Source Code for Module prompt.select

  1  ############################################################################### 
  2  #                                                                             # 
  3  # Copyright (C) 2003-2011 Edward d'Auvergne                                   # 
  4  #                                                                             # 
  5  # This file is part of the program relax.                                     # 
  6  #                                                                             # 
  7  # relax 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 2 of the License, or           # 
 10  # (at your option) any later version.                                         # 
 11  #                                                                             # 
 12  # relax 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 relax; if not, write to the Free Software                        # 
 19  # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA   # 
 20  #                                                                             # 
 21  ############################################################################### 
 22   
 23  # Module docstring. 
 24  """Module containing the 'select' user function class.""" 
 25  __docformat__ = 'plaintext' 
 26   
 27  # relax module imports. 
 28  from base_class import User_fn_class, _build_doc 
 29  import arg_check 
 30  from generic_fns import selection 
 31   
 32   
 33  boolean_doc = ["Boolean operators", """ 
 34  The boolean operator can be used to change how spin systems are selected.  The allowed values are: 'OR', 'NOR', 'AND', 'NAND', 'XOR', 'XNOR'.  The following table details how the selections will occur for the different boolean operators. 
 35  __________________________________________________________ 
 36  |                    |   |   |   |   |   |   |   |   |   | 
 37  | Spin system        | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 
 38  |____________________|___|___|___|___|___|___|___|___|___| 
 39  |                    |   |   |   |   |   |   |   |   |   | 
 40  | Original selection | 0 | 1 | 1 | 1 | 1 | 0 | 1 | 0 | 1 | 
 41  |                    |   |   |   |   |   |   |   |   |   | 
 42  | New selection      | 0 | 1 | 1 | 1 | 1 | 1 | 0 | 0 | 0 | 
 43  |                    |   |   |   |   |   |   |   |   |   | 
 44  | OR                 | 0 | 1 | 1 | 1 | 1 | 1 | 1 | 0 | 1 | 
 45  |                    |   |   |   |   |   |   |   |   |   | 
 46  | NOR                | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 
 47  |                    |   |   |   |   |   |   |   |   |   | 
 48  | AND                | 0 | 1 | 1 | 1 | 1 | 0 | 0 | 0 | 0 | 
 49  |                    |   |   |   |   |   |   |   |   |   | 
 50  | NAND               | 1 | 0 | 0 | 0 | 0 | 1 | 1 | 1 | 1 | 
 51  |                    |   |   |   |   |   |   |   |   |   | 
 52  | XOR                | 0 | 0 | 0 | 0 | 0 | 1 | 1 | 0 | 1 | 
 53  |                    |   |   |   |   |   |   |   |   |   | 
 54  | XNOR               | 1 | 1 | 1 | 1 | 1 | 0 | 0 | 1 | 0 | 
 55  |____________________|___|___|___|___|___|___|___|___|___| 
 56  """, """ 
 57  The boolean operator can be used to change how spin systems are selected.  The allowed values are: 'OR', 'NOR', 'AND', 'NAND', 'XOR', 'XNOR'.  The following details how the selections will occur for the different boolean operators: 
 58   
 59  Spin system:  1 2 3 4 5 6 7 8 9 
 60  Original selection:  0 1 1 1 1 0 1 0 1 
 61  New selection:  0 1 1 1 1 1 0 0 0 
 62  OR:  0 1 1 1 1 1 1 0 1 
 63  NOR:  1 0 0 0 0 0 0 1 0 
 64  AND:  0 1 1 1 1 0 0 0 0 
 65  NAND:  1 0 0 0 0 1 1 1 1 
 66  XOR:  0 0 0 0 0 1 1 0 1 
 67  XNOR:  1 1 1 1 1 0 0 1 0 
 68  """ 
 69  ] 
 70   
 71   
 72 -class Select(User_fn_class): 
 73      """Class for selecting spins.""" 
 74   
 75 -    def all(self): 
 76          # Function intro test. 
 77          if self._exec_info.intro: 
 78              text = self._exec_info.ps3 + "select.all()" 
 79              print(text) 
 80   
 81          # Execute the functional code. 
 82          selection.sel_all() 
 83   
 84      # The function doc info. 
 85      all._doc_title = "Select all spins." 
