Source Code for Module prompt.palmer

  1  ############################################################################### 
  2  #                                                                             # 
  3  # Copyright (C) 2003-2005 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   
 79              'dir/mfin', 
 80              'dir/mfdata', 
 81              'dir/mfpar', 
 82              'dir/mfmodel', 
 83              'dir/run.sh'. 
 84   
 85          The file 'run/run.sh' contains the single command, 
 86   
 87          'modelfree4 -i mfin -d mfdata -p mfpar -m mfmodel -o mfout -e out', 
 88   
 89          which can be used to execute modelfree4. 
 90          """ 
 91   
 92          # Function intro text. 
 93          if self.__relax__.interpreter.intro: 
 94              text = sys.ps3 + "palmer.create(" 
 95              text = text + "run=" + `run` 
 96              text = text + ", dir=" + `dir` 
 97              text = text + ", force=" + `force` 
 98              text = text + ", diff_search=" + `diff_search` 
 99              text = text + ", sims=" + `sims` 
100              text = text + ", sim_type=" + `sim_type` 
101              text = text + ", trim=" + `trim` 
102              text = text + ", steps=" + `steps` 
103              text = text + ", constraints=" + `constraints` 
104              text = text + ", nucleus=" + `nucleus` 
105              text = text + ", atom1=" + `atom1` 
106              text = text + ", atom2=" + `atom2` + ")" 
107              print text 
108   
109          # The run argument. 
110          if type(run) != str: 
111              raise RelaxStrError, ('run', run) 
112   
113          # Directory. 
114          if dir != None: 
115              if type(dir) != str: 
116                  raise RelaxNoneStrError, ('directory name', dir) 
117   
118          # The force flag. 
119          if type(force) != int or (force != 0 and force != 1): 
120              raise RelaxBinError, ('force flag', force) 
121   
122          # The diff_search argument. 
123          if type(diff_search) != str: 
124              raise RelaxStrError, ('diff_search', diff_search) 
125   
126          # The number of Monte Carlo simulations. 
127          if type(sims) != int: 
128              raise RelaxIntError, ('sims', sims) 
129   
130          # The sim_type argument. 
131          if type(sim_type) != str: 
132              raise RelaxStrError, ('sim_type', sim_type) 
133   
134          # The trim argument. 
135          if type(trim) != float and type(trim) != int: 
136              raise RelaxFloatError, ('trim', trim) 
137   
138          # The steps argument. 
139          if type(steps) != int: 
140              raise RelaxIntError, ('steps', steps) 
141   
142          # Constraint flag. 
143          if type(constraints) != int or (constraints != 0 and constraints != 1): 
144              raise RelaxBinError, ('constraint flag', constraints) 
145   
146          # The nucleus argument. 
147          if type(nucleus) != str: 
148              raise RelaxStrError, ('nucleus', nucleus) 
149   
150          # The atom1 argument. 
151          if type(atom1) != str: 
152              raise RelaxStrError, ('atom1', atom1) 
153   
154          # The atom2 argument. 
155          if type(atom2) != str: 
156              raise RelaxStrError, ('atom2', atom2) 
157   
158          # Execute the functional code. 
159          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) 
160   
161   
162 -    def execute(self, run=None, dir=None, force=0): 
163          """Function for executing Modelfree4. 
164   
165          Keyword Arguments 
166          ~~~~~~~~~~~~~~~~~ 
167   
168          run:  The name of the run. 
169   
170          dir:  The directory to place the files.  The default is the value of 'run'. 
171   
172          force:  A flag which if set to 1 will cause the results file to be overwritten if it already 
173          exists. 
174   
175   
176          Description 
177          ~~~~~~~~~~~ 
178   
179          Modelfree 4 will be executed as 
180   
181          $ modelfree4 -i mfin -d mfdata -p mfpar -m mfmodel -o mfout -e out 
182   
183          If a PDB file is loaded and non-isotropic diffusion is selected, then the file name will be 
184          placed on the command line as '-s pdb_file_name'. 
185          """ 
186   
187          # Function intro text. 
188          if self.__relax__.interpreter.intro: 
189              text = sys.ps3 + "palmer.execute(" 
190              text = text + "run=" + `run` 
191              text = text + ", dir=" + `dir` 
192              text = text + ", force=" + `force` + ")" 
193              print text 
194   
195          # The run argument. 
196          if type(run) != str: 
197              raise RelaxStrError, ('run', run) 
198   
199          # Directory. 
200          if dir != None: 
201              if type(dir) != str: 
202                  raise RelaxNoneStrError, ('directory name', dir) 
203   
204          # The force flag. 
205          if type(force) != int or (force != 0 and force != 1): 
206              raise RelaxBinError, ('force flag', force) 
207   
208          # Execute the functional code. 
209          self.__relax__.generic.palmer.execute(run=run, dir=dir, force=force) 
210   
211   
212 -    def extract(self, run=None, dir=None): 
213          """Function for extracting data from the Modelfree4 'mfout' star formatted file. 
214   
215          Keyword Arguments 
216          ~~~~~~~~~~~~~~~~~ 
217   
218          run:  The name of the run. 
219   
220          dir:  The directory where the file 'mfout' is found.  The default is the value of 'run'. 
221          """ 
222   
223          # Function intro text. 
224          if self.__relax__.interpreter.intro: 
225              text = sys.ps3 + "palmer.extract(" 
226              text = text + "run=" + `run` 
227              text = text + ", dir=" + `dir` + ")" 
228              print text 
229   
230          # The run argument. 
231          if type(run) != str: 
232              raise RelaxStrError, ('run', run) 
233   
234          # Directory. 
235          if dir != None: 
236              if type(dir) != str: 
237                  raise RelaxNoneStrError, ('directory name', dir) 
238   
239          # Execute the functional code. 
240          self.__relax__.generic.palmer.extract(run=run, dir=dir) 
241