90   
 91          # Space type. 
 92          if match("^[Ii]so3[Dd]", map_type): 
 93              if n != 3: 
 94                  raise RelaxError, "The 3D isosurface map requires a 3 parameter model." 
 95   
 96              # Create the map. 
 97              self.iso3d.map_space(run, index, n, inc, lower, upper, swap, file, dir, point, point_file, remap, labels) 
 98          else: 
 99              raise RelaxError, "The map type '" + map_type + "' is not supported." 
100   
101   
102 -    def run(self, file="map", dir="dx", dx_exe="dx", vp_exec=1): 
103          """Function for running OpenDX.""" 
104   
105          # Text for changing to the directory dir. 
106          dir_text = "" 
107          if dir != None: 
108              dir_text = " -directory " + dir 
109   
110          # Text for executing OpenDX. 
111          execute_text = "" 
112          if vp_exec: 
113              execute_text = " -execute" 
114   
115          # Run OpenDX. 
116          system(dx_exe + dir_text + " -program " + file + ".net" + execute_text + " &") 
117