Source Code for Module prompt.noe

  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        # 
  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   
 27   
 28 -class Noe: 
 29 -    def __init__(self, relax): 
 30          # Help. 
 31          self.__relax_help__ = \ 
 32          """Class for calculating NOE data.""" 
 33   
 34          # Add the generic help string. 
 35          self.__relax_help__ = self.__relax_help__ + "\n" + help.relax_class_help 
 36   
 37          # Place relax in the class namespace. 
 38          self.__relax__ = relax 
 39   
 40   
 41 -    def error(self, run=None, error=0.0, spectrum_type=None, res_num=None, res_name=None): 
 42          """Function for setting the errors in the reference or saturated NOE spectra. 
 43   
 44          Keyword Arguments 
 45          ~~~~~~~~~~~~~~~~~ 
 46   
 47          run:  The name of the run. 
 48   
 49          error:  The error. 
 50   
 51          spectrum_type:  The type of spectrum. 
 52   
 53          res_num:  The residue number. 
 54   
 55          res_name:  The residue name. 
 56   
 57   
 58          Description 
 59          ~~~~~~~~~~~ 
 60   
 61          The spectrum_type argument can have the following values: 
 62              'ref':  The NOE reference spectrum. 
 63              'sat':  The NOE spectrum with proton saturation turned on. 
 64   
 65          If the 'res_num' and 'res_name' arguments are left as the defaults of None, then the error 
 66          value for all residues will be set to the supplied value.  Otherwise the residue number can 
 67          be set to either an integer for selecting a single residue or a python regular expression 
 68          string for selecting multiple residues.  The residue name argument must be a string and can 
 69          use regular expression as well. 
 70          """ 
 71   
 72          # Function intro text. 
 73          if self.__relax__.interpreter.intro: 
 74              text = sys.ps3 + "noe.error(" 
 75              text = text + "run=" + `run` 
 76              text = text + ", error=" + `error` 
 77              text = text + ", spectrum_type=" + `spectrum_type` 
 78              text = text + ", res_num=" + `res_num` 
 79              text = text + ", res_name=" + `res_name` + ")" 
 80              print text 
 81   
 82          # The run argument. 
 83          if type(run) != str: 
 84              raise RelaxStrError, ('run', run) 
 85   
 86          # The error. 
 87          if type(error) != float and type(error) != int: 
 88              raise RelaxNumError, ('error', error) 
 89   
 90          # The spectrum type. 
 91          if type(spectrum_type) != str: 
 92              raise RelaxStrError, ('spectrum type', spectrum_type) 
 93   
 94          # Residue number. 
 95          if res_num != None and type(res_num) != int and type(res_num) != str: 
 96              raise RelaxNoneIntStrError, ('residue number', res_num) 
 97   
 98          # Residue name. 
 99          if res_name != None and type(res_name) != str: 
100              raise RelaxNoneStrError, ('residue name', res_name) 
101   
102          # Execute the functional code. 
103          self.__relax__.specific.noe.set_error(run=run, error=error, spectrum_type=spectrum_type, res_num=res_num, res_name=res_name) 
104   
105   
106 -    def read(self, run=None, file=None, dir=None, spectrum_type=None, format='sparky', heteronuc='N', proton='HN', int_col=None): 
107          """Function for reading peak intensities from a file for NOE calculations. 
108   
109          Keyword Arguments 
110          ~~~~~~~~~~~~~~~~~ 
111   
112          run:  The name of the run. 
113   
114          file:  The name of the file containing the sequence data. 
115   
116          dir:  The directory where the file is located. 
117   
118          spectrum_type:  The type of spectrum. 
119   
120          format:  The type of file containing peak intensities. 
121   
122          heteronuc:  The name of the heteronucleus as specified in the peak intensity file. 
123   
124          proton:  The name of the proton as specified in the peak intensity file. 
125   
126          int_col:  The column containing the peak intensity data (for a non-standard formatted file). 
127   
128   
129          Description 
130          ~~~~~~~~~~~ 
131   
132          The peak intensity can either be from peak heights or peak volumes. 
133   
134   
135          The 'spectrum_type' argument can have the following values: 
136              'ref':  The NOE reference spectrum. 
