Source Code for Module Chem.Pharm2D.SigFactory

 1  # $Id: SigFactory.py 2 2006-05-06 22:54:39Z glandrum $ 
 2  # 
 3  # Copyright (C) 2003-2006 greg Landrum and Rational Discovery LLC 
 4  # 
 5  #   @@ All Rights Reserved  @@ 
 6  # 
 7  """ contains factory class for producing signatures 
 8   
 9   
10  """ 
11  from Chem.Pharm2D.Signature import Pharm2DSig as Signature 
12   
13 -class SigFactory(object): 
14    """ 
15   
16      SigFactory's are used by creating one, setting the relevant 
17      parameters, then calling the GetSignature() method each time a 
18      signature is required. 
19   
20    """ 
21 -  def __init__(self): 
22      self._patts = None 
23      self._lables = None 
24      self._bins = None 
25      self._minCnt = 2 
26      self._maxCnt = 4 
27      self._shortestPathsOnly = 1 
28      self._includeBondOrder = 0 
29      self._labels = None 
30       
31 -  def SetPatterns(self,patts): 
32      self._patts = patts[:] 
33 -  def SetPatternsFromSmarts(self,smarts): 
34      import Chem 
35      self._patts = [None]*len(smarts) 
36      for i in range(len(smarts)): 
37        p = Chem.MolFromSmarts(smarts[i]) 
38        self._patts[i] = p 
39 -  def GetPatterns(self): 
40      return self._patts 
41 -  def GetNumPatterns(self): 
42      return len(self._patts) 
43     
44 -  def SetLabels(self,labels): 
45      self._labels = labels[:] 
46 -  def GetLabel(self,which): 
47      return self._labels[which] 
48 -  def GetLabels(self): 
49      return self._labels 
50   
51 -  def SetBins(self,bins): 
52      """ bins should be a list of 2-tuples """ 
53      self._bins = bins[:] 
54 -  def GetBins(self): 
55      return self._bins 
56 -  def GetNumBins(self): 
57      return len(self._bins) 
58   
59 -  def SetMinCount(self,min): 
60      self._minCnt = min 
61 -  def GetMinCount(self): 
62      return self._minCnt 
63   
64 -  def SetMaxCount(self,max): 
65      self._maxCnt = max 
66 -  def GetMaxCount(self): 
67      return self._maxCnt 
68   
69 -  def SetShortestPathsOnly(self,val): 
70      if not val: 
71        raise ValueError,'only shortest paths signatures are currently supported' 
72      self._shortestPathsOnly = val 
73 -  def GetShortestPathsOnly(self): 
74      return self._shortestPathsOnly 
75       
76 -  def SetIncludeBondOrder(self,val): 
77      self._includeBondOrder = val 
78 -  def GetIncludeBondOrder(self): 
79      return self._includeBondOrder 
80       
81     
82 -  def GetSignature(self,initialize=1): 
83      sig = Signature(patts=self.GetPatterns(), 
84                      bins=self.GetBins(), 
85                      labels = self.GetLabels(), 
86                      minCnt=self.GetMinCount(), 
87                      maxCnt=self.GetMaxCount(), 
88                      shortestPathsOnly=self.GetShortestPathsOnly(), 
89                      includeBondOrder=self.GetIncludeBondOrder()) 
90      if initialize: 
91        sig.Init() 
92      return sig 
93