rdkit.ML.Cluster.ClusterUtils

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

      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  """utility functions for clustering
     12
     13  """
     14
     15 -def GetNodeList(cluster):
     16    """returns an ordered list of all nodes below cluster
     17
     18    the ordering is done using the lengths of the child nodes
     19
     20     **Arguments**
     21
     22       - cluster: the cluster in question
     23
     24     **Returns**
     25
     26       - a list of the leaves below this cluster
     27
     28    """
     29    if len(cluster) == 1:
     30      return [cluster]
     31    else:
     32      children = cluster.GetChildren()
     33      children.sort(key=lambda x:len(x), reverse=True)
     34      res = []
     35      for child in children:
     36        res += GetNodeList(child)
     37      res += [cluster]
     38      return res
     39
     40 -def GetNodesDownToCentroids(cluster,above=1):
     41    """returns an ordered list of all nodes below cluster
     42
     43
     44    """
     45    if hasattr(cluster,'_isCentroid'):
     46      cluster._aboveCentroid = 0
     47      above = -1
     48    else:
     49      cluster._aboveCentroid = above
     50    if len(cluster) == 1:
     51      return [cluster]
     52    else:
     53      res = []
     54      children = cluster.GetChildren()
     55      children.sort(lambda x,y:cmp(len(y),len(x)))
     56      for child in children:
     57        res = res + GetNodesDownToCentroids(child,above)
     58      res = res + [cluster]
     59      return res
     60
     61 -def FindClusterCentroidFromDists(cluster,dists):
     62    """ find the point in a cluster which has the smallest summed
     63       Euclidean distance to all others
     64
     65     **Arguments**
     66
     67       - cluster: the cluster to work with
     68
     69       - dists: the distance matrix to use for the points
     70
     71     **Returns**
     72
     73       - the index of the centroid point
     74
     75    """
     76    children = cluster.GetPoints()
     77    pts = [x.GetData() for x in children]
     78
     79    best = 1e24
     80    bestIdx = -1
     81    for pt in pts:
     82      dAccum = 0.0
     83      # loop over others and add'em up
     84      for other in pts:
     85        if other != pt:
     86          if other > pt: row,col = pt,other
     87          else: row,col = other,pt
     88          dAccum += dists[col*(col-1)/2+row]
     89          if dAccum >= best:
     90            # minor efficiency hack
     91            break
     92      if dAccum < best:
     93        best = dAccum
     94        bestIdx = pt
     95    for i in range(len(pts)):
     96      pt = pts[i]
     97      if pt != bestIdx:
     98        if pt > bestIdx: row,col = bestIdx,pt
     99        else: row,col = pt,bestIdx
    100        children[i]._distToCenter = dists[col*(col-1)/2+row]
    101      else:
    102        children[i]._distToCenter = 0.0
    103      children[i]._clustCenter = bestIdx
    104    cluster._clustCenter=bestIdx
    105    cluster._distToCenter=0.0
    106
    107    return bestIdx
    108
    109 -def _BreadthFirstSplit(cluster,n):
    110    """  *Internal Use Only*
    111
    112    """
    113    if len(cluster)<n:
    114      raise ValueError('Cannot split cluster of length %d into %d pieces'%(len(cluster),n))
    115    if len(cluster)==n:
    116      return cluster.GetPoints()
    117    clusters = [cluster]
    118    nxtIdx = 0
    119    for i in range(n-1):
    120      while nxtIdx<len(clusters) and len(clusters[nxtIdx])==1:
    121        nxtIdx+=1
    122      assert nxtIdx<len(clusters)
    123
    124      children = clusters[nxtIdx].GetChildren()
    125      children.sort(key=lambda x: x.GetMetric(), reverse=True)
    126      for child in children:
    127        clusters.append(child)
    128      del clusters[nxtIdx]
    129    return clusters
    130
    131 -def _HeightFirstSplit(cluster,n):
    132    """  *Internal Use Only*
    133
    134    """
    135    if len(cluster)<n:
    136      raise ValueError('Cannot split cluster of length %d into %d pieces'%(len(cluster),n))
    137    if len(cluster)==n:
    138      return cluster.GetPoints()
    139    clusters = [cluster]
    140    for i in range(n-1):
    141      nxtIdx = 0
    142      while nxtIdx<len(clusters) and len(clusters[nxtIdx])==1:
    143        nxtIdx+=1
    144      assert nxtIdx<len(clusters)
    145
    146      children = clusters[nxtIdx].GetChildren()
    147      for child in children:
    148        clusters.append(child)
    149      del clusters[nxtIdx]
    150      clusters.sort(key=lambda x: x.GetMetric(), reverse=True)
    151    return clusters
    152
    153
    154 -def SplitIntoNClusters(cluster,n,breadthFirst=1):
    155    """  splits a cluster tree into a set of branches
    156
    157      **Arguments**
    158
    159        - cluster: the root of the cluster tree
    160
    161        - n: the number of clusters to include in the split
    162
    163        - breadthFirst: toggles breadth first (vs depth first) cleavage
    164          of the cluster tree.
    165
    166      **Returns**
    167
    168        - a list of sub clusters
    169
    170    """
    171    if breadthFirst:
    172      return _BreadthFirstSplit(cluster,n)
    173    else:
    174      return _HeightFirstSplit(cluster,n)
    175