Source Code for Module prompt.relax_fit

  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   
 27   
 28 -class Relax_fit: 
 29 -    def __init__(self, relax): 
 30          # Help. 
 31          self.__relax_help__ = \ 
 32          """Class for relaxation curve fitting.""" 
 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 read(self, run=None, file=None, dir=None, relax_time=0.0, fit_type='exp', format='sparky', heteronuc='N', proton='HN', int_col=None): 
 42          """Function for reading peak intensities from a file. 
 43   
 44          Keyword Arguments 
 45          ~~~~~~~~~~~~~~~~~ 
 46   
 47          run:  The name of the run. 
 48   
 49          file:  The name of the file containing the sequence data. 
 50   
 51          dir:  The directory where the file is located. 
 52   
 53          relax_time:  The time, in seconds, of the relaxation period. 
 54   
 55          fit_type:  The type of relaxation curve to fit. 
 56   
 57          format:  The type of file containing peak intensities. 
 58   
 59          heteronuc:  The name of the heteronucleus as specified in the peak intensity file. 
 60   
 61          proton:  The name of the proton as specified in the peak intensity file. 
 62   
 63          int_col:  The column containing the peak intensity data (for a non-standard formatted file). 
 64   
 65   
 66          Description 
 67          ~~~~~~~~~~~ 
 68   
 69          The peak intensity can either be from peak heights or peak volumes. 
 70   
 71   
 72          The supported relaxation experiments include the default two parameter exponential fit, 
 73          selected by setting the 'fit_type' argument to 'exp', and the three parameter inversion 
 74          recovery experiment in which the peak intensity limit is a non-zero value, selected by 
 75          setting the argument to 'inv'. 
 76   
 77   
 78          The format argument can currently be set to: 
 79              'sparky' 
 80              'xeasy' 
 81   
 82          If the format argument is set to 'sparky', the file should be a Sparky peak list saved after 
 83          typing the command 'lt'.  The default is to assume that columns 0, 1, 2, and 3 (1st, 2nd, 
 84          3rd, and 4th) contain the Sparky assignment, w1, w2, and peak intensity data respectively. 
 85          The frequency data w1 and w2 are ignored while the peak intensity data can either be the 
 86          peak height or volume displayed by changing the window options.  If the peak intensity data 
 87          is not within column 3, set the argument int_col to the appropriate value (column numbering 
 88          starts from 0 rather than 1). 
 89   
 90          If the format argument is set to 'xeasy', the file should be the saved XEasy text window 
 91          output of the list peak entries command, 'tw' followed by 'le'.  As the columns are fixed, 
 92          the peak intensity column is hardwired to number 10 (the 11th column) which contains either 
 93          the peak height or peak volume data.  Because the columns are fixed, the int_col argument 
 94          will be ignored. 
 95   
 96   
 97          The heteronuc and proton arguments should be set respectively to the name of the 
 98          heteronucleus and proton in the file.  Only those lines which match these labels will be 
 99          used. 
100   
101   
102          """ 
103   
104          # Function intro text. 
105          if self.__relax__.interpreter.intro: 
106              text = sys.ps3 + "relax_fit.read(" 
107              text = text + "run=" + `run` 
108              text = text + ", file=" + `file` 
109              text = text + ", dir=" + `dir` 
110              text = text + ", relax_time=" + `relax_time` 
111              text = text + ", fit_type=" + `fit_type` 
112              text = text + ", format=" + `format` 
113              text = text + ", heteronuc=" + `heteronuc` 
114              text = text + ", proton=" + `proton` 
115              text = text + ", int_col=" + `int_col` + ")" 
116              print text 
117   
118          # The run argument. 
119          if type(run) != str: 
120              raise RelaxStrError, ('run', run) 
121   
122          # The file name. 
123          if type(file) != str: 
124              raise RelaxStrError, ('file name', file) 
125   
126          # Directory. 
127          if dir != None and type(dir) != str: 
128              raise RelaxNoneStrError, ('directory name', dir) 
129   
130          # The relaxation time. 
131          if type(relax_time) != float: 
132              raise RelaxFloatError, ('relaxation time', relax_time) 
133   
134          # The fit type. 
135          if type(fit_type) != str: 
136              raise RelaxStrError, ('fit type', fit_type) 
137   
138          # The format. 
139          if type(format) != str: 
140              raise RelaxStrError, ('format', format) 
141   
142          # The heteronucleus name. 
143          if type(heteronuc) != str: 
144              raise RelaxStrError, ('heteronucleus name', heteronuc) 
145   
146          # The proton name. 
147          if type(proton) != str: 
148              raise RelaxStrError, ('proton name', proton) 
149   
150          # The intensity column. 
151          if int_col and type(int_col) != int: 
152              raise RelaxNoneIntError, ('intensity column', int_col) 
153   
154          # Execute the functional code. 
155          self.__relax__.specific.relax_fit.read(run=run, file=file, dir=dir, relax_time=relax_time, fit_type=fit_type, format=format, heteronuc=heteronuc, proton=proton, int_col=int_col) 
156