Source Code for Module generic_fns.grace

  1  ############################################################################### 
  2  #                                                                             # 
  3  # Copyright (C) 2003, 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 system 
 24  from re import match 
 25   
 26   
 27 -class Grace: 
 28 -    def __init__(self, relax): 
 29          """Operations, functions, etc common to the different model-free analysis methods.""" 
 30   
 31          self.relax = relax 
 32   
 33   
 34 -    def data(self): 
 35          """Write the data into the grace file.""" 
 36   
 37          # Determine the graph type. 
 38          errors = 0 
 39          for i in xrange(len(self.relax.data.res[self.run])): 
 40              # Remap the data structure 'self.relax.data.res[self.run][i]'. 
 41              data = self.relax.data.res[self.run][i] 
 42   
 43              # Get the value and error. 
 44              value, error = self.return_value(self.run, i, self.data_type) 
 45   
 46              # Skip the data if there is no value. 
 47              if value == None: 
 48                  continue 
 49   
 50              # Test if there is an error. 
 51              if error != None: 
 52                  errors = 1 
 53                  break 
 54   
 55          if errors: 
 56              graph_type = 'xydy' 
 57          else: 
 58              graph_type = 'xy' 
 59   
 60   
 61          # Graph 0, set 0. 
 62          self.file.write("@target G0.S0\n") 
 63          self.file.write("@type " + graph_type + "\n") 
 64   
 65          # Loop over the sequence. 
 66          for i in xrange(len(self.relax.data.res[self.run])): 
 67              # Remap the data structure 'self.relax.data.res[self.run][i]'. 
 68              data = self.relax.data.res[self.run][i] 
 69   
 70              # Get the value and error. 
 71              value, error = self.return_value(self.run, i, self.data_type) 
 72   
 73              # Skip the data if there is no value. 
 74              if value == None: 
 75                  continue 
 76   
 77              # Graph type xy. 
 78              if graph_type == 'xy': 
 79                  # Write the data. 
 80                  self.file.write("%-5i%-30s\n" % (data.num, `value`)) 
 81   
 82              # Graph type xydy. 
 83              elif graph_type == 'xydy': 
 84                  # Missing error. 
 85                  if error == None: 
 86                      error = 0.0 
 87   
 88                  # Write the data. 
 89                  self.file.write("%-5i%-30s%-30s\n" % (data.num, `value`, `error`)) 
 90   
 91          # End of graph 0, set 0. 
 92          self.file.write("&\n") 
 93   
 94   
 95 -    def header(self): 
 96          """Write the grace header.""" 
 97   
 98          # Grace version number (presumably for grace to interpret the header info). 
 99          self.file.write("@version 50114\n") 
100   
101          # Graph G0. 
102          self.file.write("@with g0\n") 
103   
104          # X axis start and end. 
105          self.file.write("@    world xmin " + `self.relax.data.res[self.run][0].num - 1` + "\n") 
106          self.file.write("@    world xmax " + `self.relax.data.res[self.run][-1].num + 1` + "\n") 
107   
108          # Y axis start and end. 
109          min_value = 0.0 
110          max_value = -1e99 
111          for i in xrange(len(self.relax.data.res[self.run])): 
112              # Remap the data structure 'self.relax.data.res[self.run][i]'. 
113              data = self.relax.data.res[self.run][i] 
114   
115              # Get the value and error. 
116              value, error = self.return_value(self.run, i, self.data_type) 
117   
118              # Skip the data if there is no value. 
119              if value == None: 
120                  continue 
121   
122              # Max check. 
123              if value > max_value: 
124                  max_value = value 
125   
126              # Min check. 
127              if value < min_value: 
128                  min_value = value 
129   
130          self.file.write("@    world ymin " + `min_value - min_value * 0.05` + "\n") 
131          self.file.write("@    world ymax " + `max_value + max_value * 0.05` + "\n") 
132   
133          # Residue specific ticks. 
134          self.file.write("@    xaxis  tick major 10\n") 
135          self.file.write("@    xaxis  tick major size 0.48\n") 
136          self.file.write("@    xaxis  tick major linewidth 0.5\n") 
137          self.file.write("@    xaxis  tick minor linewidth 0.5\n") 
138          self.file.write("@    xaxis  tick minor size 0.24\n") 
139          self.file.write("@    xaxis  ticklabel char size 0.79\n") 
140   
141          # Data specific ticks. 
142          self.file.write("@    yaxis  tick major size 0.48\n") 
143          self.file.write("@    yaxis  tick major linewidth 0.5\n") 
144          self.file.write("@    yaxis  tick minor linewidth 0.5\n") 
145          self.file.write("@    yaxis  tick minor size 0.24\n") 
146          self.file.write("@    yaxis  ticklabel char size 0.79\n") 
147   
148          # Frame. 
149          self.file.write("@    frame linewidth 0.5\n") 
150   
151          # Symbols. 
152          self.file.write("@    s0 symbol 1\n") 
153          self.file.write("@    s0 symbol size 0.35\n") 
154          self.file.write("@    s0 symbol fill pattern 1\n") 
155          self.file.write("@    s0 symbol linewidth 0.5\n") 
156          self.file.write("@    s0 line linestyle 0\n") 
157   
158          # Error bars. 
159          self.file.write("@    s0 errorbar size 0.5\n") 
160          self.file.write("@    s0 errorbar linewidth 0.5\n") 
161          self.file.write("@    s0 errorbar riser linewidth 0.5\n") 
162   
163   
164 -    def view(self, run=None, data_type=None, file=None, dir=None, grace_exe='xmgrace', force=0): 
165          """Function for running Grace.""" 
166   
167          # Write the grace file (if the run in not None). 
168          if run != None: 
169              self.write(run=run, data_type=data_type, file=file, dir=dir, force=force) 
170   
171          # File path. 
172          self.file_path = self.relax.IO.file_path(file, dir) 
173   
174          # Run Grace. 
175          system(grace_exe + " " + self.file_path + " &") 
176   
177   
178 -    def write(self, run=None, data_type=None, file=None, dir=None, force=0): 
179          """Function for writing data to a file.""" 
180   
181          # Arguments. 
182          self.run = run 
183          self.data_type = data_type 
184   
185          # Test if the run exists. 
186          if not self.run in self.relax.data.run_names: 
187              raise RelaxNoRunError, self.run 
188   
189          # Test if the sequence data is loaded. 
190          if not self.relax.data.res.has_key(self.run): 
191              raise RelaxNoSequenceError, self.run 
192   
193          # Open the file for writing. 
194          self.file = self.relax.IO.open_write_file(file, dir, force) 
195   
196          # Function type. 
197          function_type = self.relax.data.run_types[self.relax.data.run_names.index(run)] 
198   
199          # Specific value and error returning function. 
200          self.return_value = self.relax.specific_setup.setup('return_value', function_type) 
201   
202          # Write the header. 
203          self.header() 
204   
205          # Write the data. 
206          self.data() 
207   
208          # Close the file. 
209          self.file.close() 
210