rdkit.ML.Cluster.Clusters

Package rdkit :: Package ML :: Package Cluster :: Module Clusters |
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# Source Code for Module rdkit.ML.Cluster.Clusters

      1  # $Id$
      2  #
      3  # Copyright (C) 2001-2008  greg Landrum
      4  #
      5  #   @@ All Rights Reserved @@
      6  #  This file is part of the RDKit.
      7  #  The contents are covered by the terms of the BSD license
      8  #  which is included in the file license.txt, found at the root
      9  #  of the RDKit source tree.
     10  #
     11  """ contains the Cluster class for representing hierarchical cluster trees
     12
     13  """
     14  from __future__ import print_function
     15  import numpy
     16
     17  from rdkit.six.moves import reduce
     18  from rdkit.six import cmp
     19
     20  CMPTOL=1e-6
     21
     22 -class Cluster(object):
     23    """a class for storing clusters/data
     24
     25      **General Remarks**
     26
     27       - It is assumed that the bottom of any cluster hierarchy tree is composed of
     28         the individual data points which were clustered.
     29
     30       - Clusters objects store the following pieces of data, most are
     31          accessible via standard Setters/Getters:
     32
     33         - Children: *Not Settable*, the list of children.  You can add children
     34           with the _AddChild()_ and _AddChildren()_ methods.
     35
     36           **Note** this can be of arbitrary length,
     37           but the current algorithms I have only produce trees with two children
     38           per cluster
     39
     40         - Metric: the metric for this cluster (i.e. how far apart its children are)
     41
     42         - Index: the order in which this cluster was generated
     43
     44         - Points: *Not Settable*, the list of original points in this cluster
     45              (calculated recursively from the children)
     46
     47         - PointsPositions: *Not Settable*, the list of positions of the original
     48            points in this cluster (calculated recursively from the children)
     49
     50         - Position: the location of the cluster **Note** for a cluster this
     51           probably means the location of the average of all the Points which are
     52           its children.
     53
     54         - Data: a data field.  This is used with the original points to store their
     55           data value (i.e. the value we're using to classify)
     56
     57         - Name: the name of this cluster
     58
     59    """
     60 -  def __init__(self,metric=0.0,children=None,position=None,index=-1,name=None,data=None):
     61      """Constructor
     62
     63        **Arguments**
     64
     65          see the class documentation for the meanings of these arguments
     66
     67          *my wrists are tired*
     68
     69      """
     70      if children is None:
     71        children = []
     72      if position is None:
     73        position = []
     74      self.metric = metric
     75      self.children = children
     76      self._UpdateLength()
     77      self.pos = position
     78      self.index = index
     79      self.name = name
     80      self._points = None
     81      self._pointsPositions = None
     82      self.data = data
     83
     84 -  def SetMetric(self,metric):
     85      self.metric = metric
     86 -  def GetMetric(self):
     87      return self.metric
     88
     89 -  def SetIndex(self,index):
     90      self.index = index
     91 -  def GetIndex(self):
     92      return self.index
     93
     94 -  def SetPosition(self,pos):
     95      self.pos = pos
     96 -  def GetPosition(self):
     97      return self.pos
     98
     99 -  def GetPointsPositions(self):
    100      if self._pointsPositions is not None:
    101        return self._pointsPositions
    102      else:
    103        self._GenPoints()
    104        return self._pointsPositions
    105
    106 -  def GetPoints(self):
    107      if self._points is not None:
    108        return self._points
    109      else:
    110        self._GenPoints()
    111        return self._points
    112
    113 -  def FindSubtree(self,index):
    114      """ finds and returns the subtree with a particular index
    115      """
    116      res = None
    117      if index == self.index:
    118        res = self
    119      else:
    120        for child in self.children:
    121          res = child.FindSubtree(index)
    122          if res:
    123            break
    124      return res
    125
    126 -  def _GenPoints(self):
    127      """ Generates the _Points_ and _PointsPositions_ lists
    128
    129       *intended for internal use*
    130
    131      """
    132      if len(self) == 1:
    133        self._points = [self]
    134        self._pointsPositions = [self.GetPosition()]
    135        return self._points
    136      else:
    137        res = []
    138        children = self.GetChildren()
    139        # children.sort(lambda x,y:cmp(len(y),len(x)))
    140        children.sort(key=lambda x:len(x), reverse=True)
    141        for child in children:
    142          res += child.GetPoints()
