Source Code for Module specific_analyses.frame_order.data

  1  ############################################################################### 
  2  #                                                                             # 
  3  # Copyright (C) 2009-2014 Edward d'Auvergne                                   # 
  4  #                                                                             # 
  5  # This file is part of the program relax (http://www.nmr-relax.com).          # 
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  8  # it under the terms of the GNU General Public License as published by        # 
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 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.                                # 
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 18  # along with this program.  If not, see <http://www.gnu.org/licenses/>.       # 
 19  #                                                                             # 
 20  ############################################################################### 
 21   
 22  # Module docstring. 
 23  """Module for handling the frame order data in the relax data store.""" 
 24   
 25  # relax module imports. 
 26  from lib.errors import RelaxError 
 27  from pipe_control.interatomic import interatomic_loop 
 28  from pipe_control.mol_res_spin import spin_loop 
 29   
 30   
 31 -def base_data_types(): 
 32      """Determine all the base data types. 
 33   
 34      The base data types can include:: 
 35          - 'rdc', residual dipolar couplings. 
 36          - 'pcs', pseudo-contact shifts. 
 37   
 38      @return:    A list of all the base data types. 
 39      @rtype:     list of str 
 40      """ 
 41   
 42      # Array of data types. 
 43      list = [] 
 44   
 45      # RDC search. 
 46      for interatom in interatomic_loop(selection1=domain_moving()): 
 47          if hasattr(interatom, 'rdc'): 
 48              list.append('rdc') 
 49              break 
 50   
 51      # PCS search. 
 52      for spin in spin_loop(selection=domain_moving()): 
 53          if hasattr(spin, 'pcs'): 
 54              list.append('pcs') 
 55              break 
 56   
 57      # No data is present. 
 58      if not list: 
 59          raise RelaxError("Neither RDCs nor PCSs are present.") 
 60   
 61      # Return the list. 
 62      return list 
 63   
 64   
 65 -def domain_moving(): 
 66      """Return the spin ID string corresponding to the moving domain. 
 67   
 68      @return:    The spin ID string defining the moving domain. 
 69      @rtype:     str 
 70      """ 
 71   
 72      # Check that the domain is defined. 
 73      if not hasattr(cdp, 'domain'): 
 74          raise RelaxError("No domains have been defined.  Please use the domain user function.") 
 75   
 76      # Only support for 2 domains. 
 77      if len(list(cdp.domain.keys())) > 2: 
 78          raise RelaxError("Only two domains are supported in the frame order analysis.") 
 79   
 80      # Reference domain not set yet, so return nothing. 
 81      if not hasattr(cdp, 'ref_domain'): 
 82          return None 
 83   
 84      # Loop over the domains. 
 85      for id in list(cdp.domain.keys()): 
 86          # Reference domain. 
 87          if id == cdp.ref_domain: 
 88              continue 
 89   
 90          # Return the ID. 
 91          return cdp.domain[id] 
 92   
 93   
 94 -def pivot_fixed(): 
 95      """Determine if the pivot is fixed or not. 
 96   
 97      @return:    The answer to the question. 
 98      @rtype:     bool 
 99      """ 
100   
101      # A pivot point is not supported by the model. 
102      if cdp.model in ['rigid']: 
103          return True 
104   
105      # The PCS is loaded. 
106      if 'pcs' in base_data_types(): 
107          # The fixed flag is not set. 
108          if hasattr(cdp, 'pivot_fixed') and not cdp.pivot_fixed: 
109              return False 
110   
111      # The point is fixed. 
112      return True 
113   
114   
115 -def tensor_loop(red=False): 
116      """Generator method for looping over the full or reduced tensors. 
117   
118      @keyword red:   A flag which if True causes the reduced tensors to be returned, and if False 
119                      the full tensors are returned. 
120      @type red:      bool 
121      @return:        The tensor index and the tensor. 
122      @rtype:         (int, AlignTensorData instance) 
123      """ 
124   
125      # Number of tensor pairs. 
126      n = len(cdp.align_tensors.reduction) 
127   
128      # Alias. 
129      data = cdp.align_tensors 
130      list = data.reduction 
131   
132      # Full or reduced index. 
133      if red: 
134          index = 1 
135      else: 
136          index = 0 
137   
138      # Loop over the reduction list. 
139      for i in range(n): 
140          yield i, data[list[i][index]] 
141   
142   
143 -def translation_fixed(): 
144      """Is the translation of the average domain position fixed? 
145   
146      @return:    The answer to the question. 
147      @rtype:     bool 
148      """ 
149   
150      # PCS data must be present. 
151      if 'pcs' in base_data_types(): 
152          # The fixed flag is not set. 
153          if hasattr(cdp, 'ave_pos_translation') and cdp.ave_pos_translation: 
154              return False 
155   
156      # Default to being fixed. 
157      return True 
158