Source Code for Module prompt.grace

  1  ############################################################################### 
  2  #                                                                             # 
  3  # Copyright (C) 2004-2005 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        # 
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 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.                                # 
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 17  # You should have received a copy of the GNU General Public License           # 
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 19  # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA   # 
 20  #                                                                             # 
 21  ############################################################################### 
 22   
 23  import sys 
 24   
 25  from doc_string import regexp_doc 
 26  import help 
 27  from generic_fns.minimise import Minimise 
 28  from specific_fns.model_free import Model_free 
 29  from specific_fns.jw_mapping import Jw_mapping 
 30  from specific_fns.noe import Noe 
 31   
 32   
 33 -class Grace: 
 34 -    def __init__(self, relax): 
 35          # Help. 
 36          self.__relax_help__ = \ 
 37          """Class for interfacing with Grace.""" 
 38   
 39          # Add the generic help string. 
 40          self.__relax_help__ = self.__relax_help__ + "\n" + help.relax_class_help 
 41   
 42          # Place relax in the class namespace. 
 43          self.__relax__ = relax 
 44   
 45   
 46 -    def view(self, file=None, dir='grace', grace_exe='xmgrace'): 
 47          """Function for running Grace. 
 48   
 49          Keyword Arguments 
 50          ~~~~~~~~~~~~~~~~~ 
 51   
 52          file:  The name of the file. 
 53   
 54          dir:  The directory name. 
 55   
 56          grace_exe:  The Grace executable file. 
 57   
 58   
 59          Description 
 60          ~~~~~~~~~~~ 
 61   
 62          This function can be used to execute Grace to view the specified file the Grace '.agr' file 
 63          and the execute Grace. If the directory name is set to None, the file will be assumed to be 
 64          in the current working directory. 
 65   
 66   
 67          Examples 
 68          ~~~~~~~~ 
 69   
 70          To view the file 's2.agr' in the directory 'grace', type: 
 71   
 72          relax> grace.view(file='s2.agr') 
 73          relax> grace.view(file='s2.agr', dir='grace') 
 74          """ 
 75   
 76          # Function intro text. 
 77          if self.__relax__.interpreter.intro: 
 78              text = sys.ps3 + "grace.view(" 
 79              text = text + "file=" + `file` 
 80              text = text + ", dir=" + `dir` 
 81              text = text + ", grace_exe=" + `grace_exe` + ")" 
 82              print text 
 83   
 84          # File. 
 85          if type(file) != str: 
 86              raise RelaxStrError, ('file name', file) 
 87   
 88          # Directory. 
 89          if dir != None and type(dir) != str: 
 90              raise RelaxNoneStrError, ('directory name', dir) 
 91   
 92          # Grace executable file. 
 93          if type(grace_exe) != str: 
 94              raise RelaxStrError, ('Grace executable file', grace_exe) 
 95   
 96          # Execute the functional code. 
 97          self.__relax__.generic.grace.view(file=file, dir=dir, grace_exe=grace_exe) 
 98   
 99   
100 -    def write(self, run=None, x_data_type='res', y_data_type=None, res_num=None, res_name=None, plot_data='value', file=None, dir='grace', force=0): 
101          """Function for creating a grace '.agr' file. 
102   
103          Keyword Arguments 
104          ~~~~~~~~~~~~~~~~~ 
105   
106          run:  The name of the run. 
107   
108          x_data_type:  The data type for the X-axis (no regular expression is allowed). 
109   
110          y_data_type:  The data type for the Y-axis (no regular expression is allowed). 
111   
112          res_num:  The residue number (regular expression is allowed). 
113   
114          res_name:  The residue name (regular expression is allowed). 
115   
116          plot_data:  The data to use for the plot. 
117   
118          file:  The name of the file. 
119   
120          dir:  The directory name. 
121   
122          force:  A flag which, if set to 1, will cause the file to be overwritten. 
123   
124   
125          Description 
126          ~~~~~~~~~~~ 
127   
128          This function is designed to be as flexible as possible so that any combination of data can 
129          be plotted.  The output is in the format of a Grace plot (also known as ACE/gr, Xmgr, and 
130          xmgrace) which only supports two dimensional plots.  Three types of keyword arguments can 
131          be used to create various types of plot.  These include the X-axis and Y-axis data types, 
132          the residue number and name selection arguments, and an argument for selecting what to 
133          actually plot. 
134   
135          The X-axis and Y-axis data type arguments should be plain strings, regular expression is not 
136          allowed.  If the X-axis data type argument is not given, the plot will default to having the 
137          residue number along the x-axis.  The two axes of the Grace plot can be absolutely any of 
138          the data types listed in the tables below.  The only limitation, currently anyway, is that 
139          the data must belong to the same run. 
