Source Code for Module prompt.palmer

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  2  #                                                                             # 
  3  # Copyright (C) 2003-2006, 2009-2010 Edward d'Auvergne                        # 
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 22   
 23  # Module docstring. 
 24  """Module containing the 'palmer' user function class for controlling the Modelfree4 software.""" 
 25  __docformat__ = 'plaintext' 
 26   
 27  # relax module imports. 
 28  from base_class import User_fn_class 
 29  import arg_check 
 30  from generic_fns import palmer 
 31   
 32   
 33 -class Palmer(User_fn_class): 
 34      """Class for interfacing with Art Palmer's Modelfree 4.""" 
 35   
 36 -    def create(self, dir=None, force=False, binary='modelfree4', diff_search='none', sims=0, sim_type='pred', trim=0, steps=20, constraints=True, heteronuc_type='15N', atom1='N', atom2='H', spin_id=None): 
 37          """Function for creating the Modelfree4 input files. 
 38   
 39          Keyword Arguments 
 40          ~~~~~~~~~~~~~~~~~ 
 41   
 42          dir:  The directory to place the files. 
 43   
 44          force:  A flag which if set to True will cause the results file to be overwritten if it 
 45          already exists. 
 46   
 47          binary:  The name of the executable Modelfree program file. 
 48   
 49          diff_search:  See the Modelfree4 manual for 'diffusion_search'. 
 50   
 51          sims:  The number of Monte Carlo simulations. 
 52   
 53          sim_type:  See the Modelfree4 manual. 
 54   
 55          trim:  See the Modelfree4 manual. 
 56   
 57          steps:  See the Modelfree4 manual. 
 58   
 59          constraints:  A flag specifying whether the parameters should be constrained.  The default 
 60          is to turn constraints on (constraints=True). 
 61   
 62          heteronuc_type:  A three letter string describing the heteronucleus type, ie 15N, 13C, etc. 
 63   
 64          atom1:  The symbol of the X heteronucleus in the pdb file. 
 65   
 66          atom2:  The symbol of the H nucleus in the pdb file. 
 67   
 68          spin_id:  The spin identification string. 
 69   
 70   
 71          Description 
 72          ~~~~~~~~~~~ 
 73   
 74          The following files are created 
 75   
 76              'dir/mfin', 
 77              'dir/mfdata', 
 78              'dir/mfpar', 
 79              'dir/mfmodel', 
 80              'dir/run.sh'. 
 81   
 82          The file 'dir/run.sh' contains the single command, 
 83   
 84          'modelfree4 -i mfin -d mfdata -p mfpar -m mfmodel -o mfout -e out', 
 85   
 86          which can be used to execute modelfree4. 
 87   
 88          If you would like to use a different Modelfree executable file, change the keyword argument 
 89          'binary' to the appropriate file name.  If the file is not located within the environment's 
 90          path, include the full path infront of the binary file name. 
 91          """ 
 92   
 93          # Function intro text. 
 94          if self._exec_info.intro: 
 95              text = self._exec_info.ps3 + "palmer.create(" 
 96              text = text + "dir=" + repr(dir) 
 97              text = text + ", force=" + repr(force) 
 98              text = text + ", binary=" + repr(binary) 
 99              text = text + ", diff_search=" + repr(diff_search) 
100              text = text + ", sims=" + repr(sims) 
101              text = text + ", sim_type=" + repr(sim_type) 
102              text = text + ", trim=" + repr(trim) 
103              text = text + ", steps=" + repr(steps) 
104              text = text + ", constraints=" + repr(constraints) 
105              text = text + ", heteronucleus=" + repr(heteronuc_type) 
106              text = text + ", atom1=" + repr(atom1) 
107              text = text + ", atom2=" + repr(atom2) 
108              text = text + ", spin_id=" + repr(spin_id) + ")" 
109              print(text) 
110   
111          # The argument checks. 
112          arg_check.is_str(dir, 'directory name', can_be_none=True) 
113          arg_check.is_bool(force, 'force flag') 
114          arg_check.is_str(binary, 'Modelfree executable file') 
115          arg_check.is_str(diff_search, 'diffusion search') 
116          arg_check.is_int(sims, 'number of Monte Carlo simulations') 
117          arg_check.is_str(sim_type, 'simulation type') 
118          arg_check.is_num(trim, 'trimming') 
119          arg_check.is_int(steps, 'steps') 
120          arg_check.is_bool(constraints, 'constraints flag') 
121          arg_check.is_str(heteronuc_type, 'heteronucleus') 
122          arg_check.is_str(atom1, 'atom1') 
123          arg_check.is_str(atom2, 'atom2') 
124   
125          # Execute the functional code. 
126          palmer.create(dir=dir, force=force, binary=binary, diff_search=diff_search, sims=sims, sim_type=sim_type, trim=trim, steps=steps, constraints=constraints, heteronuc_type=heteronuc_type, atom1=atom1, atom2=atom2, spin_id=spin_id) 
127   
128   
129 -    def execute(self, dir=None, force=False, binary='modelfree4'): 
130          """Function for executing Modelfree4. 
131   
132          Keyword Arguments 
133          ~~~~~~~~~~~~~~~~~ 
134   
135          dir:  The directory to place the files. 
136   
137          force:  A flag which if set to True will cause the results file to be overwritten if it 
138          already exists. 
139   
140          binary:  The name of the executable Modelfree program file. 
141   
142   
143          Description 
144          ~~~~~~~~~~~ 
145   
146          Modelfree 4 will be executed as 
147   
148          $ modelfree4 -i mfin -d mfdata -p mfpar -m mfmodel -o mfout -e out 
149   
150          If a PDB file is loaded and non-isotropic diffusion is selected, then the file name will be 
151          placed on the command line as '-s pdb_file_name'. 
152   
153   
154          If you would like to use a different Modelfree executable file, change the keyword argument 
155          'binary' to the appropriate file name.  If the file is not located within the environment's 
156          path, include the full path in front of the binary file name. 
157          """ 
158   
159          # Function intro text. 
160          if self._exec_info.intro: 
161              text = self._exec_info.ps3 + "palmer.execute(" 
162              text = text + "dir=" + repr(dir) 
163              text = text + ", force=" + repr(force) 
164              text = text + ", binary=" + repr(binary) + ")" 
165              print(text) 
166   
167          # The argument checks. 
168          arg_check.is_str(dir, 'directory name', can_be_none=True) 
169          arg_check.is_bool(force, 'force flag') 
170          arg_check.is_str(binary, 'Modelfree executable file') 
171   
172          # Execute the functional code. 
173          palmer.execute(dir=dir, force=force, binary=binary) 
174   
175   
176 -    def extract(self, dir=None): 
177          """Function for extracting data from the Modelfree4 'mfout' star formatted file. 
178   
179          Keyword Arguments 
180          ~~~~~~~~~~~~~~~~~ 
181   
182          dir:  The directory where the file 'mfout' is found. 
183          """ 
184   
185          # Function intro text. 
186          if self._exec_info.intro: 
187              text = self._exec_info.ps3 + "palmer.extract(" 
188              text = text + "dir=" + repr(dir) + ")" 
189              print(text) 
190   
191          # The argument checks. 
192          arg_check.is_str(dir, 'directory name', can_be_none=True) 
193   
194          # Execute the functional code. 
195          palmer.extract(dir=dir) 
196