rdkit/Python/DataStructs/VectCollection.py

# $Id$
#
#  Copyright (C) 2005-2006 greg landrum and Rational Discovery LLC
#
#   @@ All Rights Reserved  @@
#
import DataStructs
import copy,struct,cPickle

class VectCollection(object):
  """

  >>> vc = VectCollection()
  >>> bv1 = DataStructs.ExplicitBitVect(10)
  >>> bv1.SetBitsFromList((1,3,5))
  >>> vc.AddVect(1,bv1)
  >>> bv1 = DataStructs.ExplicitBitVect(10)
  >>> bv1.SetBitsFromList((6,8))
  >>> vc.AddVect(2,bv1)
  >>> len(vc)
  10
  >>> vc.GetNumBits()
  10
  >>> vc[0]
  0
  >>> vc[1]
  1
  >>> vc[9]
  0
  >>> vc[6]
  1
  >>> vc.GetBit(6)
  1
  >>> list(vc.GetOnBits())
  [1, 3, 5, 6, 8]
  
  keys must be unique, so adding a duplicate replaces the
  previous values:
  >>> bv1 = DataStructs.ExplicitBitVect(10)
  >>> bv1.SetBitsFromList((7,9))
  >>> vc.AddVect(1,bv1)
  >>> len(vc)
  10
  >>> vc[1]
  0
  >>> vc[9]
  1
  >>> vc[6]
  1

  we can also query the children:
  >>> vc.NumChildren()
  2
  >>> cs = vc.GetChildren()
  >>> id,fp = cs[0]
  >>> id
  1
  >>> list(fp.GetOnBits())
  [7, 9]
  >>> id,fp = cs[1]
  >>> id
  2
  >>> list(fp.GetOnBits())
  [6, 8]

  attach/detach operations:
  >>> bv1 = DataStructs.ExplicitBitVect(10)
  >>> bv1.SetBitsFromList((5,6))
  >>> vc.AddVect(3,bv1)
  >>> vc.NumChildren()
  3
  >>> list(vc.GetOnBits())
  [5, 6, 7, 8, 9]
  >>> vc.DetachVectsNotMatchingBit(6)
  >>> vc.NumChildren()
  2
  >>> list(vc.GetOnBits())
  [5, 6, 8]
  

  >>> bv1 = DataStructs.ExplicitBitVect(10)
  >>> bv1.SetBitsFromList((7,9))
  >>> vc.AddVect(1,bv1)
  >>> vc.NumChildren()
  3
  >>> list(vc.GetOnBits())
  [5, 6, 7, 8, 9]
  >>> vc.DetachVectsMatchingBit(6)
  >>> vc.NumChildren()
  1
  >>> list(vc.GetOnBits())
  [7, 9]


  to copy VectCollections, use the copy module:
  >>> bv1 = DataStructs.ExplicitBitVect(10)
  >>> bv1.SetBitsFromList((5,6))
  >>> vc.AddVect(3,bv1)
  >>> list(vc.GetOnBits())
  [5, 6, 7, 9]
  >>> vc2 = copy.copy(vc)
  >>> vc.DetachVectsNotMatchingBit(6)
  >>> list(vc.GetOnBits())
  [5, 6]
  >>> list(vc2.GetOnBits())
  [5, 6, 7, 9]
  
  The Uniquify() method can be used to remove duplicate vectors:
  >>> vc = VectCollection()
  >>> bv1 = DataStructs.ExplicitBitVect(10)
  >>> bv1.SetBitsFromList((7,9))
  >>> vc.AddVect(1,bv1)
  >>> vc.AddVect(2,bv1)
  >>> bv1 = DataStructs.ExplicitBitVect(10)
  >>> bv1.SetBitsFromList((2,3,5))
  >>> vc.AddVect(3,bv1)
  >>> vc.NumChildren()
  3
  >>> vc.Uniquify()
  >>> vc.NumChildren()
  2
  

