rdkit.ML.Cluster.Resemblance

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# Source Code for Module rdkit.ML.Cluster.Resemblance

      1  # $Id$
      2  #
      3  # Copyright (C) 2001-2006  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  """ code for dealing with resemblance (metric) matrices
     12
     13      Here's how the matrices are stored:
     14
     15       '[(0,1),(0,2),(1,2),(0,3),(1,3),(2,3)...]  (row,col), col>row'
     16
     17       or, alternatively the matrix can be drawn, with indices as:
     18
     19         || - || 0 || 1 || 3
     20         || - || - || 2 || 4
     21         || - || - || - || 5
     22         || - || - || - || -
     23
     24       the index of a given (row,col) pair is:
     25         '(col*(col-1))/2 + row'
     26
     27  """
     28  from __future__ import print_function
     29  import numpy
     30
     31
     32 -def EuclideanDistance(inData):
     33    """returns the euclidean metricMat between the points in _inData_
     34
     35      **Arguments**
     36
     37       - inData: a Numeric array of data points
     38
     39      **Returns**
     40
     41         a Numeric array with the metric matrix.  See the module documentation
     42         for the format.
     43
     44
     45    """
     46    nObjs = len(inData)
     47    res = numpy.zeros((nObjs*(nObjs-1)/2),numpy.float)
     48    nSoFar = 0
     49    for col in range(1,nObjs):
     50      for row in range(col):
     51        t = inData[row]-inData[col]
     52        res[nSoFar] = sum(t*t)
     53        nSoFar += 1
     54    return numpy.sqrt(res)
     55
     56 -def CalcMetricMatrix(inData,metricFunc):
     57    """ generates a metric matrix
     58
     59      **Arguments**
     60       - inData is assumed to be a list of clusters (or anything with
     61         a GetPosition() method)
     62
     63       - metricFunc is the function to be used to generate the matrix
     64
     65
     66      **Returns**
     67
     68        the metric matrix as a Numeric array
     69
     70    """
     71    nObjs = len(inData)
     72    res = []
     73    inData = map(lambda x:x.GetPosition(),inData)
     74    return metricFunc(inData)
     75
     76 -def FindMinValInList(mat,nObjs,minIdx=None):
     77    """ finds the minimum value in a metricMatrix and returns it and its indices
     78
     79      **Arguments**
     80
     81       - mat: the metric matrix
     82
     83       - nObjs: the number of objects to be considered
     84
     85       - minIdx: the index of the minimum value (value, row and column still need
     86         to be calculated
     87
     88      **Returns**
     89
     90        a 3-tuple containing:
     91
     92          1) the row
     93          2) the column
     94          3) the minimum value itself
     95
     96      **Notes**
     97
     98        -this probably ain't the speediest thing on earth
     99
    100    """
    101    assert len(mat) == nObjs*(nObjs-1)/2, 'bad matrix length in FindMinValInList'
    102    if minIdx is None:
    103      minIdx = numpy.argmin(mat)
    104
    105    nSoFar = 0
    106    col = 0
    107    while nSoFar <= minIdx:
    108      col = col + 1
    109      nSoFar += col
    110
    111    row = minIdx - nSoFar + col
    112    return row,col,mat[minIdx]
    113
    114 -def ShowMetricMat(metricMat,nObjs):
    115    """ displays a metric matrix
    116
    117     **Arguments**
    118
    119      - metricMat: the matrix to be displayed
    120
    121      - nObjs: the number of objects to display
    122
    123    """
    124    assert len(metricMat) == nObjs*(nObjs-1)/2, 'bad matrix length in FindMinValInList'
    125    for row in range(nObjs):
    126      for col in range(nObjs):
    127        if col <= row:
    128          print('   ---    ',end='')
    129        else:
    130          print('%10.6f'%metricMat[(col*(col-1))/2+row],end='')
    131      print()
    132
    133
    134
    135  methods = [
    136    ("Euclidean",EuclideanDistance,"Euclidean Distance"),
    137    ]
    138
    139
    140
    141  if __name__ == '__main__':
    142    m = [.1,.2,.3,.4,.5,.6,.7,.8,.9,1.0]
    143    nObjs = 5
    144    for i in range(10):
    145      print(i, FindMinValInList(m,nObjs,i))
    146