Python rdkit.Chem.FragmentOnBonds() Examples

The following are 7 code examples of rdkit.Chem.FragmentOnBonds(). You can vote up the ones you like or vote down the ones you don't like, and go to the original project or source file by following the links above each example. You may also want to check out all available functions/classes of the module rdkit.Chem , or try the search function .
Example #1
Source File: crossover.py    From guacamol_baselines with MIT License 6 votes vote down vote up 
def cut(mol):
    if not mol.HasSubstructMatch(Chem.MolFromSmarts('[*]-;!@[*]')):
        return None

    bis = random.choice(mol.GetSubstructMatches(Chem.MolFromSmarts('[*]-;!@[*]')))  # single bond not in ring

    bs = [mol.GetBondBetweenAtoms(bis[0], bis[1]).GetIdx()]

    fragments_mol = Chem.FragmentOnBonds(mol, bs, addDummies=True, dummyLabels=[(1, 1)])

    try:
        return Chem.GetMolFrags(fragments_mol, asMols=True, sanitizeFrags=True)
    except ValueError:
        return None

    return None
Example #2
Source File: mol_utils.py    From DeepFMPO with MIT License 6 votes vote down vote up 
def spf(mol, split_id):

    bonds = mol.GetBonds()
    for i in range(len(bonds)):
        if okToBreak(bonds[i]):
            mol = Chem.FragmentOnBonds(mol, [i], addDummies=True, dummyLabels=[(0, 0)])
            # Dummy atoms are always added last
            n_at = mol.GetNumAtoms()
            mol.GetAtomWithIdx(n_at-1).SetAtomicNum(split_id)
            mol.GetAtomWithIdx(n_at-2).SetAtomicNum(split_id)
            return Chem.rdmolops.GetMolFrags(mol, asMols=True)

    # If the molecule could not been split, return original molecule
    return [mol]



# Build up a chain of fragments from a molecule.
# This is required so that a given list of fragments can be rebuilt into the same
#   molecule as was given when splitting the molecule
Example #3
Source File: mol_utils.py    From DeepFMPO with MIT License 6 votes vote down vote up 
def spf(mol, split_id):
    
    bonds = mol.GetBonds()
    for i in range(len(bonds)):
        if okToBreak(bonds[i]):
            mol = Chem.FragmentOnBonds(mol, [i], addDummies=True, dummyLabels=[(0, 0)])
            # Dummy atoms are always added last
            n_at = mol.GetNumAtoms()
            mol.GetAtomWithIdx(n_at-1).SetAtomicNum(split_id)
            mol.GetAtomWithIdx(n_at-2).SetAtomicNum(split_id)
            return Chem.rdmolops.GetMolFrags(mol, asMols=True)
     
    # If the molecule could not been split, return original molecule
    return [mol] 



# Build up a chain of fragments from a molecule.
# This is required so that a given list of fragments can be rebuilt into the same
#   molecule as was given when splitting the molecule
Example #4
Source File: crossover.py    From guacamol_baselines with MIT License 5 votes vote down vote up 
def cut_ring(mol):

    for i in range(10):
        if random.random() < 0.5:
            if not mol.HasSubstructMatch(Chem.MolFromSmarts('[R]@[R]@[R]@[R]')):
                return None
            bis = random.choice(mol.GetSubstructMatches(Chem.MolFromSmarts('[R]@[R]@[R]@[R]')))
            bis = ((bis[0], bis[1]), (bis[2], bis[3]),)
        else:
            if not mol.HasSubstructMatch(Chem.MolFromSmarts('[R]@[R;!D2]@[R]')):
                return None
            bis = random.choice(mol.GetSubstructMatches(Chem.MolFromSmarts('[R]@[R;!D2]@[R]')))
            bis = ((bis[0], bis[1]), (bis[1], bis[2]),)

        bs = [mol.GetBondBetweenAtoms(x, y).GetIdx() for x, y in bis]

        fragments_mol = Chem.FragmentOnBonds(mol, bs, addDummies=True, dummyLabels=[(1, 1), (1, 1)])

        try:
            fragments = Chem.GetMolFrags(fragments_mol, asMols=True, sanitizeFrags=True)
            if len(fragments) == 2:
                return fragments
        except ValueError:
            return None

