Source Code for Module pipe_control.grace

  1  ############################################################################### 
  2  #                                                                             # 
  3  # Copyright (C) 2001-2005,2007-2010,2012-2014 Edward d'Auvergne               # 
  4  # Copyright (C) 2008 Sebastien Morin                                          # 
  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  """Module for interfacing with Grace (also known as Xmgrace, Xmgr, and ace).""" 
 25   
 26  # Python module imports. 
 27  from os import system 
 28   
 29  # relax module imports. 
 30  from lib.io import get_file_path, test_binary 
 31  from pipe_control.mol_res_spin import count_molecules, count_residues, count_spins 
 32  from specific_analyses.api import return_api 
 33  from status import Status; status = Status() 
 34   
 35   
 36 -def determine_seq_type(spin_id=None): 
 37      """Determine the spin sequence data type. 
 38   
 39      The purpose is to identify systems whereby only spins or only residues exist. 
 40   
 41      @keyword spin_id:   The spin identification string. 
 42      @type spin_id:      str 
 43      @return:            The spin sequence data type.  This can be one of 'spin', 'res,' or 'mixed'. 
 44      @rtype:             str 
 45      """ 
 46   
 47      # Count the molecules, residues, and spins. 
 48      num_mol = count_molecules(spin_id) 
 49      num_res = count_residues(spin_id) 
 50      num_spin = count_spins(spin_id) 
 51   
 52      # Only residues. 
 53      if num_mol == 1 and num_spin == 1: 
 54          return 'res' 
 55   
 56      # Only spins. 
 57      if num_mol == 1 and num_res == 1: 
 58          return 'spin' 
 59   
 60      # Mixed. 
 61      return 'mixed' 
 62   
 63   
 64 -def get_data_types(): 
 65      """Get all of the data types to plot for the current data pipe. 
 66   
 67      @return:    A list of lists of all the allowable data type descriptions and their values. 
 68      @rtype:     list of list of str 
 69      """ 
 70   
 71      # The specific analysis API object. 
 72      api = return_api() 
 73   
 74      # Return an empty list if the required functions are absent. 
 75      if not hasattr(api, 'data_names') or not hasattr(api, 'return_data_desc'): 
 76          return [] 
 77   
 78      # The data names, if they exist. 
 79      names = api.data_names(set='params') 
 80   
 81      # Initialise the list and then add the sequence data. 
 82      data = [] 
 83      data.append(["Spin sequence", 'spin']) 
 84   
 85      # Loop over the parameters. 
 86      for name in (api.data_names(set='params') + api.data_names(set='generic') + api.data_names(set='min')): 
 87          # Get the description. 
 88          try: 
 89              desc = api.return_data_desc(name) 
 90          except: 
 91              return [] 
 92   
 93          # No description. 
 94          if not desc: 
 95              text = name 
 96   
 97          # The text. 
 98          else: 
 99              text = "'%s':  %s" % (name, desc) 
100   
101          # Append the description. 
102          data.append([text, name]) 
103   
104      # Return the data. 
105      return data 
106   
107   
108 -def view(file=None, dir=None, grace_exe='xmgrace'): 
109      """Execute Grace. 
110   
111      @keyword file:      The name of the file to open in Grace. 
112      @type file:         str 
113      @keyword dir:       The optional directory containing the file. 
114      @type dir:          str 
115      @keyword grace_exe: The name of the Grace executable file.  This should be located within the 
116                          system path. 
117      @type grace_exe:    str 
118      """ 
119   
120      # Test the binary file string corresponds to a valid executable. 
121      test_binary(grace_exe) 
122   
123      # File path. 
124      file_path = get_file_path(file, dir) 
125   
126      # Run Grace. 
127      system(grace_exe + " \"" + file_path + "\" &") 
128