Source Code for Package user_functions

  1  ############################################################################### 
  2  #                                                                             # 
  3  # Copyright (C) 2012-2014 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  # Package docstring. 
 23  """Package containing all of the user function details. 
 24   
 25  This package contains all information and details about user functions, from documentation to icons to be used in the GUI.  This package contains a special data structure which will be used by the different UIs to automatically generate their interfaces to the user functions. 
 26  """ 
 27   
 28  # The __all__ package list (main modules). 
 29  __all__ = [ 
 30      'data', 
 31      'objects' 
 32  ] 
 33   
 34  # The __all__ package list (user function modules). 
 35  __all__ += [ 
 36      'align_tensor', 
 37      'angles', 
 38      'bmrb', 
 39      'bruker', 
 40      'chemical_shift', 
 41      'consistency_tests', 
 42      'dasha', 
 43      'deselect', 
 44      'diffusion_tensor', 
 45      'domain', 
 46      'dx', 
 47      'eliminate', 
 48      'error_analysis', 
 49      'fix', 
 50      'frame_order', 
 51      'grace', 
 52      'interatom', 
 53      'j_coupling', 
 54      'jw_mapping', 
 55      'minimisation', 
 56      'model_free', 
 57      'model_selection', 
 58      'molecule', 
 59      'molmol', 
 60      'monte_carlo', 
 61      'n_state_model', 
 62      'noe', 
 63      'palmer', 
 64      'paramag', 
 65      'pcs', 
 66      'pipe', 
 67      'pymol_control', 
 68      'rdc', 
 69      'relax_data', 
 70      'relax_disp', 
 71      'relax_fit', 
 72      'residue', 
 73      'reset', 
 74      'results', 
 75      'script', 
 76      'select', 
 77      'sequence', 
 78      'spectrometer', 
 79      'spectrum', 
 80      'spin', 
 81      'state', 
 82      'statistics', 
 83      'structure', 
 84      'sys_info', 
 85      'wildcards', 
 86      'value', 
 87      'vmd' 
 88  ] 
 89   
 90   
 91 -def initialise(): 
 92      """Initialise all of the user function definitions by importing then validating them.""" 
 93   
 94      # Import all the modules to set up the data. 
 95      import user_functions.align_tensor 
 96      import user_functions.angles 
 97      import user_functions.bmrb 
 98      import user_functions.bruker 
 99      import user_functions.chemical_shift 
100      import user_functions.consistency_tests 
101      import user_functions.dasha 
102      import user_functions.deselect 
103      import user_functions.diffusion_tensor 
104      import user_functions.domain 
105      import user_functions.dx 
106      import user_functions.eliminate 
107      import user_functions.error_analysis 
108      import user_functions.fix 
109      import user_functions.frame_order 
110      import user_functions.grace 
111      import user_functions.interatom 
112      import user_functions.j_coupling 
113      import user_functions.jw_mapping 
114      import user_functions.minimisation 
115      import user_functions.model_free 
116      import user_functions.model_selection 
117      import user_functions.molecule 
118      import user_functions.molmol 
119      import user_functions.monte_carlo 
120      import user_functions.n_state_model 
121      import user_functions.noe 
122      import user_functions.palmer 
123      import user_functions.paramag 
124      import user_functions.pcs 
125      import user_functions.pipe 
126      import user_functions.pymol_control 
127      import user_functions.rdc 
128      import user_functions.relax_data 
129      import user_functions.relax_disp 
130      import user_functions.relax_fit 
131      import user_functions.residue 
132      import user_functions.reset 
133      import user_functions.results 
134      import user_functions.script 
135      import user_functions.select 
136      import user_functions.sequence 
137      import user_functions.spectrometer 
138      import user_functions.spectrum 
139      import user_functions.spin 
140      import user_functions.state 
141      import user_functions.statistics 
142      import user_functions.structure 
143      import user_functions.sys_info 
144      import user_functions.value 
145      import user_functions.vmd 
146   
147      # Import the data structure. 
148      from user_functions.data import Uf_info; uf_info = Uf_info() 
149   
150      # Check the validity of the data. 
151      uf_info.validate() 
152   
153   
154  # A table of user function renamings - for script compatibility. 
155  uf_translation_table = { 
156      'calc': 'minimise.calculate', 
157      'dipole_pair.define': 'interatom.define', 
158      'dipole_pair.read_dist': 'interatom.read_dist', 
159      'dipole_pair.set_dist': 'interatom.set_dist', 
160      'dipole_pair.unit_vectors': 'interatom.unit_vectors', 
161      'exp_info.software_select': 'bmrb.software_select', 
162      'frq.set': 'spectrometer.frequency', 
163      'grid_search': 'minimise.grid_search', 
164      'interatomic.copy': 'interatom.copy', 
165      'interatomic.create': 'interatom.define', 
166      'minimise': 'minimise.execute', 
167      'molmol.macro_exec': 'molmol.macro_run', 
168      'molmol.write': 'molmol.macro_write', 
169      'n_state_model.set_domain': 'align_tensor.set_domain', 
170      'n_state_model.set_type': 'align_tensor.reduction', 
171      'noe.error': 'spectrum.error_analysis', 
172      'noe.read': 'spectrum.read_intensities', 
173      'pcs.centre': 'paramag_centre', 
174      'pdc.read': 'bruker.read', 
175      'pipe.list': 'pipe.display', 
176      'pymol.cmd': 'pymol.command', 
177      'pymol.macro_create': 'pymol.macro_write', 
178      'pymol.macro_exec': 'pymol.macro_run', 
179      'pymol.write': 'pymol.macro_write', 
180      'relax_data.frq': 'spectrometer.frequency', 
181      'relax_disp.cpmg_frq': 'relax_disp.cpmg_setup', 
182      'relax_disp.set_grid_r20_from_min_r2eff': 'relax_disp.r20_from_min_r2eff', 
183      'relax_fit.mean_and_error': 'spectrum.error_analysis', 
184      'relax_fit.read': 'spectrum.read_intensities', 
185      'structure.align': 'structure.superimpose', 
186      'structure.vectors': 'interatom.unit_vectors', 
187      'sys_info': 'system.sys_info', 
188      'temperature': 'spectrometer.temperature', 
189      'time': 'system.time' 
190  } 
191