137              'sat':  The NOE spectrum with proton saturation turned on. 
138   
139   
140          The 'format' argument can currently be set to: 
141              'sparky' 
142              'xeasy' 
143   
144          If the 'format' argument is set to 'sparky', the file should be a Sparky peak list saved 
145          after typing the command 'lt'.  The default is to assume that columns 0, 1, 2, and 3 (1st, 
146          2nd, 3rd, and 4th) contain the Sparky assignment, w1, w2, and peak intensity data 
147          respectively.  The frequency data w1 and w2 are ignored while the peak intensity data can 
148          either be the peak height or volume displayed by changing the window options.  If the peak 
149          intensity data is not within column 3, set the argument 'int_col' to the appropriate value 
150          (column numbering starts from 0 rather than 1). 
151   
152          If the 'format' argument is set to 'xeasy', the file should be the saved XEasy text window 
153          output of the list peak entries command, 'tw' followed by 'le'.  As the columns are fixed, 
154          the peak intensity column is hardwired to number 10 (the 11th column) which contains either 
155          the peak height or peak volume data.  Because the columns are fixed, the 'int_col' argument 
156          will be ignored. 
157   
158   
159          The 'heteronuc' and 'proton' arguments should be set respectively to the name of the 
160          heteronucleus and proton in the file.  Only those lines which match these labels will be 
161          used. 
162   
163   
164          Examples 
165          ~~~~~~~~ 
166   
167          To read the reference and saturated spectra peak heights from the Sparky formatted files 
168          'ref.list' and 'sat.list' to the run 'noe', type: 
169   
170          relax> noe.read('noe', file='ref.list', spectrum_type='ref') 
171          relax> noe.read('noe', file='sat.list', spectrum_type='sat') 
172   
173          To read the reference and saturated spectra peak heights from the XEasy formatted files 
174          'ref.text' and 'sat.text' to the run 'noe', type: 
175   
176          relax> noe.read('noe', file='ref.text', spectrum_type='ref', format='xeasy') 
177          relax> noe.read('noe', file='sat.text', spectrum_type='sat', format='xeasy') 
178          """ 
179   
180          # Function intro text. 
181          if self.__relax__.interpreter.intro: 
182              text = sys.ps3 + "noe.read(" 
183              text = text + "run=" + `run` 
184              text = text + ", file=" + `file` 
185              text = text + ", dir=" + `dir` 
186              text = text + ", spectrum_type=" + `spectrum_type` 
187              text = text + ", format=" + `format` 
188              text = text + ", heteronuc=" + `heteronuc` 
189              text = text + ", proton=" + `proton` 
190              text = text + ", int_col=" + `int_col` + ")" 
191              print text 
192   
193          # The run argument. 
194          if type(run) != str: 
195              raise RelaxStrError, ('run', run) 
196   
197          # The file name. 
198          if type(file) != str: 
199              raise RelaxStrError, ('file name', file) 
200   
201          # Directory. 
202          if dir != None and type(dir) != str: 
203              raise RelaxNoneStrError, ('directory name', dir) 
204   
205          # The spectrum type. 
206          if type(spectrum_type) != str: 
207              raise RelaxStrError, ('spectrum type', spectrum_type) 
208   
209          # The format. 
210          if type(format) != str: 
211              raise RelaxStrError, ('format', format) 
212   
213          # The heteronucleus name. 
214          if type(heteronuc) != str: 
215              raise RelaxStrError, ('heteronucleus name', heteronuc) 
216   
217          # The proton name. 
218          if type(proton) != str: 
219              raise RelaxStrError, ('proton name', proton) 
220   
221          # The intensity column. 
222          if int_col and type(int_col) != int: 
223              raise RelaxNoneIntError, ('intensity column', int_col) 
224   
225          # Execute the functional code. 
226          self.__relax__.specific.noe.read(run=run, file=file, dir=dir, spectrum_type=spectrum_type, format=format, heteronuc=heteronuc, proton=proton, int_col=int_col) 
227