Python Chem.CombineMols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 CombineMols [as 别名]
def normalize(self, mol):
        """Apply a series of Normalization transforms to correct functional groups and recombine charges.

        A series of transforms are applied to the molecule. For each Normalization, the transform is applied repeatedly
        until no further changes occur. If any changes occurred, we go back and start from the first Normalization
        again, in case the changes mean an earlier transform is now applicable. The molecule is returned once the entire
        series of Normalizations cause no further changes or if max_restarts (default 200) is reached.

        :param mol: The molecule to normalize.
        :type mol: rdkit.Chem.rdchem.Mol
        :return: The normalized fragment.
        :rtype: rdkit.Chem.rdchem.Mol
        """
        log.debug('Running Normalizer')
        # Normalize each fragment separately to get around quirky RunReactants behaviour
        fragments = []
        for fragment in Chem.GetMolFrags(mol, asMols=True):
            fragments.append(self._normalize_fragment(fragment))
        # Join normalized fragments into a single molecule again
        outmol = fragments.pop()
        for fragment in fragments:
            outmol = Chem.CombineMols(outmol, fragment)
        Chem.SanitizeMol(outmol)
        return outmol 

# 需要导入模块: from rdkit import Chem [as 别名]
# 或者: from rdkit.Chem import CombineMols [as 别名]
def normalize(self, mol):
        """Apply a series of Normalization transforms to correct functional groups and recombine charges.

        A series of transforms are applied to the molecule. For each Normalization, the transform is applied repeatedly
        until no further changes occur. If any changes occurred, we go back and start from the first Normalization
        again, in case the changes mean an earlier transform is now applicable. The molecule is returned once the entire
        series of Normalizations cause no further changes or if max_restarts (default 200) is reached.

        :param mol: The molecule to normalize.
        :type mol: :rdkit:`Mol <Chem.rdchem.Mol-class.html>`
        :return: The normalized fragment.
        :rtype: :rdkit:`Mol <Chem.rdchem.Mol-class.html>`
        """
        log.debug("Running Normalizer")
        # Normalize each fragment separately to get around quirky RunReactants behaviour
        fragments = []
        for fragment in Chem.GetMolFrags(mol, asMols=True):
            fragments.append(self._normalize_fragment(fragment))
        # Join normalized fragments into a single molecule again
        outmol = fragments.pop()
        for fragment in fragments:
            outmol = Chem.CombineMols(outmol, fragment)
        Chem.SanitizeMol(outmol)
        return outmol 

# 需要导入模块: from rdkit import Chem [as 别名]
# 或者: from rdkit.Chem import CombineMols [as 别名]
def clean_charges(mol):
    """
    This hack should not be needed anymore, but is kept just in case

    """

    Chem.SanitizeMol(mol)
    #rxn_smarts = ['[N+:1]=[*:2]-[C-:3]>>[N+0:1]-[*:2]=[C-0:3]',
    #              '[N+:1]=[*:2]-[O-:3]>>[N+0:1]-[*:2]=[O-0:3]',
    #              '[N+:1]=[*:2]-[*:3]=[*:4]-[O-:5]>>[N+0:1]-[*:2]=[*:3]-[*:4]=[O-0:5]',
    #              '[#8:1]=[#6:2]([!-:6])[*:3]=[*:4][#6-:5]>>[*-:1][*:2]([*:6])=[*:3][*:4]=[*+0:5]',
    #              '[O:1]=[c:2][c-:3]>>[*-:1][*:2][*+0:3]',
    #              '[O:1]=[C:2][C-:3]>>[*-:1][*:2]=[*+0:3]']

    rxn_smarts = ['[#6,#7:1]1=[#6,#7:2][#6,#7:3]=[#6,#7:4][CX3-,NX3-:5][#6,#7:6]1=[#6,#7:7]>>'
                  '[#6,#7:1]1=[#6,#7:2][#6,#7:3]=[#6,#7:4][-0,-0:5]=[#6,#7:6]1[#6-,#7-:7]',
                  '[#6,#7:1]1=[#6,#7:2][#6,#7:3](=[#6,#7:4])[#6,#7:5]=[#6,#7:6][CX3-,NX3-:7]1>>'
                  '[#6,#7:1]1=[#6,#7:2][#6,#7:3]([#6-,#7-:4])=[#6,#7:5][#6,#7:6]=[-0,-0:7]1']

    fragments = Chem.GetMolFrags(mol,asMols=True,sanitizeFrags=False)

