<filename>third_party_package/RDKit_2015_03_1/rdkit/Chem/Fingerprints/UnitTestFingerprints.py
# $Id$
#
#  Copyright (C) 2003-2006  <NAME> and Rational Discovery LLC
#
#   @@ All Rights Reserved @@
#  This file is part of the RDKit.
#  The contents are covered by the terms of the BSD license
#  which is included in the file license.txt, found at the root
#  of the RDKit source tree.
#
"""unit testing code for fingerprinting

"""
import unittest
from rdkit import Chem
from rdkit import DataStructs

def feq(v1,v2,tol=1e-4):
  return abs(v1-v2)<=tol


class TestCase(unittest.TestCase):
  def setUp(self):
    #print '\n%s: '%self.shortDescription(),
    pass

  def test1(self):
    # FIX: test HashAtom
    pass
  def test2(self):
    # FIX: test HashBond
    pass
  def test3(self):
    # FIX: test HashPath
    pass

  def test4(self):
    """ check containing mols, no Hs, no valence

    """
    tgts = [ ('CCC(O)C(=O)O',
              ('CCC','OCC','OCC=O','OCCO','CCCC','OC=O','CC(O)C')),
             ]
    for smi,matches in tgts:
      m = Chem.MolFromSmiles(smi)
      fp1 = Chem.RDKFingerprint(m,2,7,9192,4,0)
      obs = fp1.GetOnBits()
      for match in matches:
        m2 = Chem.MolFromSmiles(match)
        fp2 = Chem.RDKFingerprint(m2,2,7,9192,4,0)
        v1,v2 = DataStructs.OnBitProjSimilarity(fp2,fp1)
        assert feq(v1,1.0000),'substruct %s not properly contained in %s'%(match,smi)

  def test5(self):
    """ check containing mols, use Hs, no valence

    """
    tgts = [ ('CCC(O)C(=O)O',
              ('O[CH-][CH2-]','O[CH-][C-]=O')),
             ]
    for smi,matches in tgts:
      m = Chem.MolFromSmiles(smi)
      fp1 = Chem.RDKFingerprint(m,2,7,9192,4,1)
      obs = fp1.GetOnBits()
      for match in matches:
        m2 = Chem.MolFromSmiles(match)
        fp2 = Chem.RDKFingerprint(m2,2,7,9192,4,1)
        v1,v2 = DataStructs.OnBitProjSimilarity(fp2,fp1)
        assert feq(v1,1.0000),'substruct %s not properly contained in %s'%(match,smi)

  def test6(self):
    """ check that the bits in a signature of size N which has been folded in half
      are the same as those in a signature of size N/2

    """
    smis = [ 'CCC(O)C(=O)O','c1ccccc1','C1CCCCC1','C1NCCCC1','CNCNCNC']
    for smi in smis:
      m = Chem.MolFromSmiles(smi)
      fp1 = Chem.RDKFingerprint(m,2,7,4096)
      fp2 = DataStructs.FoldFingerprint(fp1,2)
      fp3 = Chem.RDKFingerprint(m,2,7,2048)
      assert tuple(fp2.GetOnBits())==tuple(fp3.GetOnBits())
      fp2 = DataStructs.FoldFingerprint(fp2,2)
      fp3 = Chem.RDKFingerprint(m,2,7,1024)
      assert tuple(fp2.GetOnBits())==tuple(fp3.GetOnBits())
      fp2 = DataStructs.FoldFingerprint(fp1,4)
      assert tuple(fp2.GetOnBits())==tuple(fp3.GetOnBits())
      
    

if __name__ == '__main__':
  unittest.main()


<filename>third_party_package/RDKit_2015_03_1/rdkit/Chem/Fingerprints/UnitTestFingerprints.py
# $Id$
#
#  Copyright (C) 2003-2006  <NAME> and Rational Discovery LLC
#
#   @@ All Rights Reserved @@
#  This file is part of the RDKit.
#  The contents are covered by the terms of the BSD license
#  which is included in the file license.txt, found at the root
#  of the RDKit source tree.
#
"""unit testing code for fingerprinting

