Source Code for Module prompt.palmer

  1  ############################################################################### 
  2  #                                                                             # 
  3  # Copyright (C) 2003, 2004 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  import sys 
 24   
 25  import help 
 26   
 27   
 28 -class Palmer: 
 29 -    def __init__(self, relax): 
 30          # Help. 
 31          self.__relax_help__ = \ 
 32          """Class for interfacing with Art Palmer's Modelfree 4.""" 
 33   
 34          # Add the generic help string. 
 35          self.__relax_help__ = self.__relax_help__ + "\n" + help.relax_class_help 
 36   
 37          # Place relax in the class namespace. 
 38          self.__relax__ = relax 
 39   
 40   
 41 -    def create(self, run=None, dir=None, force=0, diff_search='none', sims=0, sim_type='pred', trim=0, steps=20, constraints=1, nucleus='15N', atom1='N', atom2='H'): 
 42          """Function for creating the Modelfree4 input files. 
 43   
 44          Keyword Arguments 
 45          ~~~~~~~~~~~~~~~~~ 
 46   
 47          run:  The name of the run. 
 48   
 49          dir:  The directory to place the files.  The default is the value of 'run'. 
 50   
 51          force:  A flag which if set to 1 will cause the results file to be overwritten if it already 
 52          exists. 
 53   
 54          diff_search:  See the Modelfree4 manual for 'diffusion_search'. 
 55   
 56          sims:  The number of Monte Carlo simulations. 
 57   
 58          sim_type:  See the Modelfree4 manual. 
 59   
 60          trim:  See the Modelfree4 manual. 
 61   
 62          steps:  See the Modelfree4 manual. 
 63   
 64          constraints:  A flag specifying whether the parameters should be constrained.  The default 
 65          is to turn constraints on (constraints=1). 
 66   
 67          nucleus:  A three letter string describing the nucleus type, ie 15N, 13C, etc. 
 68   
 69          atom1:  The symbol of the X nucleus in the pdb file. 
 70   
 71          atom2:  The symbol of the H nucleus in the pdb file. 
 72   
 73   
 74          Description 
 75          ~~~~~~~~~~~ 
 76   
 77          The following files are created: 
 78              dir/mfin 
 79              dir/mfdata 
 80              dir/mfpar 
 81              dir/mfmodel 
 82              dir/run.sh 
 83   
 84          The file 'run/run.sh' contains the single command: 
 85              modelfree4 -i mfin -d mfdata -p mfpar -m mfmodel -o mfout -e out 
 86          This can be used to execute modelfree4. 
 87          """ 
 88   
 89          # Function intro text. 
 90          if self.__relax__.interpreter.intro: 
 91              text = sys.ps3 + "palmer.create(" 
 92              text = text + "run=" + `run` 
 93              text = text + ", dir=" + `dir` 
 94              text = text + ", force=" + `force` 
 95              text = text + ", diff_search=" + `diff_search` 
 96              text = text + ", sims=" + `sims` 
 97              text = text + ", sim_type=" + `sim_type` 
 98              text = text + ", trim=" + `trim` 
 99              text = text + ", steps=" + `steps` 
100              text = text + ", constraints=" + `constraints` 
101              text = text + ", nucleus=" + `nucleus` 
102              text = text + ", atom1=" + `atom1` 
103              text = text + ", atom2=" + `atom2` + ")" 
104              print text 
105   
106          # The run argument. 
107          if type(run) != str: 
108              raise RelaxStrError, ('run', run) 
109   
110          # Directory. 
111          if dir != None: 
112              if type(dir) != str: 
113                  raise RelaxNoneStrError, ('directory name', dir) 
114   
115          # The force flag. 
116          if type(force) != int or (force != 0 and force != 1): 
117              raise RelaxBinError, ('force flag', force) 
118   
119          # The diff_search argument. 
120          if type(diff_search) != str: 
121              raise RelaxStrError, ('diff_search', diff_search) 
122   
123          # The number of Monte Carlo simulations. 
124          if type(sims) != int: 
125              raise RelaxIntError, ('sims', sims) 
126   
127          # The sim_type argument. 
