Source Code for Module specific_fns.noe.main

  1  ############################################################################### 
  2  #                                                                             # 
  3  # Copyright (C) 2004-2012 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  # Python module imports. 
 24  from math import sqrt 
 25  from re import match 
 26  from warnings import warn 
 27   
 28  # relax module imports. 
 29  from generic_fns import pipes 
 30  from generic_fns.mol_res_spin import exists_mol_res_spin_data, spin_loop 
 31  from relax_errors import RelaxArgNotInListError, RelaxError, RelaxNoSequenceError 
 32  from relax_warnings import RelaxDeselectWarning 
 33  from specific_fns.api_common import API_common 
 34  from user_functions.data import Uf_tables; uf_tables = Uf_tables() 
 35  from user_functions.objects import Desc_container 
 36   
 37   
 38 -class Noe_main: 
 39      """Class containing functions for relaxation data.""" 
 40   
 41 -    def _assign_function(self, spin=None, intensity=None, spectrum_type=None): 
 42          """Place the peak intensity data into the spin container. 
 43   
 44          The intensity data can be either that of the reference or saturated spectrum. 
 45   
 46          @keyword spin:          The spin container. 
 47          @type spin:             SpinContainer instance 
 48          @keyword intensity:     The intensity value. 
 49          @type intensity:        float 
 50          @keyword spectrum_type: The type of spectrum, one of 'ref' or 'sat'. 
 51          @type spectrum_type:    str 
 52          """ 
 53   
 54          # Add the data. 
 55          if spectrum_type == 'ref': 
 56              spin.ref = intensity 
 57          elif spectrum_type == 'sat': 
 58              spin.sat = intensity 
 59          else: 
 60              raise RelaxError("The spectrum type '%s' is unknown." % spectrum_type) 
 61   
 62   
 63 -    def _spectrum_type(self, spectrum_type=None, spectrum_id=None): 
 64          """Set the spectrum type corresponding to the spectrum_id. 
 65   
 66          @keyword spectrum_type: The type of NOE spectrum, one of 'ref' or 'sat'. 
 67          @type spectrum_type:    str 
 68          @keyword spectrum_id:   The spectrum id string. 
 69          @type spectrum_id:      str 
 70          """ 
 71   
 72          # Test if the current pipe exists 
 73          pipes.test() 
 74   
 75          # Test the spectrum id string. 
 76          if spectrum_id not in cdp.spectrum_ids: 
 77              raise RelaxError("The peak intensities corresponding to the spectrum id '%s' does not exist." % spectrum_id) 
 78   
 79          # Initialise or update the spectrum_type data structure as necessary. 
 80          if not hasattr(cdp, 'spectrum_type'): 
 81              cdp.spectrum_type = {} 
 82   
 83          # Set the error. 
 84          cdp.spectrum_type[spectrum_id] = spectrum_type 
 85   
 86   
 87 -    def calculate(self, spin_id=None, verbosity=1, sim_index=None): 
 88          """Calculate the NOE and its error. 
 89   
 90          The error for each peak is calculated using the formula:: 
 91                            ___________________________________________ 
 92                         \/ {sd(sat)*I(unsat)}^2 + {sd(unsat)*I(sat)}^2 
 93              sd(NOE) = ----------------------------------------------- 
 94                                            I(unsat)^2 
 95   
 96          @keyword spin_id:   The spin identification string. 
 97          @type spin_id:      None or str 
 98          @keyword verbosity: The amount of information to print.  The higher the value, the greater the verbosity. 
 99          @type verbosity:    int 
100          @keyword sim_index: The MC simulation index (unused). 
101          @type sim_index:    None 
102          """ 
103   
104          # Test if the current pipe exists. 
105          pipes.test() 
106   
107          # The spectrum types have not been set. 
108          if not hasattr(cdp, 'spectrum_type'): 
109              raise RelaxError("The spectrum types have not been set.") 
110   
111          # Test if the 2 spectra types 'ref' and 'sat' exist. 
112          if not 'ref' in cdp.spectrum_type.values() or not 'sat' in cdp.spectrum_type.values(): 
113              raise RelaxError("The reference and saturated NOE spectra have not been loaded.") 
114   
115          # Loop over the spins. 
116          for spin in spin_loop(): 
117              # Skip deselected spins. 
118              if not spin.select: 
119                  continue 
120   
121              # Average intensities (if required). 
122              sat = 0.0 
123              sat_err = 0.0 
124              ref = 0.0 
125              ref_err = 0.0 
126              for id in cdp.spectrum_ids: 
127                  # Sat spectra. 
128                  if cdp.spectrum_type[id] == 'sat': 
129                      sat = sat + spin.intensities[id] 
130                      sat_err = sat_err + spin.intensity_err[id] 
131   
132                  # Ref spectra. 
133                  if cdp.spectrum_type[id] == 'ref': 
134                      ref = ref + spin.intensities[id] 
135                      ref_err = ref_err + spin.intensity_err[id] 
136   
137              # Calculate the NOE. 
138              spin.noe = sat / ref 
139   
140              # Calculate the error. 
141              spin.noe_err = sqrt((sat_err * ref)**2 + (ref_err * sat)**2) / ref**2 
142   
143   
144 -    def overfit_deselect(self): 
145          """Deselect spins which have insufficient data to support calculation.""" 
146   
147          # Print out. 
148          print("\n\nOver-fit spin deselection.\n") 
149   
150          # Test the sequence data exists. 
151          if not exists_mol_res_spin_data(): 
152              raise RelaxNoSequenceError 
153   
154          # Loop over spin data. 
155          for spin, spin_id in spin_loop(return_id=True): 
156              # Skip deselected spins. 
157              if not spin.select: 
158                  continue 
159   
160              # Check for sufficient data. 
161              if not hasattr(spin, 'intensities') or not len(spin.intensities) == 2: 
162                  warn(RelaxDeselectWarning(spin_id, 'insufficient data')) 
163                  spin.select = False 
164   
165              # Check for sufficient errors. 
166              elif not hasattr(spin, 'intensity_err') or not len(spin.intensity_err) == 2: 
167                  warn(RelaxDeselectWarning(spin_id, 'missing errors')) 
168                  spin.select = False 
169   
170   
171      return_data_name_doc = Desc_container("NOE calculation data type string matching patterns") 
172      _table = uf_tables.add_table(label="table: NOE data type patterns", caption="NOE data type string matching patterns.") 
173      _table.add_headings(["Data type", "Object name"]) 
174      _table.add_row(["Reference intensity", "'ref'"]) 
175      _table.add_row(["Saturated intensity", "'sat'"]) 
176      _table.add_row(["NOE", "'noe'"]) 
177      return_data_name_doc.add_table(_table.label) 
178   
179   
180 -    def return_units(self, param): 
181          """Dummy function which returns None as the stats have no units. 
182   
183          @param param:   The name of the parameter to return the units string for. 
184          @type param:    str 
185          @return:        Nothing. 
186          @rtype:         None 
187          """ 
188   
189          return None 
190