示例#1
0
  def test1(self):
    " testing first 200 mols from NCI "
    suppl = Chem.SDMolSupplier(self.inFileName)
    idx = 1
    oldDonorSmarts = Chem.MolFromSmarts('[NH1,NH2,OH1]')
    OldDonorCount = lambda x,y=oldDonorSmarts:Lipinski._NumMatches(x,y)
    oldAcceptorSmarts = Chem.MolFromSmarts('[N,O]')
    OldAcceptorCount = lambda x,y=oldAcceptorSmarts:Lipinski._NumMatches(x,y)
    for m in suppl:
      if m:
        calc = Lipinski.NHOHCount(m)
        orig = int(m.GetProp('NUM_LIPINSKIHDONORS'))
        assert calc==orig,'bad num h donors for mol %d (%s): %d != %d'%(idx,m.GetProp('SMILES'),calc,orig)

        calc = Lipinski.NOCount(m)
        orig = int(m.GetProp('NUM_LIPINSKIHACCEPTORS'))
        assert calc==orig,'bad num h acceptors for mol %d (%s): %d != %d'%(idx,m.GetProp('SMILES'),calc,orig)

        calc = Lipinski.NumHDonors(m)
        orig = int(m.GetProp('NUM_HDONORS'))
        assert calc==orig,'bad num h donors for mol %d (%s): %d != %d'%(idx,m.GetProp('SMILES'),calc,orig)

        calc = Lipinski.NumHAcceptors(m)
        orig = int(m.GetProp('NUM_HACCEPTORS'))
        assert calc==orig,'bad num h acceptors for mol %d (%s): %d != %d'%(idx,m.GetProp('SMILES'),calc,orig)

        calc = Lipinski.NumHeteroatoms(m)
        orig = int(m.GetProp('NUM_HETEROATOMS'))
        assert calc==orig,'bad num heteroatoms for mol %d (%s): %d != %d'%(idx,m.GetProp('SMILES'),calc,orig)

        calc = Lipinski.NumRotatableBonds(m)
        orig = int(m.GetProp('NUM_ROTATABLEBONDS'))
        assert calc==orig,'bad num rotors for mol %d (%s): %d != %d'%(idx,m.GetProp('SMILES'),calc,orig)
      idx += 1
示例#2
0
  def test1(self):
    " testing first 200 mols from NCI "
    # figure out which rotor version we are using
    m = Chem.MolFromSmiles("CC(C)(C)c1cc(O)c(cc1O)C(C)(C)C")
    if Lipinski.NumRotatableBonds(m) == 2:
      rot_prop = NonStrict
    else:
      rot_prop = Strict
    
    suppl = Chem.SDMolSupplier(self.inFileName)
    idx = 1
    oldDonorSmarts = Chem.MolFromSmarts('[NH1,NH2,OH1]')
    OldDonorCount = lambda x,y=oldDonorSmarts:Lipinski._NumMatches(x,y)
    oldAcceptorSmarts = Chem.MolFromSmarts('[N,O]')
    OldAcceptorCount = lambda x,y=oldAcceptorSmarts:Lipinski._NumMatches(x,y)
    for m in suppl:
      if m:
        calc = Lipinski.NHOHCount(m)
        orig = int(m.GetProp('NUM_LIPINSKIHDONORS'))
        assert calc==orig,'bad num h donors for mol %d (%s): %d != %d'%(idx,m.GetProp('SMILES'),calc,orig)

        calc = Lipinski.NOCount(m)
        orig = int(m.GetProp('NUM_LIPINSKIHACCEPTORS'))
        assert calc==orig,'bad num h acceptors for mol %d (%s): %d != %d'%(idx,m.GetProp('SMILES'),calc,orig)

        calc = Lipinski.NumHDonors(m)
        orig = int(m.GetProp('NUM_HDONORS'))
        assert calc==orig,'bad num h donors for mol %d (%s): %d != %d'%(idx,m.GetProp('SMILES'),calc,orig)

        calc = Lipinski.NumHAcceptors(m)
        orig = int(m.GetProp('NUM_HACCEPTORS'))
        assert calc==orig,'bad num h acceptors for mol %d (%s): %d != %d'%(idx,m.GetProp('SMILES'),calc,orig)

        calc = Lipinski.NumHeteroatoms(m)
        orig = int(m.GetProp('NUM_HETEROATOMS'))
        assert calc==orig,'bad num heteroatoms for mol %d (%s): %d != %d'%(idx,m.GetProp('SMILES'),calc,orig)

        calc = Lipinski.NumRotatableBonds(m)
        orig = int(m.GetProp(rot_prop))
        assert calc==orig,'bad num rotors for mol %d (%s): %d != %d'%(idx,m.GetProp('SMILES'),calc,orig)

