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               # 
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 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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 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.consistency_tests import Consistency_tests 
 29  from specific_fns.model_free import Model_free 
 30  from specific_fns.jw_mapping import Jw_mapping 
 31  from specific_fns.noe import Noe 
 32  from specific_fns.relax_fit import Relax_fit 
 33   
 34   
 35 -class Grace: 
 36 -    def __init__(self, relax): 
 37          # Help. 
 38          self.__relax_help__ = \ 
 39          """Class for interfacing with Grace.""" 
 40   
 41          # Add the generic help string. 
 42          self.__relax_help__ = self.__relax_help__ + "\n" + help.relax_class_help 
 43   
 44          # Place relax in the class namespace. 
 45          self.__relax__ = relax 
 46   
 47   
 48 -    def view(self, file=None, dir='grace', grace_exe='xmgrace'): 
 49          """Function for running Grace. 
 50   
 51          Keyword Arguments 
 52          ~~~~~~~~~~~~~~~~~ 
 53   
 54          file:  The name of the file. 
 55   
 56          dir:  The directory name. 
 57   
 58          grace_exe:  The Grace executable file. 
 59   
 60   
 61          Description 
 62          ~~~~~~~~~~~ 
 63   
 64          This function can be used to execute Grace to view the specified file the Grace '.agr' file 
 65          and the execute Grace. If the directory name is set to None, the file will be assumed to be 
 66          in the current working directory. 
 67   
 68   
 69          Examples 
 70          ~~~~~~~~ 
 71   
 72          To view the file 's2.agr' in the directory 'grace', type: 
 73   
 74          relax> grace.view(file='s2.agr') 
 75          relax> grace.view(file='s2.agr', dir='grace') 
 76          """ 
 77   
 78          # Function intro text. 
 79          if self.__relax__.interpreter.intro: 
 80              text = sys.ps3 + "grace.view(" 
 81              text = text + "file=" + `file` 
 82              text = text + ", dir=" + `dir` 
 83              text = text + ", grace_exe=" + `grace_exe` + ")" 
 84              print text 
 85   
 86          # File. 
 87          if type(file) != str: 
 88              raise RelaxStrError, ('file name', file) 
 89   
 90          # Directory. 
 91          if dir != None and type(dir) != str: 
 92              raise RelaxNoneStrError, ('directory name', dir) 
 93   
 94          # Grace executable file. 
 95          if type(grace_exe) != str: 
 96              raise RelaxStrError, ('Grace executable file', grace_exe) 
 97   
 98          # Execute the functional code. 
 99          self.__relax__.generic.grace.view(file=file, dir=dir, grace_exe=grace_exe) 
100   
101   
102 -    def write(self, run=None, x_data_type='res', y_data_type=None, res_num=None, res_name=None, plot_data='value', norm=0, file=None, dir='grace', force=0): 
103          """Function for creating a grace '.agr' file. 
104   
105          Keyword Arguments 
106          ~~~~~~~~~~~~~~~~~ 
107   
108          run:  The name of the run. 
109   
110          x_data_type:  The data type for the X-axis (no regular expression is allowed). 
111   
112          y_data_type:  The data type for the Y-axis (no regular expression is allowed). 
113   
114          res_num:  The residue number (regular expression is allowed). 
115   
116          res_name:  The residue name (regular expression is allowed). 
117   
118          plot_data:  The data to use for the plot. 
119   
120          norm:  Flag for the normalisation of series type data. 
121   
122          file:  The name of the file. 
123   
124          dir:  The directory name. 
125   
126          force:  A flag which, if set to 1, will cause the file to be overwritten. 
127   
128   
129          Description 
130          ~~~~~~~~~~~ 
131   
132          This function is designed to be as flexible as possible so that any combination of data can 
133          be plotted.  The output is in the format of a Grace plot (also known as ACE/gr, Xmgr, and 
134          xmgrace) which only supports two dimensional plots.  Three types of keyword arguments can 
135          be used to create various types of plot.  These include the X-axis and Y-axis data types, 
136          the residue number and name selection arguments, and an argument for selecting what to 
137          actually plot. 
138   
139          The X-axis and Y-axis data type arguments should be plain strings, regular expression is not 
140          allowed.  If the X-axis data type argument is not given, the plot will default to having the 
141          residue number along the x-axis.  The two axes of the Grace plot can be absolutely any of 
142          the data types listed in the tables below.  The only limitation, currently anyway, is that 
143          the data must belong to the same run. 
144   
145          The residue number and name arguments can be used to limit the residues used in the plot. 
146          The default is that all residues will be used, however, these arguments can be used to 
147          select a subset of all residues, or a single residue for plots of Monte Carlo simulations, 
148          etc.  Regular expression is allowed for both the residue number and name, and the number can 
149          either be an integer or a string. 
150   
151          The property which is actually plotted can be controlled by the 'plot_data' argument.  It 
152          can be one of the following: 
153              'value':  Plot values (with errors if they exist). 
154              'error':  Plot errors. 
155              'sims':   Plot the simulation values. 
