Source Code for Module prompt.deselect

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  2  #                                                                             # 
  3  # Copyright (C) 2003-2011 Edward d'Auvergne                                   # 
  4  #                                                                             # 
  5  # This file is part of the program relax.                                     # 
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 21  ############################################################################### 
 22   
 23  # Module docstring. 
 24  """Module containing the 'deselect' user function class.""" 
 25  __docformat__ = 'plaintext' 
 26   
 27  # Python module imports. 
 28  from select import boolean_doc 
 29   
 30  # relax module imports. 
 31  from base_class import User_fn_class, _build_doc 
 32  import arg_check 
 33  from generic_fns import selection 
 34   
 35   
 36 -class Deselect(User_fn_class): 
 37      """Class for deselecting spins.""" 
 38   
 39 -    def all(self): 
 40          # Function intro test. 
 41          if self._exec_info.intro: 
 42              text = self._exec_info.ps3 + "deselect.all()" 
 43              print(text) 
 44   
 45          # Execute the functional code. 
 46          selection.desel_all() 
 47   
 48      # The function doc info. 
 49      all._doc_title = "Deselect all spins." 
 50      all._doc_desc = """ 
 51          This will deselect all spins, irregardless of their current state. 
 52          """ 
 53      all._doc_examples = """ 
 54          To deselect all spins, simply type: 
 55   
 56          relax> deselect.all() 
 57          """ 
 58      _build_doc(all) 
 59   
 60   
 61 -    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='AND', change_all=False): 
 62          # Function intro test. 
 63          if self._exec_info.intro: 
 64              text = self._exec_info.ps3 + "deselect.read(" 
 65              text = text + "file=" + repr(file) 
 66              text = text + ", dir=" + repr(dir) 
 67              text = text + ", spin_id_col=" + repr(spin_id_col) 
 68              text = text + ", mol_name_col=" + repr(mol_name_col) 
 69              text = text + ", res_num_col=" + repr(res_num_col) 
 70              text = text + ", res_name_col=" + repr(res_name_col) 
 71              text = text + ", spin_num_col=" + repr(spin_num_col) 
 72              text = text + ", spin_name_col=" + repr(spin_name_col) 
 73              text = text + ", sep=" + repr(sep) 
 74              text = text + ", spin_id=" + repr(spin_id) 
 75              text = text + ", boolean=" + repr(boolean) 
 76              text = text + ", change_all=" + repr(change_all) + ")" 
 77              print(text) 
 78   
 79          # The argument checks. 
 80          arg_check.is_str_or_inst(file, 'file name') 
 81          arg_check.is_str(dir, 'directory name', can_be_none=True) 
 82          arg_check.is_int(spin_id_col, 'spin ID string column', can_be_none=True) 
 83          arg_check.is_int(mol_name_col, 'molecule name column', can_be_none=True) 
 84          arg_check.is_int(res_num_col, 'residue number column', can_be_none=True) 
 85          arg_check.is_int(res_name_col, 'residue name column', can_be_none=True) 
 86          arg_check.is_int(spin_num_col, 'spin number column', can_be_none=True) 
 87          arg_check.is_int(spin_name_col, 'spin name column', can_be_none=True) 
 88          arg_check.is_str(sep, 'column separator', can_be_none=True) 
 89          arg_check.is_str(spin_id, 'spin ID string', can_be_none=True) 
 90          arg_check.is_str(boolean, 'boolean operator') 
 91          arg_check.is_bool(change_all, 'change all') 
 92   
 93          # Execute the functional code. 
 94          selection.desel_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) 
 95   
 96      # The function doc info. 
 97      read._doc_title = "Deselect the spins contained in a file." 
 98      read._doc_title_short = "Deselecting spins from file." 