        # test the underlying numrotatable bonds
        calc = rdMolDescriptors.CalcNumRotatableBonds(m, rdMolDescriptors.NumRotatableBondsOptions.NonStrict)
        orig = int(m.GetProp(NonStrict))
        assert calc==orig,'bad num rotors for mol %d (%s): %d != %d'%(idx,m.GetProp('SMILES'),calc,orig)
        
        calc = rdMolDescriptors.CalcNumRotatableBonds(m, rdMolDescriptors.NumRotatableBondsOptions.Strict)
        orig = int(m.GetProp(Strict))
        assert calc==orig,'bad num rotors for mol %d (%s): %d != %d'%(idx,m.GetProp('SMILES'),calc,orig)
        
      idx += 1
示例#3
0
    def test1(self):
        " testing first 200 mols from NCI "
        suppl = Chem.SDMolSupplier(self.inFileName)
        idx = 1
        oldDonorSmarts = Chem.MolFromSmarts('[NH1,NH2,OH1]')
        OldDonorCount = lambda x, y=oldDonorSmarts: Lipinski._NumMatches(x, y)
        oldAcceptorSmarts = Chem.MolFromSmarts('[N,O]')
        OldAcceptorCount = lambda x, y=oldAcceptorSmarts: Lipinski._NumMatches(
            x, y)
        for m in suppl:
            if m:
                calc = Lipinski.NHOHCount(m)
                orig = int(m.GetProp('NUM_LIPINSKIHDONORS'))
                assert calc == orig, 'bad num h donors for mol %d (%s): %d != %d' % (
                    idx, m.GetProp('SMILES'), calc, orig)

                calc = Lipinski.NOCount(m)
                orig = int(m.GetProp('NUM_LIPINSKIHACCEPTORS'))
                assert calc == orig, 'bad num h acceptors for mol %d (%s): %d != %d' % (
                    idx, m.GetProp('SMILES'), calc, orig)

                calc = Lipinski.NumHDonors(m)
                orig = int(m.GetProp('NUM_HDONORS'))
                assert calc == orig, 'bad num h donors for mol %d (%s): %d != %d' % (
                    idx, m.GetProp('SMILES'), calc, orig)

                calc = Lipinski.NumHAcceptors(m)
                orig = int(m.GetProp('NUM_HACCEPTORS'))
                assert calc == orig, 'bad num h acceptors for mol %d (%s): %d != %d' % (
                    idx, m.GetProp('SMILES'), calc, orig)

                calc = Lipinski.NumHeteroatoms(m)
                orig = int(m.GetProp('NUM_HETEROATOMS'))
                assert calc == orig, 'bad num heteroatoms for mol %d (%s): %d != %d' % (
                    idx, m.GetProp('SMILES'), calc, orig)

                calc = Lipinski.NumRotatableBonds(m)
                orig = int(m.GetProp('NUM_ROTATABLEBONDS'))
                assert calc == orig, 'bad num rotors for mol %d (%s): %d != %d' % (
                    idx, m.GetProp('SMILES'), calc, orig)
            idx += 1
示例#4
0
    def test1(self):
        " testing first 200 mols from NCI "
        # figure out which rotor version we are using
        m = Chem.MolFromSmiles("CC(C)(C)c1cc(O)c(cc1O)C(C)(C)C")
        if Lipinski.NumRotatableBonds(m) == 2:
            rot_prop = NonStrict
        else:
            rot_prop = Strict

        suppl = Chem.SDMolSupplier(self.inFileName)
        idx = 1
        oldDonorSmarts = Chem.MolFromSmarts('[NH1,NH2,OH1]')
        OldDonorCount = lambda x, y=oldDonorSmarts: Lipinski._NumMatches(x, y)
        oldAcceptorSmarts = Chem.MolFromSmarts('[N,O]')
        OldAcceptorCount = lambda x, y=oldAcceptorSmarts: Lipinski._NumMatches(
            x, y)
        for m in suppl:
            if m:
                calc = Lipinski.NHOHCount(m)
                orig = int(m.GetProp('NUM_LIPINSKIHDONORS'))
                assert calc == orig, 'bad num h donors for mol %d (%s): %d != %d' % (
                    idx, m.GetProp('SMILES'), calc, orig)

                calc = Lipinski.NOCount(m)
                orig = int(m.GetProp('NUM_LIPINSKIHACCEPTORS'))
                assert calc == orig, 'bad num h acceptors for mol %d (%s): %d != %d' % (
                    idx, m.GetProp('SMILES'), calc, orig)

                calc = Lipinski.NumHDonors(m)
                orig = int(m.GetProp('NUM_HDONORS'))
                assert calc == orig, 'bad num h donors for mol %d (%s): %d != %d' % (
                    idx, m.GetProp('SMILES'), calc, orig)

                calc = Lipinski.NumHAcceptors(m)
                orig = int(m.GetProp('NUM_HACCEPTORS'))
                assert calc == orig, 'bad num h acceptors for mol %d (%s): %d != %d' % (
                    idx, m.GetProp('SMILES'), calc, orig)

                calc = Lipinski.NumHeteroatoms(m)
                orig = int(m.GetProp('NUM_HETEROATOMS'))
                assert calc == orig, 'bad num heteroatoms for mol %d (%s): %d != %d' % (
                    idx, m.GetProp('SMILES'), calc, orig)

                calc = Lipinski.NumRotatableBonds(m)
                orig = int(m.GetProp(rot_prop))
                assert calc == orig, 'bad num rotors for mol %d (%s): %d != %d' % (
                    idx, m.GetProp('SMILES'), calc, orig)

                # test the underlying numrotatable bonds
                calc = rdMolDescriptors.CalcNumRotatableBonds(
                    m, rdMolDescriptors.NumRotatableBondsOptions.NonStrict)
                orig = int(m.GetProp(NonStrict))
                assert calc == orig, 'bad num rotors for mol %d (%s): %d != %d' % (
                    idx, m.GetProp('SMILES'), calc, orig)

                calc = rdMolDescriptors.CalcNumRotatableBonds(
                    m, rdMolDescriptors.NumRotatableBondsOptions.Strict)
                orig = int(m.GetProp(Strict))
                assert calc == orig, 'bad num rotors for mol %d (%s): %d != %d' % (
                    idx, m.GetProp('SMILES'), calc, orig)

            idx += 1