Source Code for Module prompt.grace

  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  import sys 
 24   
 25  import help 
 26  from specific_fns.model_free import Model_free 
 27  from specific_fns.jw_mapping import Jw_mapping 
 28  from specific_fns.noe import Noe 
 29   
 30   
 31 -class Grace: 
 32 -    def __init__(self, relax): 
 33          # Help. 
 34          self.__relax_help__ = \ 
 35          """Class for interfacing with Grace.""" 
 36   
 37          # Add the generic help string. 
 38          self.__relax_help__ = self.__relax_help__ + "\n" + help.relax_class_help 
 39   
 40          # Place relax in the class namespace. 
 41          self.__relax__ = relax 
 42   
 43   
 44 -    def view(self, run=None, data_type=None, file=None, dir='grace', grace_exe='xmgrace', force=0): 
 45          """Function for running Grace. 
 46   
 47          Keyword Arguments 
 48          ~~~~~~~~~~~~~~~~~ 
 49   
 50          run:  The name of the run. 
 51   
 52          data_type:  The data type. 
 53   
 54          file:  The name of the file. 
 55   
 56          dir:  The directory name. 
 57   
 58          grace_exe:  The Grace executable file. 
 59   
 60          force:  A flag which, if set to 1, will cause the file to be overwritten. 
 61   
 62   
 63          Description 
 64          ~~~~~~~~~~~ 
 65   
 66          This function can be used either to execute grace, opening the specified file, or to create 
 67          the grace '.agr' file and the execute grace.  If the run and data_type arguments are 
 68          supplied, the second of these two options is pursued.  To simply execute grace, leave the 
 69          run and data_type arguments as None. 
 70   
 71          If the directory name is set to None, the file will be placed in the current working 
 72          directory. 
 73   
 74          The force flag will only have an effect if the run argument is not None. 
 75   
 76   
 77          Examples 
 78          ~~~~~~~~ 
 79   
 80          To view the file 's2.agr' in the directory 'grace', type: 
 81   
 82          relax> grace.view(file='s2.agr') 
 83          relax> grace.view(file='s2.agr', dir='grace') 
 84   
 85   
 86          To write the NOE values from the run 'noe' to the grace file 'noe.agr' and then view the 
 87          file, type: 
 88   
 89          relax> grace.view('noe', 'noe', 'noe.agr') 
 90          relax> grace.view('noe', data_type='noe', file='noe.agr') 
 91          relax> grace.view(run='noe', data_type='noe', file='noe.agr', dir='grace') 
 92          """ 
 93   
 94          # Function intro text. 
 95          if self.__relax__.interpreter.intro: 
 96              text = sys.ps3 + "grace.view(" 
 97              text = text + "run=" + `run` 
 98              text = text + ", data_type=" + `data_type` 
 99              text = text + ", file=" + `file` 
100              text = text + ", dir=" + `dir` 
101              text = text + ", grace_exe=" + `grace_exe` + ")" 
102              print text 
103   
104          # The run name. 
105          if run != None and type(run) != str: 
106              raise RelaxNoneStrError, ('run', run) 
107   
108          # Data type. 
109          if data_type != None and type(data_type) != str: 
110              raise RelaxNoneStrError, ('data type', data_type) 
111   
112          # File. 
113          if type(file) != str: 
114              raise RelaxStrError, ('file name', file) 
115   
116          # Directory. 
117          if dir != None and type(dir) != str: 
118              raise RelaxNoneStrError, ('directory name', dir) 
119   
120          # Grace executable file. 
121          if type(grace_exe) != str: 
122              raise RelaxStrError, ('Grace executable file', grace_exe) 
123   
124          # The force flag. 
125          if type(force) != int or (force != 0 and force != 1): 
126              raise RelaxBinError, ('force flag', force) 
127   
128          # Execute the functional code. 
129          self.__relax__.generic.grace.view(run=run, data_type=data_type, file=file, dir=dir, grace_exe=grace_exe, force=force) 
130   
131   
132 -    def write(self, run=None, data_type=None, file=None, dir='grace', force=0): 
133          """Function for creating a grace '.agr' file. 
