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.errors import RelaxError, RelaxNoSequenceError, RelaxNoSimError 
 30  from lib.io import get_file_path, open_write_file, test_binary 
 31  from pipe_control.mol_res_spin import count_molecules, count_residues, count_spins, exists_mol_res_spin_data 
 32  from pipe_control import pipes 
 33  from pipe_control.plotting import assemble_data 
 34  from specific_analyses.api import return_api 
 35  from status import Status; status = Status() 
 36   
 37   
 38 -def determine_seq_type(spin_id=None): 
 39      """Determine the spin sequence data type. 
 40   
 41      The purpose is to identify systems whereby only spins or only residues exist. 
 42   
 43      @keyword spin_id:   The spin identification string. 
 44      @type spin_id:      str 
 45      @return:            The spin sequence data type.  This can be one of 'spin', 'res,' or 'mixed'. 
 46      @rtype:             str 
 47      """ 
 48   
 49      # Count the molecules, residues, and spins. 
 50      num_mol = count_molecules(spin_id) 
 51      num_res = count_residues(spin_id) 
 52      num_spin = count_spins(spin_id) 
 53   
 54      # Only residues. 
 55      if num_mol == 1 and num_spin == 1: 
 56          return 'res' 
 57   
 58      # Only spins. 
 59      if num_mol == 1 and num_res == 1: 
 60          return 'spin' 
 61   
 62      # Mixed. 
 63      return 'mixed' 
 64   
 65   
 66 -def get_data_types(): 
 67      """Get all of the data types to plot for the current data pipe. 
 68   
 69      @return:    A list of lists of all the allowable data type descriptions and their values. 
 70      @rtype:     list of list of str 
 71      """ 
 72   
 73      # The specific analysis API object. 
 74      api = return_api() 
 75   
 76      # Return an empty list if the required functions are absent. 
 77      if not hasattr(api, 'data_names') or not hasattr(api, 'return_data_desc'): 
 78          return [] 
 79   
 80      # The data names, if they exist. 
 81      names = api.data_names(set='params') 
 82   
 83      # Initialise the list and then add the sequence data. 
 84      data = [] 
 85      data.append(["Spin sequence", 'spin']) 
 86   
 87      # Loop over the parameters. 
 88      for name in (api.data_names(set='params') + api.data_names(set='generic') + api.data_names(set='min')): 
 89          # Get the description. 
 90          try: 
 91              desc = api.return_data_desc(name) 
 92          except: 
 93              return [] 
 94   
 95          # No description. 
 96          if not desc: 
 97              text = name 
 98   
 99          # The text. 
100          else: 
101              text = "'%s':  %s" % (name, desc) 
102   
103          # Append the description. 
104          data.append([text, name]) 
105   
106      # Return the data. 
107      return data 
108   
109   
110 -def view(file=None, dir=None, grace_exe='xmgrace'): 
111      """Execute Grace. 
112   
113      @keyword file:      The name of the file to open in Grace. 
114      @type file:         str 
115      @keyword dir:       The optional directory containing the file. 
116      @type dir:          str 
117      @keyword grace_exe: The name of the Grace executable file.  This should be located within the 
118                          system path. 
119      @type grace_exe:    str 
120      """ 
121   
122      # Test the binary file string corresponds to a valid executable. 
123      test_binary(grace_exe) 
124   
125      # File path. 
126      file_path = get_file_path(file, dir) 
127   
128      # Run Grace. 
129      system(grace_exe + " \"" + file_path + "\" &") 
130