Python Chem.FragmentOnBonds方法代码示例

# 需要导入模块: from rdkit import Chem [as 别名]
# 或者: from rdkit.Chem import FragmentOnBonds [as 别名]
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 

# 需要导入模块: from rdkit import Chem [as 别名]
# 或者: from rdkit.Chem import FragmentOnBonds [as 别名]
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 

# 需要导入模块: from rdkit import Chem [as 别名]
# 或者: from rdkit.Chem import FragmentOnBonds [as 别名]
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 

# 需要导入模块: from rdkit import Chem [as 别名]
# 或者: from rdkit.Chem import FragmentOnBonds [as 别名]
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 

# 需要导入模块: from rdkit import Chem [as 别名]
# 或者: from rdkit.Chem import FragmentOnBonds [as 别名]
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 

# 需要导入模块: from rdkit import Chem [as 别名]
# 或者: from rdkit.Chem import FragmentOnBonds [as 别名]
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 

# 需要导入模块: from rdkit import Chem [as 别名]
# 或者: from rdkit.Chem import FragmentOnBonds [as 别名]
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))