    return None
Example #5
Source File: crossover.py    From GB-GA with MIT License 5 votes vote down vote up 
def cut(mol):
  if not mol.HasSubstructMatch(Chem.MolFromSmarts('[*]-;!@[*]')): 
  	return None
  bis = random.choice(mol.GetSubstructMatches(Chem.MolFromSmarts('[*]-;!@[*]'))) #single bond not in ring
  #print bis,bis[0],bis[1]
  bs = [mol.GetBondBetweenAtoms(bis[0],bis[1]).GetIdx()]

  fragments_mol = Chem.FragmentOnBonds(mol,bs,addDummies=True,dummyLabels=[(1, 1)])

  try:
    fragments = Chem.GetMolFrags(fragments_mol,asMols=True)
    return fragments
  except:
    return None
Example #6
Source File: crossover.py    From GB-GA with MIT License 5 votes vote down vote up 
def cut_ring(mol):
  for i in range(10):
    if random.random() < 0.5:
      if not mol.HasSubstructMatch(Chem.MolFromSmarts('[R]@[R]@[R]@[R]')): 
      	return None
      bis = random.choice(mol.GetSubstructMatches(Chem.MolFromSmarts('[R]@[R]@[R]@[R]')))
      bis = ((bis[0],bis[1]),(bis[2],bis[3]),)
    else:
      if not mol.HasSubstructMatch(Chem.MolFromSmarts('[R]@[R;!D2]@[R]')): 
      	return None
      bis = random.choice(mol.GetSubstructMatches(Chem.MolFromSmarts('[R]@[R;!D2]@[R]')))
      bis = ((bis[0],bis[1]),(bis[1],bis[2]),)
    
    #print bis
    bs = [mol.GetBondBetweenAtoms(x,y).GetIdx() for x,y in bis]

    fragments_mol = Chem.FragmentOnBonds(mol,bs,addDummies=True,dummyLabels=[(1, 1),(1,1)])

    try:
      fragments = Chem.GetMolFrags(fragments_mol,asMols=True)
    except:
      return None

    if len(fragments) == 2:
      return fragments
    
  return None
Example #7
Source File: scaffold.py    From reinvent-scaffold-decorator with MIT License 5 votes vote down vote up 
def enumerate(self, mol, cuts):
        """
        Enumerates all possible combination of slicings of a molecule given a number of cuts.
        :param mol: A mol object with the molecule to slice.
        :param cuts: The number of cuts to perform.
        :return : A list with all the possible (scaffold, decorations) pairs as SlicedMol objects.
        """
        matches = self._get_matches(mol)
        sliced_mols = set()
        for atom_pairs_to_cut in itertools.combinations(matches, cuts):
            to_cut_bonds = list(sorted(mol.GetBondBetweenAtoms(aidx, oaidx).GetIdx()
                                       for aidx, oaidx in atom_pairs_to_cut))
            attachment_point_idxs = [(i, i) for i in range(len(to_cut_bonds))]
            cut_mol = rkc.FragmentOnBonds(mol, bondIndices=to_cut_bonds, dummyLabels=attachment_point_idxs)
            for atom in cut_mol.GetAtoms():
                if atom.GetSymbol() == ATTACHMENT_POINT_TOKEN:
                    num = atom.GetIsotope()
                    atom.SetIsotope(0)
                    atom.SetProp("molAtomMapNumber", str(num))

            cut_mol.UpdatePropertyCache()
            fragments = rkc.GetMolFrags(cut_mol, asMols=True, sanitizeFrags=True)

            # detect whether there is one fragment with as many attachment points as cuts (scaffold)
            # the rest are decorations
            if cuts == 1:
                sliced_mols.add(SlicedMol(fragments[0], [fragments[1]]))
                sliced_mols.add(SlicedMol(fragments[1], [fragments[0]]))
            else:
                scaffold = None
                decorations = []
                for frag in fragments:
                    num_att = len([atom for atom in frag.GetAtoms() if atom.GetSymbol() == ATTACHMENT_POINT_TOKEN])
                    if num_att == cuts and not scaffold:
                        scaffold = frag
                    else:
                        decorations.append(frag)
                if scaffold:
                    sliced_mols.add(SlicedMol(scaffold, decorations))

        return list(filter(self._filter, sliced_mols))