Source Code for Module pipe_control.grace

  1  ############################################################################### 
  2  #                                                                             # 
  3  # Copyright (C) 2003-2015 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  """Module for interfacing with Grace (also known as Xmgrace, Xmgr, and ace).""" 
 24   
 25  # Python module imports. 
 26  from os import system 
 27   
 28  # relax module imports. 
 29  from lib.io import get_file_path, test_binary 
 30  from pipe_control.mol_res_spin import count_molecules, count_residues, count_spins 
 31  from specific_analyses.api import return_api 
 32  from status import Status; status = Status() 
 33   
 34   
 35 -def determine_seq_type(spin_id=None): 
 36      """Determine the spin sequence data type. 
 37   
 38      The purpose is to identify systems whereby only spins or only residues exist. 
 39   
 40      @keyword spin_id:   The spin identification string. 
 41      @type spin_id:      str 
 42      @return:            The spin sequence data type.  This can be one of 'spin', 'res,' or 'mixed'. 
 43      @rtype:             str 
 44      """ 
 45   
 46      # Count the molecules, residues, and spins. 
 47      num_mol = count_molecules(spin_id) 
 48      num_res = count_residues(spin_id) 
 49      num_spin = count_spins(spin_id) 
 50   
 51      # Only residues. 
 52      if num_mol == 1 and num_spin == 1: 
 53          return 'res' 
 54   
 55      # Only spins. 
 56      if num_mol == 1 and num_res == 1: 
 57          return 'spin' 
 58   
 59      # Mixed. 
 60      return 'mixed' 
 61   
 62   
 63 -def get_data_types(): 
 64      """Get all of the data types to plot for the current data pipe. 
 65   
 66      @return:    A list of lists of all the allowable data type descriptions and their values. 
 67      @rtype:     list of list of str 
 68      """ 
 69   
 70      # The specific analysis API object. 
 71      api = return_api() 
 72   
 73      # Return an empty list if the required functions are absent. 
 74      if not hasattr(api, 'data_names') or not hasattr(api, 'return_data_desc'): 
 75          return [] 
 76   
 77      # The data names, if they exist. 
 78      names = api.data_names(set='params') 
 79   
 80      # Initialise the list and then add the sequence data. 
 81      data = [] 
 82      data.append(["Spin sequence", 'spin']) 
 83   
 84      # Loop over the parameters. 
 85      for name in (api.data_names(set='params') + api.data_names(set='generic') + api.data_names(set='min')): 
 86          # Get the description. 
 87          try: 
 88              desc = api.return_data_desc(name) 
 89          except: 
 90              return [] 
 91   
 92          # No description. 
 93          if not desc: 
 94              text = name 
 95   
 96          # The text. 
 97          else: 
 98              text = "'%s':  %s" % (name, desc) 
 99   
100          # Append the description. 
101          data.append([text, name]) 
102   
103      # Return the data. 
104      return data 
105   
106   
107 -def view(file=None, dir=None, grace_exe='xmgrace'): 
108      """Execute Grace. 
109   
110      @keyword file:      The name of the file to open in Grace. 
111      @type file:         str 
112      @keyword dir:       The optional directory containing the file. 
113      @type dir:          str 
114      @keyword grace_exe: The name of the Grace executable file.  This should be located within the 
115                          system path. 
116      @type grace_exe:    str 
117      """ 
118   
119      # Test the binary file string corresponds to a valid executable. 
120      test_binary(grace_exe) 
121   
122      # File path. 
123      file_path = get_file_path(file, dir) 
124   
125      # Run Grace. 
126      system(grace_exe + " \"" + file_path + "\" &") 
127