"""
import unittest
from rdkit import Chem
from rdkit import DataStructs

def feq(v1,v2,tol=1e-4):
  return abs(v1-v2)<=tol


class TestCase(unittest.TestCase):
  def setUp(self):
    #print '\n%s: '%self.shortDescription(),
    pass

  def test1(self):
    # FIX: test HashAtom
    pass
  def test2(self):
    # FIX: test HashBond
    pass
  def test3(self):
    # FIX: test HashPath
    pass

  def test4(self):
    """ check containing mols, no Hs, no valence

    """
    tgts = [ ('CCC(O)C(=O)O',
              ('CCC','OCC','OCC=O','OCCO','CCCC','OC=O','CC(O)C')),
             ]
    for smi,matches in tgts:
      m = Chem.MolFromSmiles(smi)
      fp1 = Chem.RDKFingerprint(m,2,7,9192,4,0)
      obs = fp1.GetOnBits()
      for match in matches:
        m2 = Chem.MolFromSmiles(match)
        fp2 = Chem.RDKFingerprint(m2,2,7,9192,4,0)
        v1,v2 = DataStructs.OnBitProjSimilarity(fp2,fp1)
        assert feq(v1,1.0000),'substruct %s not properly contained in %s'%(match,smi)

  def test5(self):
    """ check containing mols, use Hs, no valence

    """
    tgts = [ ('CCC(O)C(=O)O',
              ('O[CH-][CH2-]','O[CH-][C-]=O')),
             ]
    for smi,matches in tgts:
      m = Chem.MolFromSmiles(smi)
      fp1 = Chem.RDKFingerprint(m,2,7,9192,4,1)
      obs = fp1.GetOnBits()
      for match in matches:
        m2 = Chem.MolFromSmiles(match)
        fp2 = Chem.RDKFingerprint(m2,2,7,9192,4,1)
        v1,v2 = DataStructs.OnBitProjSimilarity(fp2,fp1)
        assert feq(v1,1.0000),'substruct %s not properly contained in %s'%(match,smi)

  def test6(self):
    """ check that the bits in a signature of size N which has been folded in half
      are the same as those in a signature of size N/2

    """
    smis = [ 'CCC(O)C(=O)O','c1ccccc1','C1CCCCC1','C1NCCCC1','CNCNCNC']
    for smi in smis:
      m = Chem.MolFromSmiles(smi)
      fp1 = Chem.RDKFingerprint(m,2,7,4096)
      fp2 = DataStructs.FoldFingerprint(fp1,2)
      fp3 = Chem.RDKFingerprint(m,2,7,2048)
      assert tuple(fp2.GetOnBits())==tuple(fp3.GetOnBits())
      fp2 = DataStructs.FoldFingerprint(fp2,2)
      fp3 = Chem.RDKFingerprint(m,2,7,1024)
      assert tuple(fp2.GetOnBits())==tuple(fp3.GetOnBits())
      fp2 = DataStructs.FoldFingerprint(fp1,4)
      assert tuple(fp2.GetOnBits())==tuple(fp3.GetOnBits())
      
    

if __name__ == '__main__':
  unittest.main()


# $Id$ # #  Copyright (C) 2003-2006  <NAME> and Rational Discovery LLC # #   @@ All Rights Reserved @@ #  This file is part of the RDKit. #  The contents are covered by the terms of the BSD license #  which is included in the file license.txt, found at the root #  of the RDKit source tree. # unit testing code for fingerprinting #print '\n%s: '%self.shortDescription(), # FIX: test HashAtom # FIX: test HashBond # FIX: test HashPath check containing mols, no Hs, no valence check containing mols, use Hs, no valence check that the bits in a signature of size N which has been folded in half       are the same as those in a signature of size N/2