Source Code for Module specific_analyses.relax_disp.sherekhan

  1  ############################################################################### 
  2  #                                                                             # 
  3  # Copyright (C) 2013-2014 Edward d'Auvergne                                   # 
  4  #                                                                             # 
  5  # This file is part of the program relax (http://www.nmr-relax.com).          # 
  6  #                                                                             # 
  7  # This program 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 3 of the License, or           # 
 10  # (at your option) any later version.                                         # 
 11  #                                                                             # 
 12  # This program 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 this program.  If not, see <http://www.gnu.org/licenses/>.       # 
 19  #                                                                             # 
 20  ############################################################################### 
 21   
 22  # Module docstring. 
 23  """Functions for interfacing with Adam Mazur's ShereKhan program.""" 
 24   
 25  # Dependencies. 
 26  import dep_check 
 27   
 28  # Python module imports. 
 29  from os import sep 
 30  PIPE, Popen = None, None 
 31  if dep_check.subprocess_module: 
 32      from subprocess import PIPE, Popen 
 33   
 34  # relax module imports. 
 35  from lib.errors import RelaxError, RelaxNoSequenceError 
 36  from lib.io import mkdir_nofail, open_write_file 
 37  from lib.physical_constants import g1H, g15N 
 38  from pipe_control import pipes 
 39  from pipe_control.mol_res_spin import exists_mol_res_spin_data, return_residue 
 40  from specific_analyses.relax_disp.data import loop_cluster, loop_exp_frq, loop_offset_point, loop_time, return_param_key_from_data, spin_ids_to_containers 
 41   
 42   
 43 -def sherekhan_input(spin_id=None, force=False, dir='ShereKhan'): 
 44      """Create the ShereKhan input files. 
 45   
 46      @keyword spin_id:           The spin ID string to restrict the file creation to. 
 47      @type spin_id:              str 
 48      @keyword force:             A flag which if True will cause all pre-existing files to be overwritten. 
 49      @type force:                bool 
 50      @keyword dir:               The optional directory to place the files into.  If None, then the files will be placed into the current directory. 
 51      @type dir:                  str or None 
 52      """ 
 53   
 54      # Test if the current pipe exists. 
 55      pipes.test() 
 56   
 57      # Test if sequence data is loaded. 
 58      if not exists_mol_res_spin_data(): 
 59          raise RelaxNoSequenceError 
 60   
 61      # Test if the experiment type has been set. 
 62      if not hasattr(cdp, 'exp_type'): 
 63          raise RelaxError("The relaxation dispersion experiment type has not been specified.") 
 64   
 65      # Test if the model has been set. 
 66      if not hasattr(cdp, 'model_type'): 
 67          raise RelaxError("The relaxation dispersion model has not been specified.") 
 68   
 69      # Directory creation. 
 70      if dir != None: 
 71          mkdir_nofail(dir, verbosity=0) 
 72   
 73      # Loop over the spin blocks. 
 74      cluster_index = 0 
 75      for spin_ids in loop_cluster(): 
 76          # The spin containers. 
 77          spins = spin_ids_to_containers(spin_ids) 
 78   
 79          # Loop over the magnetic fields. 
 80          for exp_type, frq, ei, mi in loop_exp_frq(return_indices=True): 
 81              # Loop over the time, and count it. 
 82              time_i = 0 
 83              for time, ti in loop_time(exp_type=exp_type, frq=frq, return_indices=True): 
 84                  time_i += 1 
 85   
 86              # Check that not more than one time point is returned. 
 87              if time_i > 1: 
 88                  raise RelaxError("Number of returned time poins is %i. Only 1 time point is expected."%time_i) 
 89   
 90              # The ShereKhan input file for the spin cluster. 
 91              file_name = 'sherekhan_frq%s.in' % (mi+1) 
 92              if dir != None: 
 93                  dir_name = dir + sep + 'cluster%s' % (cluster_index+1) 
 94              else: 
 95                  dir_name = 'cluster%s' % (cluster_index+1) 
 96              file = open_write_file(file_name=file_name, dir=dir_name, force=force) 
 97   
 98              # The B0 field for the nuclei of interest in MHz (must be positive to be accepted by the server). 
 99              file.write("%.10f\n" % abs(frq / g1H * g15N / 1e6)) 
100   
101              # The constant relaxation time for the CPMG experiment in seconds. 
102              file.write("%s\n" % (time)) 
103   
104              # The comment line. 
105              file.write("# %-18s %-20s %-20s\n" % ("nu_cpmg (Hz)", "R2eff (rad/s)", "Error")) 
106   
107              # Loop over the spins of the cluster. 
108              for i in range(len(spins)): 
109                  # Get the residue container. 
110                  res = return_residue(spin_ids[i]) 
111   
112                  # Name the residue if needed. 
113                  res_name = res.name 
114                  if res_name == None: 
115                      res_name = 'X' 
116   
117                  # Initialise the lines to output (to be able to catch missing data). 
118                  lines = [] 
119   
120                  # The residue ID line. 
121                  lines.append("# %s%s\n" % (res_name, res.num)) 
122   
123                  # Loop over the dispersion points. 
124                  for offset, point in loop_offset_point(exp_type=exp_type, frq=frq, skip_ref=True): 
125                      # The parameter key. 
126                      param_key = return_param_key_from_data(exp_type=exp_type, frq=frq, offset=offset, point=point) 
127   
128                      # No data. 
129                      if param_key not in spins[i].r2eff: 
130                          continue 
131   
132                      # Store the data. 
133                      lines.append("%20.15g %20.13g %20.13g\n" % (point, spins[i].r2eff[param_key], spins[i].r2eff_err[param_key])) 
134   
135                  # No data. 
136                  if len(lines) == 1: 
137                      continue 
138   
139                  # Write out the data. 
140                  for line in lines: 
141                      file.write(line) 
142   
143              # Close the file. 
144              file.close() 
145   
146          # Increment the cluster index. 
147          cluster_index += 1 
148