 86      all._doc_desc = """ 
 87          This will select all spins, irregardless of their current state. 
 88          """ 
 89      all._doc_examples = """ 
 90          To select all spins, simply type: 
 91   
 92          relax> select.all() 
 93          """ 
 94      _build_doc(all) 
 95   
 96   
 97 -    def read(self, file=None, dir=None, spin_id_col=None, mol_name_col=None, res_num_col=None, res_name_col=None, spin_num_col=None, spin_name_col=None, sep=None, spin_id=None, boolean='OR', change_all=False): 
 98          # Function intro test. 
 99          if self._exec_info.intro: 
100              text = self._exec_info.ps3 + "select.read(" 
101              text = text + "file=" + repr(file) 
102              text = text + ", dir=" + repr(dir) 
103              text = text + ", spin_id_col=" + repr(spin_id_col) 
104              text = text + ", mol_name_col=" + repr(mol_name_col) 
105              text = text + ", res_num_col=" + repr(res_num_col) 
106              text = text + ", res_name_col=" + repr(res_name_col) 
107              text = text + ", spin_num_col=" + repr(spin_num_col) 
108              text = text + ", spin_name_col=" + repr(spin_name_col) 
109              text = text + ", sep=" + repr(sep) 
110              text = text + ", spin_id=" + repr(spin_id) 
111              text = text + ", boolean=" + repr(boolean) 
112              text = text + ", change_all=" + repr(change_all) + ")" 
113              print(text) 
114   
115          # The argument checks. 
116          arg_check.is_str_or_inst(file, 'file name') 
117          arg_check.is_str(dir, 'directory name', can_be_none=True) 
118          arg_check.is_int(spin_id_col, 'spin ID string column', can_be_none=True) 
119          arg_check.is_int(mol_name_col, 'molecule name column', can_be_none=True) 
120          arg_check.is_int(res_num_col, 'residue number column', can_be_none=True) 
121          arg_check.is_int(res_name_col, 'residue name column', can_be_none=True) 
122          arg_check.is_int(spin_num_col, 'spin number column', can_be_none=True) 
123          arg_check.is_int(spin_name_col, 'spin name column', can_be_none=True) 
124          arg_check.is_str(sep, 'column separator', can_be_none=True) 
125          arg_check.is_str(spin_id, 'spin ID string', can_be_none=True) 
126          arg_check.is_str(boolean, 'boolean operator') 
127          arg_check.is_bool(change_all, 'change all') 
128   
129          # Execute the functional code. 
130          selection.sel_read(file=file, dir=dir, spin_id_col=spin_id_col, mol_name_col=mol_name_col, res_num_col=res_num_col, res_name_col=res_name_col, spin_num_col=spin_num_col, spin_name_col=spin_name_col, sep=sep, spin_id=spin_id, boolean=boolean, change_all=change_all) 
131   
132      # The function doc info. 
133      read._doc_title = "Select the spins contained in a file." 
134      read._doc_title_short = "Selecting spins from file." 
135      read._doc_args = [ 
136          ["file", "The name of the file containing the list of spins to select."], 
137          ["dir", "The directory where the file is located."], 
138          ["spin_id_col", "The spin ID string column (an alternative to the mol, res, and spin name and number columns)."], 
139          ["mol_name_col", "The molecule name column (alternative to the spin_id_col)."], 
140          ["res_num_col", "The residue number column (alternative to the spin_id_col)."], 
141          ["res_name_col", "The residue name column (alternative to the spin_id_col)."], 
142          ["spin_num_col", "The spin number column (alternative to the spin_id_col)."], 
143          ["spin_name_col", "The spin name column (alternative to the spin_id_col)."], 
144          ["data_col", "The RDC data column."], 
145          ["error_col", "The experimental error column."], 
146          ["sep", "The column separator (the default is white space)."], 
147          ["spin_id", "The spin ID string to restrict the loading of data to certain spin subsets."], 
148          ["boolean", "The boolean operator specifying how spins should be selected."], 
149          ["change_all", "A flag specifying if all other spins should be changed."] 
