Source Code for Module rdkit.ML.Cluster.Clusters

  1  # $Id: Clusters.py 997 2009-02-25 06:12:43Z glandrum $ 
  2  # 
  3  # Copyright (C) 2001-2008  greg Landrum 
  4  # 
  5  #   @@ All Rights Reserved  @@ 
  6  # 
  7  """ contains the Cluster class for representing hierarchical cluster trees 
  8   
  9  """ 
 10  import numpy 
 11   
 12  CMPTOL=1e-6 
 13   
 14 -class Cluster(object): 
 15    """a class for storing clusters/data 
 16   
 17      **General Remarks** 
 18   
 19       - It is assumed that the bottom of any cluster hierarchy tree is composed of 
 20         the individual data points which were clustered. 
 21   
 22       - Clusters objects store the following pieces of data, most are 
 23          accessible via standard Setters/Getters: 
 24   
 25         - Children: *Not Settable*, the list of children.  You can add children 
 26           with the _AddChild()_ and _AddChildren()_ methods. 
 27            
 28           **Note** this can be of arbitrary length, 
 29           but the current algorithms I have only produce trees with two children 
 30           per cluster 
 31         
 32         - Metric: the metric for this cluster (i.e. how far apart its children are) 
 33   
 34         - Index: the order in which this cluster was generated 
 35   
 36         - Points: *Not Settable*, the list of original points in this cluster 
 37              (calculated recursively from the children) 
 38   
 39         - PointsPositions: *Not Settable*, the list of positions of the original 
 40            points in this cluster (calculated recursively from the children) 
 41   
 42         - Position: the location of the cluster **Note** for a cluster this 
 43           probably means the location of the average of all the Points which are 
 44           its children. 
 45   
 46         - Data: a data field.  This is used with the original points to store their 
 47           data value (i.e. the value we're using to classify) 
 48   
 49         - Name: the name of this cluster 
 50    
 51    """ 
 52 -  def __init__(self,metric=0.0,children=None,position=None,index=-1,name=None,data=None): 
 53      """Constructor 
 54   
 55        **Arguments** 
 56   
 57          see the class documentation for the meanings of these arguments 
 58   
 59          *my wrists are tired* 
 60   
 61      """ 
 62      if children is None: 
 63        children = [] 
 64      if position is None: 
 65        position = [] 
 66      self.metric = metric 
 67      self.children = children 
 68      self._UpdateLength() 
 69      self.pos = position 
 70      self.index = index 
 71      self.name = name 
 72      self._points = None 
 73      self._pointsPositions = None 
 74      self.data = data 
 75   
 76 -  def SetMetric(self,metric): 
 77      self.metric = metric 
 78 -  def GetMetric(self): 
 79      return self.metric 
 80   
 81 -  def SetIndex(self,index): 
 82      self.index = index 
 83 -  def GetIndex(self): 
 84      return self.index 
 85   
 86 -  def SetPosition(self,pos): 
 87      self.pos = pos 
 88 -  def GetPosition(self): 
 89      return self.pos 
 90   
 91 -  def GetPointsPositions(self): 
 92      if self._pointsPositions is not None: 
 93        return self._pointsPositions 
 94      else: 
 95        self._GenPoints() 
 96        return self._pointsPositions 
 97   
 98 -  def GetPoints(self): 
 99      if self._points is not None: 
100        return self._points 
101      else: 
102        self._GenPoints() 
103        return self._points 
104   
105 -  def FindSubtree(self,index): 
106      """ finds and returns the subtree with a particular index 
107      """ 
108      res = None 
109      if index == self.index: 
110        res = self 
111      else: 
112        for child in self.children: 
113          res = child.FindSubtree(index) 
114          if res: 
115            break 
116      return res 
117       
118 -  def _GenPoints(self): 
119      """ Generates the _Points_ and _PointsPositions_ lists 
120   
121       *intended for internal use* 
122        
123      """ 
124      if len(self) == 1: 
125        self._points = [self] 
126        self._pointsPositions = [self.GetPosition()] 
127        return self._points 
128      else: 
129        res = [] 
130        children = self.GetChildren() 
131        children.sort(lambda x,y:cmp(len(y),len(x))) 
132        for child in children: 
133          res += child.GetPoints() 
134        self._points=res 
135        self._pointsPositions = [x.GetPosition() for x in res] 
136   
137 -  def AddChild(self,child): 
138      """Adds a child to our list 
