Source Code for Module MolKit.moleculeParser

 1  ############################################################################# 
 2  # 
 3  # Author: Michel F. SANNER 
 4  # 
 5  # Copyright: M. Sanner TSRI 2000 
 6  # 
 7  ############################################################################# 
 8   
 9  # 
10  # $Header: /opt/cvs/python/packages/share1.5/MolKit/moleculeParser.py,v 1.5 2005/06/01 19:51:31 sanner Exp $ 
11  # 
12  # $Id: moleculeParser.py,v 1.5 2005/06/01 19:51:31 sanner Exp $ 
13  # 
14   
15  from MolKit.molecule import Atom 
16  import warnings 
17   
18 -class MoleculeParser: 
19 -    def __init__(self, filename=None, allLines=None): 
20          """Supply the filename for reading by readFile, or 
21          supply the lines directly via allLines 
22          """ 
23          self.filename = filename 
24          self.allLines = allLines #stores all lines from file 
25   
26           
27 -    def readFile(self): 
28          try: 
29              f = open(self.filename) 
30              self.allLines = f.readlines() 
31              if len(self.allLines)==1: 
32                  # this file probably has \r instead or \n 
33                  self.allLines = self.allLines[0].split('\r') 
34                  warnings.warn('Only 1 line read from PDB file, splitting on \r') 
35              f.close() 
36              import string 
37              self.allLines = filter( lambda x,s=string.strip: len(s(x)), 
38                                      self.allLines ) 
39          except: 
40              self.allLines = None 
41