Source Code for Module specific_analyses.relax_disp.uf

  1  ############################################################################### 
  2  #                                                                             # 
  3  # Copyright (C) 2004-2014 Edward d'Auvergne                                   # 
  4  # Copyright (C) 2009 Sebastien Morin                                          # 
  5  # Copyright (C) 2013-2014 Troels E. Linnet                                    # 
  6  #                                                                             # 
  7  # This file is part of the program relax (http://www.nmr-relax.com).          # 
  8  #                                                                             # 
  9  # This program is free software: you can redistribute it and/or modify        # 
 10  # it under the terms of the GNU General Public License as published by        # 
 11  # the Free Software Foundation, either version 3 of the License, or           # 
 12  # (at your option) any later version.                                         # 
 13  #                                                                             # 
 14  # This program is distributed in the hope that it will be useful,             # 
 15  # but WITHOUT ANY WARRANTY; without even the implied warranty of              # 
 16  # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the               # 
 17  # GNU General Public License for more details.                                # 
 18  #                                                                             # 
 19  # You should have received a copy of the GNU General Public License           # 
 20  # along with this program.  If not, see <http://www.gnu.org/licenses/>.       # 
 21  #                                                                             # 
 22  ############################################################################### 
 23   
 24  # Module docstring. 
 25  """The relaxation dispersion API object.""" 
 26   
 27  # relax module imports. 
 28  from lib.errors import RelaxError 
 29  from pipe_control import pipes 
 30  from pipe_control.mol_res_spin import check_mol_res_spin_data, spin_loop 
 31  from specific_analyses.relax_disp.api import Relax_disp 
 32  from specific_analyses.relax_disp.checks import check_c_modules, check_exp_type, check_pipe_type 
 33  from specific_analyses.relax_disp.data import get_curve_type 
 34  from specific_analyses.relax_disp.variables import MODEL_DESC, MODEL_LIST_FULL, MODEL_PARAMS, MODEL_R2EFF 
 35   
 36   
 37  # The API object. 
 38  api_relax_disp = Relax_disp() 
 39   
 40   
 41 -def cluster(cluster_id=None, spin_id=None): 
 42      """Define spin clustering. 
 43   
 44      @keyword cluster_id:    The cluster ID string. 
 45      @type cluster_id:       str 
 46      @keyword spin_id:       The spin ID string for the spin or group of spins to add to the cluster. 
 47      @type spin_id:          str 
 48      """ 
 49   
 50      # Initialise. 
 51      if not hasattr(cdp, 'clustering'): 
 52          # Create the dictionary. 
 53          cdp.clustering = {} 
 54          cdp.clustering['free spins'] = [] 
 55   
 56          # Add all spin IDs to the cluster. 
 57          for spin, id in spin_loop(return_id=True): 
 58              cdp.clustering['free spins'].append(id) 
 59   
 60      # Add the key. 
 61      if cluster_id not in cdp.clustering: 
 62          cdp.clustering[cluster_id] = [] 
 63   
 64      # Loop over the spins to add to the cluster. 
 65      for spin, id in spin_loop(selection=spin_id, return_id=True): 
 66          # First remove the ID from all clusters. 
 67          for key in cdp.clustering.keys(): 
 68              if id in cdp.clustering[key]: 
 69                  cdp.clustering[key].pop(cdp.clustering[key].index(id)) 
 70   
 71          # Then add the ID to the cluster. 
 72          cdp.clustering[cluster_id].append(id) 
 73   
 74      # Clean up - delete any empty clusters (except the free spins). 
 75      clean = [] 
 76      for key in cdp.clustering.keys(): 
 77          if key == 'free spins': 
 78              continue 
 79          if cdp.clustering[key] == []: 
 80              clean.append(key) 
 81      for key in clean: 
 82          cdp.clustering.pop(key) 
 83   
 84   
 85 -def cluster_ids(): 
 86      """Return the current list of cluster ID strings. 
 87   
 88      @return:    The list of cluster IDs. 
 89      @rtype:     list of str 
 90      """ 
 91   
 92      # Initialise. 
 93      ids = ['free spins'] 
 94   
 95      # Add the defined IDs. 
 96      if hasattr(cdp, 'clustering'): 
 97          for key in list(cdp.clustering.keys()): 
 98              if key not in ids: 
 99                  ids.append(key) 
100   
101      # Return the IDs. 
102      return ids 
103   
104   
105 -def model_setup(model, params): 
106      """Update various model specific data structures. 
107   
108      @param model:   The relaxation dispersion curve type. 
109      @type model:    str 
110      @param params:  A list consisting of the model parameters. 
111      @type params:   list of str 
112      """ 
113   
114      # The model group. 
115      if model == MODEL_R2EFF: 
116          cdp.model_type = 'R2eff' 
117      else: 
118          cdp.model_type = 'disp' 
119   
120      # Loop over the sequence. 
121      for spin in spin_loop(skip_desel=True): 
122          # The model and parameter names. 
123          spin.model = model 
124          spin.params = params 
125   
126          # Initialise the data structures (if needed). 
127          api_relax_disp.data_init(spin) 
128   
129   
130 -def select_model(model=MODEL_R2EFF): 
131      """Set up the model for the relaxation dispersion analysis. 
132   
133      @keyword model: The relaxation dispersion analysis type. 
134      @type model:    str 
135      """ 
136   
137      # Data checks. 
138      pipes.test() 
139      check_pipe_type() 
140      check_mol_res_spin_data() 
141      check_exp_type() 
142   
143      # The curve type. 
144      curve_type = get_curve_type() 
145      if model == MODEL_R2EFF and curve_type == 'exponential': 
146          check_c_modules() 
147   
148      # Invalid model. 
149      if model not in MODEL_DESC: 
150          raise RelaxError("The model '%s' must be one of %s." % (model, MODEL_LIST_FULL)) 
151   
152      # R2eff/R1rho model. 
153      if model == MODEL_R2EFF: 
154          if curve_type == 'exponential': 
155              params = ['r2eff', 'i0'] 
156          else: 
157              params = ['r2eff'] 
158   
159      # All other models. 
160      else: 
161          params = MODEL_PARAMS[model] 
162   
163      # Printout. 
164      print(MODEL_DESC[model]) 
165   
166      # Set up the model. 
167      model_setup(model, params) 
168