139   
140        **Arguments** 
141   
142          - child: a Cluster 
143         
144      """ 
145      self.children.append(child) 
146      self._GenPoints() 
147      self._UpdateLength() 
148 -  def AddChildren(self,children): 
149      """Adds a bunch of children to our list 
150   
151        **Arguments** 
152   
153          - children: a list of Clusters 
154         
155      """ 
156      self.children += children 
157      self._GenPoints() 
158      self._UpdateLength() 
159 -  def RemoveChild(self,child): 
160      """Removes a child from our list 
161   
162        **Arguments** 
163   
164          - child: a Cluster 
165         
166      """ 
167      self.children.remove(child) 
168      self._UpdateLength() 
169   
170 -  def GetChildren(self): 
171      self.children.sort(lambda x,y:cmp(x.GetMetric(),y.GetMetric())) 
172      return self.children 
173   
174 -  def SetData(self,data): 
175      self.data = data 
176 -  def GetData(self): 
177      return self.data 
178   
179 -  def SetName(self,name): 
180      self.name = name 
181 -  def GetName(self): 
182      if self.name is None: 
183        return 'Cluster(%d)'%(self.GetIndex()) 
184      else: 
185        return self.name 
186   
187 -  def Print(self,level=0,showData=0,offset='\t'): 
188      if not showData or self.GetData() is None: 
189        print '%s%s%s Metric: %f'%('  '*level,self.GetName(),offset,self.GetMetric()) 
190      else: 
191        print '%s%s%s Data: %f\t Metric: %f'%('  '*level,self.GetName(),offset,self.GetData(),self.GetMetric()) 
192           
193      for child in self.GetChildren(): 
194        child.Print(level=level+1,showData=showData,offset=offset) 
195       
196 -  def Compare(self,other,ignoreExtras=1): 
197      """ not as choosy as self==other 
198   
199      """ 
200      if cmp(type(self),type(other)): 
201        return cmp(type(self),type(other)) 
202   
203      if cmp(len(self),len(other)): 
204        return cmp(len(self),len(other)) 
205         
206      if not ignoreExtras: 
207        m1,m2=self.GetMetric(),other.GetMetric() 
208        if abs(m1-m2)>CMPTOL: 
209          return cmp(m1,m2) 
210   
211        if cmp(self.GetName(),other.GetName()): 
212          return cmp(self.GetName(),other.GetName()) 
213   
214        sP = self.GetPosition() 
215        oP = other.GetPosition() 
216        try: 
217          r = cmp(len(sP),len(oP)) 
218        except: 
219          pass 
220        else: 
221          if r: 
222            return r 
223   
224        try: 
225          r = cmp(sP,oP)  
226        except: 
227          r = sum(sP-oP) 
228        if r: 
229          return r 
230           
231      c1,c2=self.GetChildren(),other.GetChildren() 
232      if cmp(len(c1),len(c2)): 
233        return cmp(len(c1),len(c2)) 
234      for i in range(len(c1)): 
235        t = c1[i].Compare(c2[i],ignoreExtras=ignoreExtras) 
236        if t: 
237          return t 
238         
239      return 0 
240   
241 -  def _UpdateLength(self): 
242      """ updates our length 
243   
244       *intended for internal use* 
245        
246      """ 
247      self._len = reduce(lambda x,y: len(y)+x,self.children,1)   
248   
249 -  def IsTerminal(self): 
250      return self._len<=1 
251   
252 -  def __len__(self): 
253      """ allows _len(cluster)_ to work 
254   
255      """ 
256      return self._len 
257   
258 -  def __cmp__(self,other): 
259      """ allows _cluster1 == cluster2_ to work 
260   
261      """ 
262      if cmp(type(self),type(other)): 
263        return cmp(type(self),type(other)) 
264   
265      m1,m2=self.GetMetric(),other.GetMetric() 
266      if abs(m1-m2)>CMPTOL: 
267        return cmp(m1,m2) 
268       
269      if cmp(self.GetName(),other.GetName()): 
270        return cmp(self.GetName(),other.GetName()) 
271   
272      c1,c2=self.GetChildren(),other.GetChildren() 
273      return cmp(c1,c2) 
274       
275   
276  if __name__ == '__main__': 
277      from rdkit.ML.Cluster import ClusterUtils 
278      root = Cluster(index=1,metric=1000) 
279      c1 = Cluster(index=10,metric=100) 
280      c1.AddChild(Cluster(index=30,metric=10)) 
281      c1.AddChild(Cluster(index=31,metric=10)) 
282      c1.AddChild(Cluster(index=32,metric=10)) 
283       
284      c2 = Cluster(index=11,metric=100) 
285      c2.AddChild(Cluster(index=40,metric=10)) 
286      c2.AddChild(Cluster(index=41,metric=10)) 
287   
288      root.AddChild(c1) 
289      root.AddChild(c2) 
290   
291      nodes = ClusterUtils.GetNodeList(root) 
292   
293      indices = [x.GetIndex() for x in nodes] 
294      print 'XXX:',indices 
295