156   
157          Normalisation is only allowed for series type data, for example the R2 exponential curves, 
158          and will be ignored for all other data types.  If the norm flag is set to one then the 
159          y-value of the first point of the series will be set to 1.  This normalisation is useful for 
160          emphasising errors in the data sets. 
161   
162   
163          Examples 
164          ~~~~~~~~ 
165   
166          To write the NOE values for all residues from the run 'noe' to the Grace file 'noe.agr', 
167          type: 
168   
169          relax> grace.write('noe', 'res', 'noe', file='noe.agr') 
170          relax> grace.write('noe', y_data_type='noe', file='noe.agr') 
171          relax> grace.write('noe', x_data_type='res', y_data_type='noe', file='noe.agr') 
172          relax> grace.write(run='noe', y_data_type='noe', file='noe.agr', force=1) 
173   
174   
175          To create a Grace file of 'S2' vs. 'te' for all residues, type: 
176   
177          relax> grace.write('m2', 'S2', 'te', file='s2_te.agr') 
178          relax> grace.write('m2', x_data_type='S2', y_data_type='te', file='s2_te.agr') 
179          relax> grace.write(run='m2', x_data_type='S2', y_data_type='te', file='s2_te.agr', force=1) 
180   
181   
182          To create a Grace file of the Monte Carlo simulation values of 'Rex' vs. 'te' for residue 
183          123, type: 
184   
185          relax> grace.write('m4', 'Rex', 'te', res_num=123, plot_data='sims', file='s2_te.agr') 
186          relax> grace.write(run='m4', x_data_type='Rex', y_data_type='te', res_num=123, 
187                             plot_data='sims', file='s2_te.agr') 
188   
189   
190          By plotting the peak intensities, the integrity of exponential relaxation curves can be 
191          checked and anomalies searched for prior to model-free analysis or reduced spectral density 
192          mapping.  For example the normalised average peak intensities can be plotted verses the 
193          relaxation time periods for the relaxation curves of all residues of a protein.  The 
194          normalisation, whereby the initial peak intensity of each residue I(0) is set to 1, 
195          emphasises any problems.  To produce this Grace file, type: 
196   
197          relax> grace.write(name, x_data_type='relax_times', y_data_type='ave_int', 
198                             norm=1, file='intensities_norm.agr', force=1) 
199          """ 
200   
201          # Function intro text. 
202          if self.__relax__.interpreter.intro: 
203              text = sys.ps3 + "grace.write(" 
204              text = text + "run=" + `run` 
205              text = text + ", x_data_type=" + `x_data_type` 
206              text = text + ", y_data_type=" + `y_data_type` 
207              text = text + ", res_num=" + `res_num` 
208              text = text + ", res_name=" + `res_name` 
209              text = text + ", plot_data=" + `plot_data` 
210              text = text + ", norm=" + `norm` 
211              text = text + ", file=" + `file` 
212              text = text + ", dir=" + `dir` 
213              text = text + ", force=" + `force` + ")" 
214              print text 
215   
216          # The run name. 
217          if type(run) != str: 
218              raise RelaxStrError, ('run', run) 
219   
220          # Data type for x-axis. 
221          if type(x_data_type) != str: 
222              raise RelaxStrError, ('x data type', x_data_type) 
223   
224          # Data type for y-axis. 
225          if type(y_data_type) != str: 
226              raise RelaxStrError, ('y data type', y_data_type) 
227   
228          # Residue number. 
229          if res_num != None and type(res_num) != int and type(res_num) != str: 
230              raise RelaxNoneIntStrError, ('residue number', res_num) 
231   
232          # Residue name. 
233          if res_name != None and type(res_name) != str: 
234              raise RelaxNoneStrError, ('residue name', res_name) 
235   
236          # The plot data. 
237          if type(plot_data) != str: 
238              raise RelaxStrError, ('plot data', plot_data) 
239   
240          # File. 
241          if type(file) != str: 
242              raise RelaxStrError, ('file name', file) 
243   
244          # Directory. 
245          if dir != None and type(dir) != str: 
246              raise RelaxNoneStrError, ('directory name', dir) 
247   
248          # The force flag. 
249          if type(force) != int or (force != 0 and force != 1): 
250              raise RelaxBinError, ('force flag', force) 
251   
252          # Execute the functional code. 
253          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, norm=norm, file=file, dir=dir, force=force) 
254   
255   
256   
257      # Docstring modification. 
258      ######################### 
259   
260      # Write function. 
261      write.__doc__ = write.__doc__ + "\n\n" + regexp_doc() + "\n" 
262      write.__doc__ = write.__doc__ + Consistency_tests.return_data_name.__doc__ + "\n\n" 
263      write.__doc__ = write.__doc__ + Minimise.return_data_name.__doc__ + "\n\n" 
264      write.__doc__ = write.__doc__ + Noe.return_data_name.__doc__ + "\n" 
265      write.__doc__ = write.__doc__ + Relax_fit.return_data_name.__doc__ + "\n" 
266      write.__doc__ = write.__doc__ + Jw_mapping.return_data_name.__doc__ + "\n\n" 
267      write.__doc__ = write.__doc__ + Model_free.return_data_name.__doc__ + "\n\n" 
268