Source Code for Module csb.bio.io.whatif

 1  """ 
 2  Simple WhatIf/WhatCheck Summary parser 
 3  """ 
 4   
 5  import re 
 6  import os 
 7  import shutil 
 8   
 9  from csb.io import Shell 
10  from csb.io import TempFolder 
11   
12 -class WhatCheckParser(object): 
13      """ 
14      Simple WhatIf/WhatCheck Summary parser 
15      """ 
16   
17 -    def __init__(self, binary='DO_WHATCHECK.COM'): 
18          self.binary = binary 
19       
20 -    def parse_summary(self, fn): 
21          """ 
22          @param fn: whatif pdbout.txt file to parse 
23          @type fn: str 
24   
25          @return: A dict containing some of the WhatCheck results 
26          @rtype: a dict 
27          """ 
28          f_handler = open(os.path.expanduser(fn)) 
29          text = f_handler.read() 
30   
31          info = dict() 
32          re_ramachandran = re.compile('Ramachandran\s*Z-score\s*:\s*([0-9.Ee-]+)') 
33          re_1st = re.compile('1st\s*generation\s*packing\s*quality\s*:\s*([0-9.Ee-]+)') 
34          re_2nd = re.compile('2nd\s*generation\s*packing\s*quality\s*:\s*([0-9.Ee-]+)') 
35          re_backbone = re.compile('Backbone\s*conformation\s*Z-score\s*:\s*([0-9.Ee-]+)') 
36          re_rotamer = re.compile('chi-1\S*chi-2\s*rotamer\s*normality\s*:\s*([0-9.Ee-]+)') 
37           
38   
39          info['rama_z_score'] = float(re_ramachandran.search(text).groups(0)[0]) 
40          info['bb_z_score'] = float(re_backbone.search(text).groups(0)[0]) 
41          info['1st_packing_z_score'] = float(re_1st.search(text).groups(0)[0]) 
42          info['2nd_packing_z_score'] = float(re_2nd.search(text).groups(0)[0]) 
43          info['rotamer_score'] = float(re_rotamer.search(text).groups(0)[0]) 
44   
45          f_handler.close() 
46          return info 
47   
48      parse = parse_summary 
49   
50   
51 -    def run(self, pdb_file): 
52          """ 
53          Runs WhatCheck for the given pdbfile and parses the output. 
54          Will fail if the WhatCheck binary is not in the path. 
55           
56          @param pdb_file: file to parse 
57          @return: dict of parsed values 
58          """ 
59          wd = os.getcwd() 
60          base = os.path.basename(pdb_file) 
61   
62          with TempFolder() as tmp: 
63              shutil.copy(os.path.expanduser(pdb_file), tmp.name) 
64              os.chdir(tmp.name) 
65              Shell.run('{0} {1}'.format(self.binary, 
66                                         os.path.join(tmp.name, base))) 
67              out = self.parse_summary(os.path.join(tmp.name, 'pdbout.txt')) 
68              os.chdir(wd) 
69   
70          return out 
71