 99      read._doc_args = [ 
100          ["file", "The name of the file containing the list of spins to deselect."], 
101          ["dir", "The directory where the file is located."], 
102          ["spin_id_col", "The spin ID string column (an alternative to the mol, res, and spin name and number columns)."], 
103          ["mol_name_col", "The molecule name column (alternative to the spin_id_col)."], 
104          ["res_num_col", "The residue number column (alternative to the spin_id_col)."], 
105          ["res_name_col", "The residue name column (alternative to the spin_id_col)."], 
106          ["spin_num_col", "The spin number column (alternative to the spin_id_col)."], 
107          ["spin_name_col", "The spin name column (alternative to the spin_id_col)."], 
108          ["data_col", "The RDC data column."], 
109          ["error_col", "The experimental error column."], 
110          ["sep", "The column separator (the default is white space)."], 
111          ["spin_id", "The spin ID string to restrict the loading of data to certain spin subsets."], 
112          ["boolean", "The boolean operator specifying how spins should be selected."], 
113          ["change_all", "A flag specifying if all other spins should be changed."] 
114      ] 
115      read._doc_desc = """ 
116          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. 
117   
118          Empty lines and lines beginning with a hash are ignored. 
119   
120          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 selected. 
121          """ 
122      read._doc_examples = """ 
123          To deselect all overlapped residues listed with residue numbers in the first column of the 
124          file 'unresolved', type one of: 
125   
126          relax> deselect.read('unresolved', res_num_col=1) 
127          relax> deselect.read(file='unresolved', res_num_col=1) 
128   
129          To deselect the spins in the second column of the relaxation data file 'r1.600' while 
130          selecting all other spins, for example type: 
131   
132          relax> deselect.read('r1.600', spin_num_col=2, change_all=True) 
133          relax> deselect.read(file='r1.600', spin_num_col=2, change_all=True) 
134          """ 
135      read._doc_additional = [boolean_doc] 
136      _build_doc(read) 
137   
138   
139 -    def reverse(self, spin_id=None): 
140          # Function intro test. 
141          if self._exec_info.intro: 
142              text = self._exec_info.ps3 + "deselect.reverse(" 
143              text = text + "spin_id=" + repr(spin_id) + ")" 
144              print(text) 
145   
146          # The argument checks. 
147          arg_check.is_str(spin_id, 'spin ID string', can_be_none=True) 
148   
149          # Execute the functional code. 
150          selection.reverse(spin_id=spin_id) 
151   
152      # The function doc info. 
153      reverse._doc_title = "Reversal of the spin selection for the given spins." 
154      reverse._doc_title_short = "Spin selection reversal." 
155      reverse._doc_args = [ 
156          ["spin_id", "The spin ID string."] 
157      ] 
158      reverse._doc_desc = """ 
159          By supplying the spin ID string, a subset of spins can have their selection status reversed. 
160          """ 
161      reverse._doc_examples = """ 
162          To deselect all currently selected spins and select those which are deselected type: 
163   
164          relax> deselect.reverse() 
165          """ 
166      _build_doc(reverse) 
167   
168   
169 -    def spin(self, spin_id=None, change_all=False): 
170          # Function intro test. 
171          if self._exec_info.intro: 
172              text = self._exec_info.ps3 + "deselect.spin(" 
173              text = text + "spin_id=" + repr(spin_id) 
174              text = text + ", change_all=" + repr(change_all) + ")" 
175              print(text) 
176   
177          # The argument checks. 
178          arg_check.is_str(spin_id, 'spin ID string', can_be_none=True) 
179          arg_check.is_bool(change_all, 'change all') 
180   
181          # Execute the functional code. 
182          selection.desel_spin(spin_id=spin_id, change_all=change_all) 
183   
184      # The function doc info. 
185      spin._doc_title = "Deselect specific spins." 
186      spin._doc_args = [ 
187          ["spin_id", "The spin ID string."], 
188          ["change_all", "A flag specifying if all other spins should be changed."] 
189      ] 
190      spin._doc_desc = """ 
191          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. 
192          """ 
193      spin._doc_examples = """ 
194          To deselect all glycines and alanines, type: 
195   
196          relax> deselect.spin(spin_id=':GLY|:ALA') 
197   
198          To deselect residue 12 MET type: 
199   
200          relax> deselect.spin(':12') 
201          relax> deselect.spin(spin_id=':12') 
202          relax> deselect.spin(spin_id=':12&:MET') 
203          """ 
204      _build_doc(spin) 
205