Source Code for Module specific_analyses.relax_disp.sherekhan

  1  ############################################################################### 
  2  #                                                                             # 
  3  # Copyright (C) 2013-2014 Edward d'Auvergne                                   # 
  4  # Copyright (C) 2014 Troels E. Linnet                                         # 
  5  #                                                                             # 
  6  # This file is part of the program relax (http://www.nmr-relax.com).          # 
  7  #                                                                             # 
  8  # This program is free software: you can redistribute it and/or modify        # 
  9  # it under the terms of the GNU General Public License as published by        # 
 10  # the Free Software Foundation, either version 3 of the License, or           # 
 11  # (at your option) any later version.                                         # 
 12  #                                                                             # 
 13  # This program is distributed in the hope that it will be useful,             # 
 14  # but WITHOUT ANY WARRANTY; without even the implied warranty of              # 
 15  # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the               # 
 16  # GNU General Public License for more details.                                # 
 17  #                                                                             # 
 18  # You should have received a copy of the GNU General Public License           # 
 19  # along with this program.  If not, see <http://www.gnu.org/licenses/>.       # 
 20  #                                                                             # 
 21  ############################################################################### 
 22   
 23  # Module docstring. 
 24  """Functions for interfacing with Adam Mazur's ShereKhan program.""" 
 25   
 26  # Dependencies. 
 27  import dep_check 
 28   
 29  # Python module imports. 
 30  from os import sep 
 31  PIPE, Popen = None, None 
 32  if dep_check.subprocess_module: 
 33      from subprocess import PIPE, Popen 
 34   
 35  # relax module imports. 
 36  from lib.errors import RelaxError, RelaxNoSequenceError 
 37  from lib.io import mkdir_nofail, open_write_file 
 38  from lib.periodic_table import periodic_table 
 39  from pipe_control.mol_res_spin import exists_mol_res_spin_data, return_residue 
 40  from pipe_control.pipes import check_pipe 
 41  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 
 42   
 43   
 44 -def sherekhan_input(spin_id=None, force=False, dir='ShereKhan'): 
 45      """Create the ShereKhan input files. 
 46   
 47      @keyword spin_id:           The spin ID string to restrict the file creation to. 
 48      @type spin_id:              str 
 49      @keyword force:             A flag which if True will cause all pre-existing files to be overwritten. 
 50      @type force:                bool 
 51      @keyword dir:               The optional directory to place the files into.  If None, then the files will be placed into the current directory. 
 52      @type dir:                  str or None 
 53      """ 
 54   
 55      # Test if the current pipe exists. 
 56      check_pipe() 
 57   
 58      # Test if sequence data is loaded. 
 59      if not exists_mol_res_spin_data(): 
 60          raise RelaxNoSequenceError 
 61   
 62      # Test if the experiment type has been set. 
 63      if not hasattr(cdp, 'exp_type'): 
 64          raise RelaxError("The relaxation dispersion experiment type has not been specified.") 
 65   
 66      # Test if the model has been set. 
 67      if not hasattr(cdp, 'model_type'): 
 68          raise RelaxError("The relaxation dispersion model has not been specified.") 
 69   
 70      # Directory creation. 
 71      if dir != None: 
 72          mkdir_nofail(dir, verbosity=0) 
 73   
 74      # Loop over the spin blocks. 
 75      cluster_index = 0 
 76      for spin_ids in loop_cluster(): 
 77          # The spin containers. 
 78          spins = spin_ids_to_containers(spin_ids) 
 79   
 80          # Loop over the magnetic fields. 
 81          for exp_type, frq, ei, mi in loop_exp_frq(return_indices=True): 
 82              # Loop over the time, and count it. 
 83              time_i = 0 
 84              for time, ti in loop_time(exp_type=exp_type, frq=frq, return_indices=True): 
 85                  time_i += 1 
 86   
 87              # Check that not more than one time point is returned. 
 88              if time_i > 1: 
 89                  raise RelaxError("Number of returned time poins is %i. Only 1 time point is expected."%time_i) 
 90   
 91              # The ShereKhan input file for the spin cluster. 
 92              file_name = 'sherekhan_frq%s.in' % (mi+1) 
 93              if dir != None: 
 94                  dir_name = dir + sep + 'cluster%s' % (cluster_index+1) 
 95              else: 
 96                  dir_name = 'cluster%s' % (cluster_index+1) 
 97              file = open_write_file(file_name=file_name, dir=dir_name, force=force) 
 98   
 99              # The B0 field for the nuclei of interest in MHz (must be positive to be accepted by the server). 
100              file.write("%.10f\n" % abs(frq / periodic_table.gyromagnetic_ratio('1H') * periodic_table.gyromagnetic_ratio('15N') / 1e6)) 
101   
102              # The constant relaxation time for the CPMG experiment in seconds. 
103              file.write("%s\n" % (time)) 
104   
105              # The comment line. 
106              file.write("# %-18s %-20s %-20s\n" % ("nu_cpmg (Hz)", "R2eff (rad/s)", "Error")) 
107   
108              # Loop over the spins of the cluster. 
109              for i in range(len(spins)): 
110                  # Get the residue container. 
111                  res = return_residue(spin_ids[i]) 
112   
113                  # Name the residue if needed. 
114                  res_name = res.name 
115                  if res_name == None: 
116                      res_name = 'X' 
117   
118                  # Initialise the lines to output (to be able to catch missing data). 
119                  lines = [] 
120   
121                  # The residue ID line. 
122                  lines.append("# %s%s\n" % (res_name, res.num)) 
123   
124                  # Loop over the dispersion points. 
125                  for offset, point in loop_offset_point(exp_type=exp_type, frq=frq, skip_ref=True): 
126                      # The parameter key. 
127                      param_key = return_param_key_from_data(exp_type=exp_type, frq=frq, offset=offset, point=point) 
128   
129                      # No data. 
130                      if param_key not in spins[i].r2eff: 
131                          continue 
132   
133                      # Store the data. 
134                      lines.append("%20.15g %20.13g %20.13g\n" % (point, spins[i].r2eff[param_key], spins[i].r2eff_err[param_key])) 
135   
136                  # No data. 
137                  if len(lines) == 1: 
138                      continue 
139   
140                  # Write out the data. 
141                  for line in lines: 
142                      file.write(line) 
143   
144              # Close the file. 
145              file.close() 
146   
147          # Increment the cluster index. 
148          cluster_index += 1 
149