140   
141          The residue number and name arguments can be used to limit the residues used in the plot. 
142          The default is that all residues will be used, however, these arguments can be used to 
143          select a subset of all residues, or a single residue for plots of Monte Carlo simulations, 
144          etc.  Regular expression is allowed for both the residue number and name, and the number can 
145          either be an integer or a string. 
146   
147          The property which is actually plotted can be controlled by the 'plot_data' argument.  It 
148          can be one of the following: 
149              'value':  Plot values (with errors if they exist). 
150              'error':  Plot errors. 
151              'sims':   Plot the simulation values. 
152   
153   
154          Examples 
155          ~~~~~~~~ 
156   
157          To write the NOE values for all residues from the run 'noe' to the Grace file 'noe.agr', 
158          type: 
159   
160          relax> grace.write('noe', 'res', 'noe', file='noe.agr') 
161          relax> grace.write('noe', y_data_type='noe', file='noe.agr') 
162          relax> grace.write('noe', x_data_type='res', y_data_type='noe', file='noe.agr') 
163          relax> grace.write(run='noe', y_data_type='noe', file='noe.agr', force=1) 
164   
165   
166          To create a Grace file of 'S2' vs. 'te' for all residues, type: 
167   
168          relax> grace.write('m2', 'S2', 'te', file='s2_te.agr') 
169          relax> grace.write('m2', x_data_type='S2', y_data_type='te', file='s2_te.agr') 
170          relax> grace.write(run='m2', x_data_type='S2', y_data_type='te', file='s2_te.agr', force=1) 
171   
172   
173          To create a Grace file of the Monte Carlo simulation values of 'Rex' vs. 'te' for residue 
174          123, type: 
175   
176          relax> grace.write('m4', 'Rex', 'te', res_num=123, plot_data='sims', file='s2_te.agr') 
177          relax> grace.write(run='m4', x_data_type='Rex', y_data_type='te', res_num=123, 
178                             plot_data='sims', file='s2_te.agr') 
179          """ 
180   
181          # Function intro text. 
182          if self.__relax__.interpreter.intro: 
183              text = sys.ps3 + "grace.write(" 
184              text = text + "run=" + `run` 
185              text = text + ", x_data_type=" + `x_data_type` 
186              text = text + ", y_data_type=" + `y_data_type` 
187              text = text + ", res_num=" + `res_num` 
188              text = text + ", res_name=" + `res_name` 
189              text = text + ", plot_data=" + `plot_data` 
190              text = text + ", file=" + `file` 
191              text = text + ", dir=" + `dir` 
192              text = text + ", force=" + `force` + ")" 
193              print text 
194   
195          # The run name. 
196          if type(run) != str: 
197              raise RelaxStrError, ('run', run) 
198   
199          # Data type for x-axis. 
200          if type(x_data_type) != str: 
201              raise RelaxStrError, ('x data type', x_data_type) 
202   
203          # Data type for y-axis. 
204          if type(y_data_type) != str: 
205              raise RelaxStrError, ('y data type', y_data_type) 
206   
207          # Residue number. 
208          if res_num != None and type(res_num) != int and type(res_num) != str: 
209              raise RelaxNoneIntStrError, ('residue number', res_num) 
210   
211          # Residue name. 
212          if res_name != None and type(res_name) != str: 
213              raise RelaxNoneStrError, ('residue name', res_name) 
214   
215          # The plot data. 
216          if type(plot_data) != str: 
217              raise RelaxStrError, ('plot data', plot_data) 
218   
219          # File. 
220          if type(file) != str: 
221              raise RelaxStrError, ('file name', file) 
222   
223          # Directory. 
224          if dir != None and type(dir) != str: 
225              raise RelaxNoneStrError, ('directory name', dir) 
226   
227          # The force flag. 
228          if type(force) != int or (force != 0 and force != 1): 
229              raise RelaxBinError, ('force flag', force) 
230   
231          # Execute the functional code. 
232          self.__relax__.generic.grace.write(run=run, x_data_type=x_data_type, y_data_type=y_data_type, res_num=res_num, res_name=res_name, plot_data=plot_data, file=file, dir=dir, force=force) 
233   
234   
235   
236      # Docstring modification. 
237      ######################### 
238   
239      # Write function. 
240      write.__doc__ = write.__doc__ + "\n\n" + regexp_doc() + "\n" 
241      write.__doc__ = write.__doc__ + Minimise.return_data_name.__doc__ + "\n\n" 
242      write.__doc__ = write.__doc__ + Model_free.return_data_name.__doc__ + "\n\n" 
243      write.__doc__ = write.__doc__ + Jw_mapping.return_data_name.__doc__ + "\n\n" 
244      write.__doc__ = write.__doc__ + Noe.return_data_name.__doc__ + "\n" 
245