    143        self._points=res
    144        self._pointsPositions = [x.GetPosition() for x in res]
    145
    146 -  def AddChild(self,child):
    147      """Adds a child to our list
    148
    149        **Arguments**
    150
    151          - child: a Cluster
    152
    153      """
    154      self.children.append(child)
    155      self._GenPoints()
    156      self._UpdateLength()
    157 -  def AddChildren(self,children):
    158      """Adds a bunch of children to our list
    159
    160        **Arguments**
    161
    162          - children: a list of Clusters
    163
    164      """
    165      self.children += children
    166      self._GenPoints()
    167      self._UpdateLength()
    168 -  def RemoveChild(self,child):
    169      """Removes a child from our list
    170
    171        **Arguments**
    172
    173          - child: a Cluster
    174
    175      """
    176      self.children.remove(child)
    177      self._UpdateLength()
    178
    179 -  def GetChildren(self):
    180      #self.children.sort(lambda x,y:cmp(x.GetMetric(),y.GetMetric()))
    181      self.children.sort(key=lambda x:x.GetMetric())
    182      return self.children
    183
    184 -  def SetData(self,data):
    185      self.data = data
    186 -  def GetData(self):
    187      return self.data
    188
    189 -  def SetName(self,name):
    190      self.name = name
    191 -  def GetName(self):
    192      if self.name is None:
    193        return 'Cluster(%d)'%(self.GetIndex())
    194      else:
    195        return self.name
    196
    197 -  def Print(self,level=0,showData=0,offset='\t'):
    198      if not showData or self.GetData() is None:
    199        print('%s%s%s Metric: %f'%('  '*level,self.GetName(),offset,self.GetMetric()))
    200      else:
    201        print('%s%s%s Data: %f\t Metric: %f'%('  '*level,self.GetName(),offset,self.GetData(),self.GetMetric()))
    202
    203      for child in self.GetChildren():
    204        child.Print(level=level+1,showData=showData,offset=offset)
    205
    206 -  def Compare(self,other,ignoreExtras=1):
    207      """ not as choosy as self==other
    208
    209      """
    210      tv1,tv2 = str(type(self)),str(type(other))
    211      tv = cmp(tv1,tv2)
    212      if tv:
    213        return tv
    214      tv1,tv2 = len(self),len(other)
    215      tv = cmp(tv1,tv2)
    216      if tv:
    217        return tv
    218
    219      if not ignoreExtras:
    220        m1,m2=self.GetMetric(),other.GetMetric()
    221        if abs(m1-m2)>CMPTOL:
    222          return cmp(m1,m2)
    223
    224        if cmp(self.GetName(),other.GetName()):
    225          return cmp(self.GetName(),other.GetName())
    226
    227        sP = self.GetPosition()
    228        oP = other.GetPosition()
    229        try:
    230          r = cmp(len(sP),len(oP))
    231        except Exception:
    232          pass
    233        else:
    234          if r:
    235            return r
    236
    237        try:
    238          r = cmp(sP,oP)
    239        except Exception:
    240          r = sum(sP-oP)
    241        if r:
    242          return r
    243
    244      c1,c2=self.GetChildren(),other.GetChildren()
    245      if cmp(len(c1),len(c2)):
    246        return cmp(len(c1),len(c2))
    247      for i in range(len(c1)):
    248        t = c1[i].Compare(c2[i],ignoreExtras=ignoreExtras)
    249        if t:
    250          return t
    251
    252      return 0
    253
    254 -  def _UpdateLength(self):
    255      """ updates our length
    256
    257       *intended for internal use*
    258
    259      """
    260      self._len = reduce(lambda x,y: len(y)+x,self.children,1)
    261
    262 -  def IsTerminal(self):
    263      return self._len<=1
    264
    265 -  def __len__(self):
    266      """ allows _len(cluster)_ to work
    267
    268      """
    269      return self._len
    270
    271 -  def __cmp__(self,other):
    272      """ allows _cluster1 == cluster2_ to work
    273
    274      """
    275      if cmp(type(self),type(other)):
    276        return cmp(type(self),type(other))
    277
    278      m1,m2=self.GetMetric(),other.GetMetric()
    279      if abs(m1-m2)>CMPTOL:
    280        return cmp(m1,m2)
    281
    282      if cmp(self.GetName(),other.GetName()):
    283        return cmp(self.GetName(),other.GetName())
    284
    285      c1,c2=self.GetChildren(),other.GetChildren()
    286      return cmp(c1,c2)
    287
    288
    289  if __name__ == '__main__':
    290      from rdkit.ML.Cluster import ClusterUtils
    291      root = Cluster(index=1,metric=1000)
    292      c1 = Cluster(index=10,metric=100)
    293      c1.AddChild(Cluster(index=30,metric=10))
    294      c1.AddChild(Cluster(index=31,metric=10))
    295      c1.AddChild(Cluster(index=32,metric=10))
    296
    297      c2 = Cluster(index=11,metric=100)
    298      c2.AddChild(Cluster(index=40,metric=10))
    299      c2.AddChild(Cluster(index=41,metric=10))
    300
    301      root.AddChild(c1)
    302      root.AddChild(c2)
    303
    304      nodes = ClusterUtils.GetNodeList(root)
    305
    306      indices = [x.GetIndex() for x in nodes]
    307      print('XXX:',indices)
    308