  
  """
  def __init__(self):
    self.__vects = {}
    self.__orVect = None
    self.__numBits = -1
    self.__needReset=True


  def GetOrVect(self):
    if self.__needReset:
      self.Reset()
    return self.__orVect
  orVect = property(GetOrVect)
   
  def AddVect(self,id,vect):
    self.__vects[id]=vect
    self.__needReset=True

  def Reset(self):
    if not self.__needReset:
      return
    self.__orVect=None
    if not self.__vects:
      return
    ks = self.__vects.keys()
    self.__orVect = copy.copy(self.__vects[ks[0]])
    self.__numBits = self.__orVect.GetNumBits()
    for i in range(1,len(ks)):
      self.__orVect |= self.__vects[ks[i]]
    self.__needReset=False

  def NumChildren(self):
    return len(self.__vects.keys())

  def GetChildren(self):
    return tuple(self.__vects.iteritems())

  def GetBit(self,id):
    if self.__needReset:
      self.Reset()
    return self[id]
  def GetNumBits(self):
    return len(self)
  
  def GetOnBits(self):
    if self.__needReset:
      self.Reset()
    return self.__orVect.GetOnBits()

  def DetachVectsNotMatchingBit(self,bit):
    items = list(self.__vects.iteritems())
    for k,v in items:
      if not v.GetBit(bit):
        del(self.__vects[k])
        self.__needReset=True

  def DetachVectsMatchingBit(self,bit):
    items = list(self.__vects.iteritems())
    for k,v in items:
      if v.GetBit(bit):
        del(self.__vects[k])
        self.__needReset=True

  def Uniquify(self,verbose=False):
    obls = {}
    for k,v in self.__vects.iteritems():
      obls[k] = list(v.GetOnBits())
    
    keys = self.__vects.keys()
    nKeys = len(keys)
    keep = self.__vects.keys()
    for i in range(nKeys):
      k1 = keys[i]
      if k1 in keep:
        obl1 = obls[k1]
        idx = keys.index(k1)
        for j in range(idx+1,nKeys):
          k2 = keys[j]
          if k2 in keep:
            obl2 = obls[k2]
            if obl1==obl2:
              keep.remove(k2)

    self.__needsReset=True
    tmp = {}
    for k in keep:
      tmp[k] = self.__vects[k]
    if verbose: print 'uniquify:',len(self.__vects),'->',len(tmp)
    self.__vects=tmp
      

  def __len__(self):
    if self.__needReset:
      self.Reset()
    return self.__numBits
  def __getitem__(self,id):
    if self.__needReset:
      self.Reset()
    return self.__orVect.GetBit(id)

  # 
  # set up our support for pickling:
  #
  def __getstate__(self):
    pkl = struct.pack('I',len(self.__vects))
    for k,v in self.__vects.iteritems():
      pkl += struct.pack('I',k)
      p = v.ToBinary()
      l = len(p)
      pkl += struct.pack('I%ds'%(l),l,p)
    return pkl

  def __setstate__(self,pkl):
    self.__vects = {}
    self.__orVect = None
    self.__numBits = -1
    self.__needReset=True
    szI = struct.calcsize('I')
    offset = 0
    nToRead = struct.unpack('I',pkl[offset:offset+szI])[0]
    offset += szI
    for i in range(nToRead):
      k = struct.unpack('I',pkl[offset:offset+szI])[0]
      offset += szI
      l = struct.unpack('I',pkl[offset:offset+szI])[0]
      offset += szI
      sz = struct.calcsize('%ds'%l)
      bv = DataStructs.ExplicitBitVect(struct.unpack('%ds'%l,pkl[offset:offset+sz])[0])
      offset += sz
      self.AddVect(k,bv)
    


#------------------------------------
#
#  doctest boilerplate
#
def _test():
  import doctest,sys
  return doctest.testmod(sys.modules["__main__"])


if __name__ == '__main__':
  import sys
  failed,tried = _test()
  sys.exit(failed)