Source Code for Module prompt.noe

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  2  #                                                                             # 
  3  # Copyright (C) 2004-2011 Edward d'Auvergne                                   # 
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  5  # This file is part of the program relax.                                     # 
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 21  ############################################################################### 
 22   
 23  # Module docstring. 
 24  """Module containing the 'noe' user function class.""" 
 25  __docformat__ = 'plaintext' 
 26   
 27  # relax module imports. 
 28  from base_class import User_fn_class, _build_doc 
 29  import arg_check 
 30  from generic_fns import noesy 
 31  from specific_fns.setup import noe_obj 
 32   
 33   
 34 -class Noe(User_fn_class): 
 35      """Class for handling steady-state NOE and NOESY data.""" 
 36   
 37 -    def read_restraints(self, file=None, dir=None, proton1_col=None, proton2_col=None, lower_col=None, upper_col=None, sep=None): 
 38          # Function intro text. 
 39          if self._exec_info.intro: 
 40              text = self._exec_info.ps3 + "noe.read_restraints(" 
 41              text = text + "file=" + repr(file) 
 42              text = text + ", dir=" + repr(dir) 
 43              text = text + ", proton1_col=" + repr(proton1_col) 
 44              text = text + ", proton2_col=" + repr(proton2_col) 
 45              text = text + ", lower_col=" + repr(lower_col) 
 46              text = text + ", upper_col=" + repr(upper_col) 
 47              text = text + ", sep=" + repr(sep) + ")" 
 48              print(text) 
 49   
 50          # The argument checks. 
 51          arg_check.is_str(file, 'file name') 
 52          arg_check.is_str(dir, 'directory name', can_be_none=True) 
 53          arg_check.is_int(proton1_col, 'first proton column', can_be_none=True) 
 54          arg_check.is_int(proton2_col, 'second proton column', can_be_none=True) 
 55          arg_check.is_int(lower_col, 'lower bound column', can_be_none=True) 
 56          arg_check.is_int(upper_col, 'upper bound column', can_be_none=True) 
 57          arg_check.is_str(sep, 'column separator', can_be_none=True) 
 58   
 59          # Execute the functional code. 
 60          noesy.read_restraints(file=file, dir=dir, proton1_col=proton1_col, proton2_col=proton2_col, lower_col=lower_col, upper_col=upper_col, sep=sep) 
 61   
 62      # The function doc info. 
 63      read_restraints._doc_title = "Read NOESY or ROESY restraints from a file." 
 64      read_restraints._doc_title_short = "Restraint reading." 
 65      read_restraints._doc_args = [ 
 66          ["file", "The name of the file containing the restraint data."], 
 67          ["dir", "The directory where the file is located."], 
 68          ["proton1_col", "The column containing the first proton of the NOE or ROE cross peak."], 
 69          ["proton2_col", "The column containing the second proton of the NOE or ROE cross peak."], 
 70          ["lower_col", "The column containing the lower NOE bound."], 
 71          ["upper_col", "The column containing the upper NOE bound."], 
 72          ["sep", "The column separator (the default is white space)."] 
 73      ] 
 74      read_restraints._doc_desc = """ 
 75          The format of the file will be automatically determined, for example Xplor formatted restraint files.  A generically formatted file is also supported if it contains minimally four columns with the two proton names and the upper and lower bounds, as specified by the column numbers.  The proton names need to be in the spin ID string format. 
 76          """ 
 77      read_restraints._doc_examples = """ 
 78          To read the Xplor formatted restraint file 'NOE.xpl', type one of: 
 79   
 80          relax> noe.read_restraints('NOE.xpl') 
 81          relax> noe.read_restraints(file='NOE.xpl') 
 82   
 83   
 84          To read the generic formatted file 'noes', type one of: 
 85   
 86          relax> noe.read_restraints(file='NOE.xpl', proton1_col=0, proton2_col=1, lower_col=2, upper_col=3) 
 87          """ 
 88      _build_doc(read_restraints) 
 89   
 90   
 91 -    def spectrum_type(self, spectrum_type=None, spectrum_id=None): 
 92          # Function intro text. 
 93          if self._exec_info.intro: 
 94              text = self._exec_info.ps3 + "noe.spectrum_type(" 
 95              text = text + "spectrum_type=" + repr(spectrum_type) 
 96              text = text + ", spectrum_id=" + repr(spectrum_id) + ")" 
 97              print(text) 
 98   
 99          # The argument checks. 
100          arg_check.is_str(spectrum_type, 'spectrum type') 
101          arg_check.is_str(spectrum_id, 'spectrum ID string') 
102   
103          # Execute the functional code. 
104          noe_obj._spectrum_type(spectrum_type=spectrum_type, spectrum_id=spectrum_id) 
105   
106      # The function doc info. 
107      spectrum_type._doc_title = "Set the steady-state NOE spectrum type for pre-loaded peak intensities." 
108      spectrum_type._doc_title_short = "Steady-state NOE spectrum type." 
109      spectrum_type._doc_args = [ 
110          ["spectrum_type", "The type of steady-state NOE spectrum, one of 'ref' for the reference spectrum or 'sat' for the saturated spectrum."], 
111          ["spectrum_id", "The spectrum ID string."] 
112      ] 
113      spectrum_type._doc_desc = """ 
114          The spectrum type can be one of the following: 
115   
116              The steady-state NOE reference spectrum. 
117              The steady-state NOE spectrum with proton saturation turned on. 
118   
119          Peak intensities should be loaded before this user function via the spectrum.read_intensities user function.  The intensity values will then be associated with a spectrum ID string which can be used here. 
120          """ 
121      _build_doc(spectrum_type) 
122