134   
135          Keyword Arguments 
136          ~~~~~~~~~~~~~~~~~ 
137   
138          run:  The name of the run. 
139   
140          data_type:  The data type. 
141   
142          file:  The name of the file. 
143   
144          dir:  The directory name. 
145   
146          force:  A flag which, if set to 1, will cause the file to be overwritten. 
147   
148   
149          Description 
150          ~~~~~~~~~~~ 
151   
152          If no directory name is given, the file will be placed in the current working directory. 
153   
154          The data type argument should be a string. 
155   
156   
157          Examples 
158          ~~~~~~~~ 
159   
160          To write the NOE values from the run 'noe' to the grace file 'noe.agr', type: 
161   
162          relax> grace.write('noe', 'noe', 'noe.agr') 
163          relax> grace.write('noe', data_type='noe', file='noe.agr') 
164          relax> grace.write(run='noe', data_type='noe', file='noe.agr', dir='grace') 
165          """ 
166   
167          # Function intro text. 
168          if self.__relax__.interpreter.intro: 
169              text = sys.ps3 + "grace.write(" 
170              text = text + "run=" + `run` 
171              text = text + ", data_type=" + `data_type` 
172              text = text + ", file=" + `file` 
173              text = text + ", dir=" + `dir` 
174              text = text + ", force=" + `force` + ")" 
175              print text 
176   
177          # The run name. 
178          if type(run) != str: 
179              raise RelaxStrError, ('run', run) 
180   
181          # Data type. 
182          if type(data_type) != str: 
183              raise RelaxStrError, ('data type', data_type) 
184   
185          # File. 
186          if type(file) != str: 
187              raise RelaxStrError, ('file name', file) 
188   
189          # Directory. 
190          if dir != None and type(dir) != str: 
191              raise RelaxNoneStrError, ('directory name', dir) 
192   
193          # The force flag. 
194          if type(force) != int or (force != 0 and force != 1): 
195              raise RelaxBinError, ('force flag', force) 
196   
197          # Execute the functional code. 
198          self.__relax__.generic.grace.write(run=run, data_type=data_type, file=file, dir=dir, force=force) 
199   
200   
201      # Docstring modification. 
202      ######################### 
203   
204      __re_doc__ = """ 
205   
206          Regular expression 
207          ~~~~~~~~~~~~~~~~~~ 
208   
209          The python function 'match', which uses regular expression, is used to determine which data 
210          type to set values to, therefore various data_type strings can be used to select the same 
211          data type.  Patterns used for matching for specific data types are listed below.  Regular 
212          expression is also used in residue name and number selections, except this time the user 
213          supplies the regular expression string. 
214   
215          This is a short description of python regular expression, for more information, see the 
216          regular expression syntax section of the Python Library Reference.  Some of the regular 
217          expression syntax used in this function is: 
218   
219              [] - A sequence or set of characters to match to a single character.  For example, 
220              '[Ss]2' will match both 'S2' and 's2'. 
221   
222              ^ - Match the start of the string. 
223   
224              $ - Match the end of the string.  For example, '^[Ss]2$' will match 's2' but not 'S2f' 
225              or 's2s'. 
226   
227      """ 
228   
229      # View function. 
230      view.__doc__ = view.__doc__ + "\n\n" + __re_doc__ + "\n" 
231      view.__doc__ = view.__doc__ + Model_free.get_data_name.__doc__ + "\n\n" 
232      view.__doc__ = view.__doc__ + Jw_mapping.get_data_name.__doc__ + "\n\n" 
233      view.__doc__ = view.__doc__ + Noe.get_data_name.__doc__ + "\n" 
234   
235      # Write function. 
236      write.__doc__ = write.__doc__ + "\n\n" + __re_doc__ + "\n" 
237      write.__doc__ = write.__doc__ + Model_free.get_data_name.__doc__ + "\n\n" 
238      write.__doc__ = write.__doc__ + Jw_mapping.get_data_name.__doc__ + "\n\n" 
239      write.__doc__ = write.__doc__ + Noe.get_data_name.__doc__ + "\n" 
240