128          if type(sim_type) != str: 
129              raise RelaxStrError, ('sim_type', sim_type) 
130   
131          # The trim argument. 
132          if type(trim) != float and type(trim) != int: 
133              raise RelaxFloatError, ('trim', trim) 
134   
135          # The steps argument. 
136          if type(steps) != int: 
137              raise RelaxIntError, ('steps', steps) 
138   
139          # Constraint flag. 
140          if type(constraints) != int or (constraints != 0 and constraints != 1): 
141              raise RelaxBinError, ('constraint flag', constraints) 
142   
143          # The nucleus argument. 
144          if type(nucleus) != str: 
145              raise RelaxStrError, ('nucleus', nucleus) 
146   
147          # The atom1 argument. 
148          if type(atom1) != str: 
149              raise RelaxStrError, ('atom1', atom1) 
150   
151          # The atom2 argument. 
152          if type(atom2) != str: 
153              raise RelaxStrError, ('atom2', atom2) 
154   
155          # Execute the functional code. 
156          self.__relax__.generic.palmer.create(run=run, dir=dir, force=force, diff_search=diff_search, sims=sims, sim_type=sim_type, trim=trim, steps=steps, constraints=constraints, nucleus=nucleus, atom1=atom1, atom2=atom2) 
157   
158   
159 -    def execute(self, run=None, dir=None, force=0): 
160          """Function for executing Modelfree4. 
161   
162          Keyword Arguments 
163          ~~~~~~~~~~~~~~~~~ 
164   
165          run:  The name of the run. 
166   
167          dir:  The directory to place the files.  The default is the value of 'run'. 
168   
169          force:  A flag which if set to 1 will cause the results file to be overwritten if it already 
170          exists. 
171   
172   
173          Description 
174          ~~~~~~~~~~~ 
175   
176          Modelfree 4 will be executed as: 
177              modelfree4 -i mfin -d mfdata -p mfpar -m mfmodel -o mfout -e out 
178   
179          If a PDB file is loaded and non-isotropic diffusion is selected, then the file name will be 
180          placed on the command line as '-s pdb_file_name'. 
181          """ 
182   
183          # Function intro text. 
184          if self.__relax__.interpreter.intro: 
185              text = sys.ps3 + "palmer.execute(" 
186              text = text + "run=" + `run` 
187              text = text + ", dir=" + `dir` 
188              text = text + ", force=" + `force` + ")" 
189              print text 
190   
191          # The run argument. 
192          if type(run) != str: 
193              raise RelaxStrError, ('run', run) 
194   
195          # Directory. 
196          if dir != None: 
197              if type(dir) != str: 
198                  raise RelaxNoneStrError, ('directory name', dir) 
199   
200          # The force flag. 
201          if type(force) != int or (force != 0 and force != 1): 
202              raise RelaxBinError, ('force flag', force) 
203   
204          # Execute the functional code. 
205          self.__relax__.generic.palmer.execute(run=run, dir=dir, force=force) 
206   
207   
208 -    def extract(self, run=None, dir=None): 
209          """Function for extracting data from the Modelfree4 'mfout' star formatted file. 
210   
211          Keyword Arguments 
212          ~~~~~~~~~~~~~~~~~ 
213   
214          run:  The name of the run. 
215   
216          dir:  The directory where the file 'mfout' is found.  The default is the value of 'run'. 
217          """ 
218   
219          # Function intro text. 
220          if self.__relax__.interpreter.intro: 
221              text = sys.ps3 + "palmer.extract(" 
222              text = text + "run=" + `run` 
223              text = text + ", dir=" + `dir` + ")" 
224              print text 
225   
226          # The run argument. 
227          if type(run) != str: 
228              raise RelaxStrError, ('run', run) 
229   
230          # Directory. 
231          if dir != None: 
232              if type(dir) != str: 
233                  raise RelaxNoneStrError, ('directory name', dir) 
234   
235          # Execute the functional code. 
236          self.__relax__.generic.palmer.extract(run=run, dir=dir) 
237