Source Code for Module user_functions.dasha

  1  ############################################################################### 
  2  #                                                                             # 
  3  # Copyright (C) 2003-2006,2009,2012-2013 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  """The dasha user function definitions for controlling the Dasha model-free software.""" 
 25   
 26  # relax module imports. 
 27  from pipe_control import dasha 
 28  from user_functions.data import Uf_info; uf_info = Uf_info() 
 29  from user_functions.objects import Desc_container 
 30   
 31   
 32  # The user function class. 
 33  uf_class = uf_info.add_class('dasha') 
 34  uf_class.title = "Class for interfacing with the program Dasha." 
 35  uf_class.menu_text = "&dasha" 
 36   
 37   
 38  # The dasha.create user function. 
 39  uf = uf_info.add_uf('dasha.create') 
 40  uf.title = "Create the Dasha script." 
 41  uf.title_short = "Script creation." 
 42  uf.add_keyarg( 
 43      name = "algor", 
 44      default = "LM", 
 45      basic_types = ["str"], 
 46      desc_short = "optimisation algorithm", 
 47      desc = "The minimisation algorithm.", 
 48      wiz_element_type = "combo", 
 49      wiz_combo_choices = ["Levenberg-Marquardt", "Newton-Raphson"], 
 50      wiz_combo_data = ["LM", "NR"], 
 51      wiz_read_only = True 
 52  ) 
 53  uf.add_keyarg( 
 54      name = "dir", 
 55      arg_type = "dir sel", 
 56      desc_short = "directory name", 
 57      desc = "The directory to place the files.", 
 58      can_be_none = True 
 59  ) 
 60  uf.add_keyarg( 
 61      name = "force", 
 62      default = False, 
 63      basic_types = ["bool"], 
 64      desc_short = "force flag", 
 65      desc = "A flag which if set to True will cause the results file to be overwritten if it already exists." 
 66  ) 
 67  # Description. 
 68  uf.desc.append(Desc_container()) 
 69  uf.desc[-1].add_paragraph("The script file created is called 'dir/dasha_script'.") 
 70  # Optimisation algorithms. 
 71  uf.desc.append(Desc_container("Optimisation algorithms")) 
 72  uf.desc[-1].add_paragraph("The two minimisation algorithms within Dasha are accessible through the algorithm which can be set to:") 
 73  uf.desc[-1].add_item_list_element("'LM'", "The Levenberg-Marquardt algorithm,") 
 74  uf.desc[-1].add_item_list_element("'NR'", "Newton-Raphson algorithm.") 
 75  uf.desc[-1].add_paragraph("For Levenberg-Marquardt minimisation, the function 'lmin' will be called, while for Newton-Raphson, the function 'min' will be executed.") 
 76  uf.backend = dasha.create 
 77  uf.menu_text = "&create" 
 78  uf.gui_icon = "oxygen.actions.list-add-relax-blue" 
 79  uf.wizard_height_desc = 400 
 80  uf.wizard_size = (800, 700) 
 81  uf.wizard_apply_button = False 
 82   
 83   
 84  # The dasha.execute user function. 
 85  uf = uf_info.add_uf('dasha.execute') 
 86  uf.title = "Perform a model-free optimisation using Dasha." 
 87  uf.title_short = "Dasha execution." 
 88  uf.add_keyarg( 
 89      name = "dir", 
 90      arg_type = "dir sel", 
 91      desc_short = "directory name", 
 92      desc = "The directory to place the files.", 
 93      can_be_none = True 
 94  ) 
 95  uf.add_keyarg( 
 96      name = "force", 
 97      default = False, 
 98      basic_types = ["bool"], 
 99      desc_short = "force flag", 
100      desc = "A flag which if set to True will cause the results file to be overwritten if it already exists." 
101  ) 
102  uf.add_keyarg( 
103      name = "binary", 
104      default = "dasha", 
105      arg_type = "file sel read", 
106      desc_short = "Dasha executable file", 
107      desc = "The name of the executable Dasha program file.", 
108      wiz_filesel_preview = False 
109  ) 
110  # Description. 
111  uf.desc.append(Desc_container()) 
112  uf.desc[-1].add_paragraph("Dasha will be executed as") 
113  uf.desc[-1].add_prompt("$ dasha < dasha_script | tee dasha_results") 
114  uf.desc[-1].add_paragraph("If you would like to use a different Dasha executable file, change the binary name to the appropriate file name.  If the file is not located within the environment's path, include the full path in front of the binary file name.") 
115  uf.backend = dasha.execute 
116  uf.gui_icon = "oxygen.categories.applications-education" 
117  uf.menu_text = "&execute" 
118  uf.wizard_size = (700, 500) 
119  uf.wizard_apply_button = False 
120   
121   
122  # The dasha.extract user function. 
123  uf = uf_info.add_uf('dasha.extract') 
124  uf.title = "Extract data from the Dasha results file." 
125  uf.title_short = "Dasha data extraction." 
126  uf.add_keyarg( 
127      name = "dir", 
128      arg_type = "dir sel", 
129      desc_short = "directory name", 
130      desc = "The directory where the file 'dasha_results' is found.", 
131      can_be_none = True 
132  ) 
133  # Description. 
134  uf.desc.append(Desc_container()) 
135  uf.desc[-1].add_paragraph("The model-free results will be extracted from the Dasha results file 'dasha_results' located in the given directory.") 
136  uf.backend = dasha.extract 
137  uf.menu_text = "ex&tract" 
138  uf.gui_icon = "oxygen.actions.archive-extract" 
139  uf.wizard_apply_button = False 
140