Source Code for Module generic_fns.noesy

  1  ############################################################################### 
  2  #                                                                             # 
  3  # Copyright (C) 2008-2009 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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 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  #                                                                             # 
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 19  # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA   # 
 20  #                                                                             # 
 21  ############################################################################### 
 22   
 23  # Module docstring. 
 24  """Module for NOESY related operations.""" 
 25   
 26  # Python module imports. 
 27  from re import search 
 28  from string import split 
 29  from warnings import warn 
 30   
 31  # relax module imports. 
 32  from generic_fns import pipes 
 33  from generic_fns.mol_res_spin import exists_mol_res_spin_data, return_spin, tokenise 
 34  from generic_fns import xplor 
 35  from relax_errors import RelaxError, RelaxNoSequenceError 
 36  from relax_io import open_read_file 
 37  from relax_warnings import RelaxWarning 
 38   
 39   
 40 -def __file_format(lines): 
 41      """Determine the format of the NOE restraints data. 
 42   
 43      @param lines:   The file data converted to a list of file lines. 
 44      @type lines:    list of str 
 45      @return:        The format of the file. 
 46      @rtype:         str 
 47      """ 
 48   
 49      # Loop over the lines. 
 50      for line in lines: 
 51          # Xplor format. 
 52          if search('^assign ', line): 
 53              print("Xplor formatted file.") 
 54              return 'xplor' 
 55   
 56      # Print out. 
 57      print("Generic formatted file.") 
 58      return 'generic' 
 59   
 60   
 61 -def parse_noe_restraints(lines, proton1_col=None, proton2_col=None, lower_col=None, upper_col=None, sep=None): 
 62      """Parse and return the NOE restraints from the generic formatted file. 
 63   
 64      @param lines:           The file, or file fragment, split into lines. 
 65      @type lines:            list of str 
 66      @keyword proton1_col:   The column containing the first proton of the NOE or ROE cross peak. 
 67      @type proton1_col:      None or int 
 68      @keyword proton2_col:   The column containing the second proton of the NOE or ROE cross peak. 
 69      @type proton2_col:      None or int 
 70      @keyword lower_col:     The column containing the lower NOE bound. 
 71      @type lower_col:        None or int 
 72      @keyword upper_col:     The column containing the upper NOE bound. 
 73      @type upper_col:        None or int 
 74      @keyword sep:           The column separator (the default is white space). 
 75      @type sep:              None or str 
 76      @return:                The NOE restraint list in the format of two atom identification strings 
 77                              and the lower and upper restraints. 
 78      @rtype:                 list of lists of [str, str, float, float] 
 79      """ 
 80   
 81      # Default column numbers. 
 82      if proton1_col == None: 
 83          warn(RelaxWarning("The proton1_col argument has not been supplied, defaulting to column 1.")) 
 84          proton1_col = 1 
 85      if proton2_col == None: 
 86          warn(RelaxWarning("The proton2_col argument has not been supplied, defaulting to column 2.")) 
 87          proton2_col = 2 
 88      if lower_col == None: 
 89          warn(RelaxWarning("The lower_col argument has not been supplied, defaulting to column 3.")) 
 90          lower_col = 3 
 91      if upper_col == None: 
 92          warn(RelaxWarning("The upper_col argument has not been supplied, defaulting to column 4.")) 
 93          upper_col = 4 
 94   
 95      # Loop over the lines. 
 96      data = [] 
 97      for line in lines: 
 98          # Split the line. 
 99          row = split(line, sep) 
100   
101          # Header lines: 
102          if len(row) < 4: 
103              continue 
104          try: 
105              tokenise(row[proton1_col-1]) 
106          except RelaxError: 
107              continue 
108   
109          # Pack the data. 
110          data.append([row[proton1_col-1], row[proton2_col-1], float(row[lower_col-1]), float(row[upper_col-1])]) 
111   
112      # Return the data. 
113      return data 
114   
115   
116 -def read_restraints(file=None, dir=None, proton1_col=None, proton2_col=None, lower_col=None, upper_col=None, sep=None): 
117      """Load NOESY or ROESY constraint information from file. 
118   
119      If the input file is a pre-formatted Xplor file, the column number and separator arguments will 
120      be ignored. 
121   
122   
123      @keyword file:          The name of the file containing the relaxation data. 
124      @type file:             str 
125      @keyword dir:           The directory where the file is located. 
126      @type dir:              None or str 
127      @keyword proton1_col:   The column containing the first proton of the NOE or ROE cross peak. 
128      @type proton1_col:      None or int 
129      @keyword proton2_col:   The column containing the second proton of the NOE or ROE cross peak. 
130      @type proton2_col:      None or int 
131      @keyword lower_col:     The column containing the lower NOE bound. 
132      @type lower_col:        None or int 
133      @keyword upper_col:     The column containing the upper NOE bound. 
134      @type upper_col:        None or int 
135      @keyword sep:           The column separator (the default is white space). 
136      @type sep:              None or str 
137      """ 
138   
139      # Test if the current data pipe exists. 
140      pipes.test() 
141   
142      # Test if sequence data is loaded. 
143      if not exists_mol_res_spin_data(): 
144          raise RelaxNoSequenceError 
145   
146      # Open the file. 
147      file = open_read_file(file_name=file, dir=dir) 
148      lines = file.readlines() 
149      file.close() 
150   
151      # Determine the file type. 
152      format = __file_format(lines) 
153   
154      # Parse and extract the NOE restraints. 
155      if format == 'xplor': 
156          noe_restraints = xplor.parse_noe_restraints(lines) 
157      elif format == 'generic': 
158          noe_restraints = parse_noe_restraints(lines, proton1_col=proton1_col, proton2_col=proton2_col, lower_col=lower_col, upper_col=upper_col, sep=sep) 
159   
160      # Pseudoatom conversion. 
161      for i in range(len(noe_restraints)): 
162          # Loop over atom IDs. 
163          for j in range(2): 
164              # Skip normal atoms. 
165              if isinstance(noe_restraints[i][j], str): 
166                  continue 
167   
168              # Loop over the pseudoatoms. 
169              pseudo_name = None 
170              for k in range(len(noe_restraints[i][j])): 
171                  # Get the spin. 
172                  spin = return_spin(noe_restraints[i][j][k]) 
173   
174                  # Check the pseudoatom consistency. 
175                  if pseudo_name and pseudo_name != spin.pseudo_name: 
176                      raise RelaxError("The pseudoatom names '%s' and '%s' do not match." % (pseudo_name, spin.pseudo_name)) 
177   
178                  # Set the name. 
179                  pseudo_name = spin.pseudo_name 
180   
181              # No pseudoatom. 
182              if not pseudo_name: 
183                  raise RelaxError("Cannot find the pseudoatom corresponding to the atoms in %s." % noe_restraints[i][j]) 
184   
185              # Otherwise, place the pseudoatom name into the NOE restraint list. 
186              noe_restraints[i][j] = pseudo_name 
187   
188      # Place the restraints into the current data pipe. 
189      cdp.noe_restraints = noe_restraints 
190   
191      # Check for the presence of the spin containers corresponding to the atom ids. 
192      for restraint in cdp.noe_restraints: 
193          if not return_spin(restraint[0]): 
194              raise RelaxError("The spin container corresponding to '%s' cannot be found." % restraint[0]) 
195          if not return_spin(restraint[1]): 
196              raise RelaxError("The spin container corresponding to '%s' cannot be found." % restraint[1]) 
197