Source Code for Module Biskit.Prosa

  1  ## 
  2  ## 
  3  ## Biskit, a toolkit for the manipulation of macromolecular structures 
  4  ## Copyright (C) 2004-2005 Raik Gruenberg & Johan Leckner 
  5  ## 
  6  ## This program is free software; you can redistribute it and/or 
  7  ## modify it under the terms of the GNU General Public License as 
  8  ## published by the Free Software Foundation; either version 2 of the 
  9  ## License, or any later version. 
 10  ## 
 11  ## This program is distributed in the hope that it will be useful, 
 12  ## but WITHOUT ANY WARRANTY; without even the implied warranty of 
 13  ## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU 
 14  ## General Public License for more details. 
 15  ## 
 16  ## You find a copy of the GNU General Public License in the file 
 17  ## license.txt along with this program; if not, write to the Free 
 18  ## Software Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA. 
 19  ## 
 20  ## 
 21  ## Author:        Wolfgang Rieping 
 22  ## Created:       04/02/02 
 23  ## Last modified: 04/06/02 
 24  ## 
 25  """ 
 26  Run a ProsaII job. 
 27   
 28  @attention: This class should be replaced by L{Prosa2003}. It will only stay 
 29  for a while unitl  all transitions are made to the new version of Prosa. 
 30  """ 
 31   
 32  import tempfile 
 33  import os 
 34  import Numeric as N 
 35   
 36  import tools as T 
 37  import Table 
 38   
 39 -class ProsaII: 
 40   
 41 -    def __init__(self, executable = 'prosaII', temp_dir = T.tempDir() ): 
 42   
 43          self.executable = executable 
 44          self.setCleanup() 
 45          self.temp_dir = temp_dir 
 46          self.script_name = tempfile.mktemp() 
 47   
 48          ## set default values 
 49   
 50          self.setPairWindowSize() 
 51          self.setSurfaceRange() 
 52          self.setSurfaceFactor() 
 53   
 54 -    def setCleanup(self, value = 1): 
 55   
 56          self.cleanup = int(value) 
 57   
 58 -    def getCleanup(self): 
 59   
 60          return self.cleanup 
 61   
 62 -    def setPairWindowSize(self, window = (1, 600)): 
 63          """ 
 64          pair-interactions are calculated for residue pairs 
 65          whose sequence separation lies in 'window'. 
 66          window must be a tuple. 
 67          default values come from prosaII manual  
 68          """ 
 69   
 70          self.pairWindowSize = tuple(window) 
 71   
 72 -    def getPairWindowSize(self): 
 73   
 74          return self.pairWindowSize 
 75   
 76 -    def setSurfaceRange(self, interval = (0., 15.)): 
 77          """ 
 78          surface energy for a residue pair is calculated only, 
 79          if their distance lies within the 'interval'. otherwise 
 80          energy is 0. 
 81          interval must be tuple. 
 82          default values come from prosaII manual 
 83          """ 
 84   
 85          self.surfaceRange = tuple(interval) 
 86   
 87 -    def getSurfaceRange(self): 
 88   
 89          return self.surfaceRange 
 90   
 91 -    def setSurfaceFactor(self, factor = 5.): 
 92          """ 
 93          E_total = factor * E_surface + E_pair 
 94          see manual for further recommendations 
 95          """ 
 96   
 97          self.surface_factor = factor 
 98   
 99 -    def getSurfaceFactor(self): 
100   
101          return self.surface_factor 
102   
103 -    def run(self, command): 
104   
105          script = self.script_name 
106   
107          f = open(script, 'w') 
108          f.write(command) 
109          f.close() 
110   
111          os.system('%s -d -f %s > /dev/null' % (self.executable, script)) 
112   
113          if self.getCleanup(): 
114   
115              try: 
116                  os.unlink(script) 
117              except: 
118                  pass 
119   
120 -    def analyseEnergy(self, filename, object_name = None): 
121          """ 
122          supports user-expansion 
123          """ 
124   
125          if not os.path.exists(filename): 
126              raise IOError, 'file %s does not exist. Check the ProsaII license' % filename 
127   
128          filename = os.path.expanduser(filename) 
129          path, filename = os.path.split(filename) 
130          name, ext = os.path.splitext(filename) 
131   
132          if path == '': 
133              path = '.' 
134   
135          lower_k, upper_k = self.getPairWindowSize() 
136          surface_lower, surface_upper = self.getSurfaceRange() 
137   
138          if object_name is None: 
139              object_name = name 
140   
141          values = {'pdb_path': path, 
142                    'pdb_file': filename, 
143                    'obj_name': object_name, 
144                    'lower_k': lower_k, 
145                    'upper_k': upper_k, 
146                    'surface_lower': surface_lower, 
147                    'surface_upper': surface_upper, 
148                    'factor_surface': self.getSurfaceFactor()} 
149   
150          command = 'pdb_dir = %(pdb_path)s\n' + \ 
151                    'read pdb %(pdb_file)s %(obj_name)s\n' + \ 
152                    'lower_k = %(lower_k)d\n' + \ 
153                    'upper_k = %(upper_k)d\n' + \ 
154                    'pot_lb = %(surface_lower)f\n' + \ 
155                    'pot_ub = %(surface_upper)f\n' + \ 
156                    'analyse energy %(obj_name)s\n' + \ 
157                    'print energy %(obj_name)s\n' 
158   
159          ## save current path 
160   
161          old_path = os.getcwd() 
162          os.chdir(self.temp_dir) 
163   
164          self.run(command % values) 
165   
166          ## output is in .ana-file 
167   
168          prosa_output = values['obj_name'] + '.ana' 
169   
170          result = parse_ANA_output(prosa_output) 
171   
172          ## if cleanup-flag is set, remove ana-files 
173   
174          if self.getCleanup(): 
175              os.unlink(prosa_output) 
176   
177          ## restore old path 
178   
179          os.chdir(old_path) 
180   
181          return result[:,1:] 
182   
183   
184 -def parse_ANA_output(prosa_output): 
185   
186      if not os.path.exists(prosa_output): 
187          raise 'prosa output %s is missing.' % prosa_output 
188   
189      t = Table.fromFile(prosa_output) 
190   
191      return N.array(t[2:]).astype(N.Float) 
192