150      ] 
151      read._doc_desc = """ 
152          The spin system can be identified in the file using two different formats.  The first is the spin ID string column which can include the molecule name, the residue name and number, and the spin name and number.  Alternatively the molecule name, residue number, residue name, spin number and/or spin name columns can be supplied allowing this information to be in separate columns.  Note that the numbering of columns starts at one.  The spin ID string can be used to restrict the reading to certain spin types, for example only 15N spins when only residue information is in the file. 
153   
154          Empty lines and lines beginning with a hash are ignored. 
155   
156          The 'change all' flag default is False meaning that all spins currently either selected or deselected will remain that way.  Setting this to True will cause all spins not specified in the file to be deselected. 
157          """ 
158      read._doc_examples = """ 
159          To select all residues listed with residue numbers in the first column of the file 
160          'isolated_peaks', type one of: 
161   
162          relax> select.read('isolated_peaks', res_num_col=1) 
163          relax> select.read(file='isolated_peaks', res_num_col=1) 
164   
165          To select the spins in the second column of the relaxation data file 'r1.600' while 
166          deselecting all other spins, for example type: 
167   
168          relax> select.read('r1.600', spin_num_col=2, change_all=True) 
169          relax> select.read(file='r1.600', spin_num_col=2, change_all=True) 
170          """ 
171      read._doc_additional = [boolean_doc] 
172      _build_doc(read) 
173   
174   
175 -    def reverse(self, spin_id=None): 
176          # Function intro test. 
177          if self._exec_info.intro: 
178              text = self._exec_info.ps3 + "select.reverse(" 
179              text = text + "spin_id=" + repr(spin_id) + ")" 
180              print(text) 
181   
182          # The argument checks. 
183          arg_check.is_str(spin_id, 'spin ID string', can_be_none=True) 
184   
185          # Execute the functional code. 
186          selection.reverse(spin_id=spin_id) 
187   
188      # The function doc info. 
189      reverse._doc_title = "Reversal of the spin selection for the given spins." 
190      reverse._doc_title_short = "Spin selection reversal." 
191      reverse._doc_args = [ 
192          ["spin_id", "The spin ID string."] 
193      ] 
194      reverse._doc_desc = """ 
195          By supplying the spin ID string, a subset of spins can have their selection status reversed. 
196          """ 
197      reverse._doc_examples = """ 
198          To select all currently deselected spins and deselect those which are selected type: 
199   
200          relax> select.reverse() 
201          """ 
202      _build_doc(reverse) 
203   
204   
205 -    def spin(self, spin_id=None, boolean='OR', change_all=False): 
206          # Function intro test. 
207          if self._exec_info.intro: 
208              text = self._exec_info.ps3 + "select.spin(" 
209              text = text + "spin_id=" + repr(spin_id) 
210              text = text + ", boolean=" + repr(boolean) 
211              text = text + ", change_all=" + repr(change_all) + ")" 
212              print(text) 
213   
214          # The argument checks. 
215          arg_check.is_str(spin_id, 'spin ID string', can_be_none=True) 
216          arg_check.is_str(boolean, 'boolean operator') 
217          arg_check.is_bool(change_all, 'change all') 
218   
219          # Execute the functional code. 
220          selection.sel_spin(spin_id=spin_id, boolean=boolean, change_all=change_all) 
221   
222      # The function doc info. 
223      spin._doc_title = "Select specific spins." 
224      spin._doc_args = [ 
225          ["spin_id", "The spin ID string."], 
226          ["boolean", "The boolean operator specifying how spins should be selected."], 
227          ["change_all", "A flag specifying if all other spins should be changed."] 
228      ] 
229      spin._doc_desc = """ 
230          The 'change all' flag default is False meaning that all spins currently either selected or deselected will remain that way.  Setting this to True will cause all spins not specified by the spin ID string to be selected. 
231          """ 
232      spin._doc_examples = """ 
233          To select only glycines and alanines, assuming they have been loaded with the names GLY and 
234          ALA, type one of: 
235   
236          relax> select.spin(spin_id=':GLY|:ALA') 
237   
238          To select residue 5 CYS in addition to the currently selected residues, type one of: 
239   
240          relax> select.spin(':5') 
241          relax> select.spin(':5&:CYS') 
242          relax> select.spin(spin_id=':5&:CYS') 
243          """ 
244      spin._doc_additional = [boolean_doc] 
245      _build_doc(spin) 
246