Package rdkit :: Package ML :: Module files

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# Source Code for Module rdkit.ML.files

      1  # copyright 2000 greg landrum
      2
      3  """ Generic file manipulation stuff
      4
      5  """
      6  from __future__ import print_function
      7  import numpy
      8  import string,re
      9
     10 -class ReFile:
     11    """convenience class for dealing with files with comments
     12
     13    blank (all whitespace) lines, and lines beginning with comment
     14      characters are skipped.
     15
     16    anything following a comment character on a line is stripped off
     17    """
     18 -  def readline(self):
     19      """ read the next line and return it.
     20
     21      return '' on EOF
     22
     23      """
     24      result = ''
     25      while result == '':
     26        inLine = self.inFile.readline()
     27        if inLine == '':
     28          return ''
     29        result = string.strip(self.regExp.split(inLine)[0])
     30      return result
     31
     32 -  def readlines(self):
     33      """ return a list of all the lines left in the file
     34
     35      return [] if there are none
     36
     37      """
     38      res = []
     39      inLines = self.inFile.readlines()
     40      for line in inLines:
     41        result = string.strip(self.regExp.split(line)[0])
     42        if result != '':
     43          res.append(result)
     44
     45      return res
     46
     47 -  def rewind(self):
     48      """ rewinds the file (seeks to the beginning)
     49
     50      """
     51      self.inFile.seek(0)
     52
     53 -  def __init__(self,fileName,mode='r',comment=r'#',trailer=r'\n'):
     54      if trailer is not None and trailer != '':
     55        comment = comment + r'|' + trailer
     56      self.regExp = re.compile(comment)
     57      self.inFile = open(fileName,mode)
     58
     59
     60 -def ReadDataFile(fileName,comment=r'#',depVarCol=0,dataType=numpy.float):
     61    """ read in the data file and return a tuple of two Numeric arrays:
     62    (independant variables, dependant variables).
     63
     64    **ARGUMENTS:**
     65
     66    - fileName: the fileName
     67
     68    - comment: the comment character for the file
     69
     70    - depVarcol: the column number containing the dependant variable
     71
     72    - dataType: the Numeric short-hand for the data type
     73
     74    RETURNS:
     75
     76     a tuple of two Numeric arrays:
     77
     78      (independant variables, dependant variables).
     79
     80    """
     81    inFile = ReFile(fileName)
     82    dataLines = inFile.readlines()
     83    nPts = len(dataLines)
     84
     85    if dataType in [numpy.float, numpy.float32, numpy.float64]:
     86      _convfunc = float
     87    else:
     88      _convfunc = int
     89
     90    nIndVars = len(string.split(dataLines[0]))-1
     91    indVarMat = numpy.zeros((nPts,nIndVars),dataType)
     92    depVarVect = numpy.zeros(nPts,dataType)
     93    for i in range(nPts):
     94      splitLine = string.split(dataLines[i])
     95      depVarVect[i] = _convfunc(splitLine[depVarCol])
     96      del splitLine[depVarCol]
     97      indVarMat[i,:] = map(_convfunc,splitLine)
     98
     99    return indVarMat,depVarVect
    100
    101
    102  if __name__ == '__main__':
    103    import sys
    104
    105    fileN = sys.argv[1]
    106    iV,dV = ReadDataFile(fileN)
    107    print('iV:', iV)
    108    print('dV:', dV)
    109