    for i, fragment in enumerate(fragments):
        for smarts in rxn_smarts:
            patt = Chem.MolFromSmarts(smarts.split(">>")[0])
            while fragment.HasSubstructMatch(patt):
                rxn = AllChem.ReactionFromSmarts(smarts)
                ps = rxn.RunReactants((fragment,))
                fragment = ps[0][0]
                Chem.SanitizeMol(fragment)
        if i == 0:
            mol = fragment
        else:
            mol = Chem.CombineMols(mol, fragment)

    return mol 

# 需要导入模块: from rdkit import Chem [as 别名]
# 或者: from rdkit.Chem import CombineMols [as 别名]
def connect_mols(mol1, mol2, atom1, atom2):
        combined = Chem.CombineMols(mol1, mol2)
        emol = Chem.EditableMol(combined)
        neighbor1_idx = atom1.GetNeighbors()[0].GetIdx()
        neighbor2_idx = atom2.GetNeighbors()[0].GetIdx()
        atom1_idx = atom1.GetIdx()
        atom2_idx = atom2.GetIdx()
        bond_order = atom2.GetBonds()[0].GetBondType()
        emol.AddBond(neighbor1_idx,
                     neighbor2_idx + mol1.GetNumAtoms(),
                     order=bond_order)
        emol.RemoveAtom(atom2_idx + mol1.GetNumAtoms())
        emol.RemoveAtom(atom1_idx)
        mol = emol.GetMol()
        return mol 

# 需要导入模块: from rdkit import Chem [as 别名]
# 或者: from rdkit.Chem import CombineMols [as 别名]
def clean_charges(mol):
# this hack should not be needed any more but is kept just in case
#

    rxn_smarts = ['[N+:1]=[*:2]-[C-:3]>>[N+0:1]-[*:2]=[C-0:3]',
                  '[N+:1]=[*:2]-[O-:3]>>[N+0:1]-[*:2]=[O-0:3]',
                  '[N+:1]=[*:2]-[*:3]=[*:4]-[O-:5]>>[N+0:1]-[*:2]=[*:3]-[*:4]=[O-0:5]',
                  '[#8:1]=[#6:2]([!-:6])[*:3]=[*:4][#6-:5]>>[*-:1][*:2]([*:6])=[*:3][*:4]=[*+0:5]',
                  '[O:1]=[c:2][c-:3]>>[*-:1][*:2][*+0:3]',
                  '[O:1]=[C:2][C-:3]>>[*-:1][*:2]=[*+0:3]']

    fragments = Chem.GetMolFrags(mol,asMols=True,sanitizeFrags=False)

    for i,fragment in enumerate(fragments):
        for smarts in rxn_smarts:
            patt = Chem.MolFromSmarts(smarts.split(">>")[0])
            while fragment.HasSubstructMatch(patt):
                rxn = AllChem.ReactionFromSmarts(smarts)
                ps = rxn.RunReactants((fragment,))
                fragment = ps[0][0]
        if i == 0:
            mol = fragment
        else:
            mol = Chem.CombineMols(mol,fragment)

    return mol 

# 需要导入模块: from rdkit import Chem [as 别名]
# 或者: from rdkit.Chem import CombineMols [as 别名]
def join_fragments(fragments):

    to_join = []
    bonds = []
    pairs = []
    del_atoms = []
    new_mol = fragments[0]

    j,b,r = get_join_list(fragments[0])
    to_join += j
    del_atoms += r
    bonds += b
    offset = fragments[0].GetNumAtoms()

    for f in fragments[1:]:

        j,b,r = get_join_list(f)
        p = to_join.pop()
        pb = bonds.pop()

        # Check bond types if b[:-1] == pb
        if b[:-1] != pb:
            assert("Can't connect bonds")



        pairs.append((p, j[-1] + offset,pb))

        for x in j[:-1]:
            to_join.append(x + offset)
        for x in r:
            del_atoms.append(x + offset)
        bonds += b[:-1]

        offset += f.GetNumAtoms()
        new_mol = Chem.CombineMols(new_mol, f)


    new_mol =  Chem.EditableMol(new_mol)

    for a1,a2,b in pairs:
        new_mol.AddBond(a1,a2, order=b)

    # Remove atom with greatest number first:
    for s in sorted(del_atoms, reverse=True):
        new_mol.RemoveAtom(s)
    return new_mol.GetMol()





# Decide the class of a fragment
#   Either R-group, Linker or Scaffold 

# 需要导入模块: from rdkit import Chem [as 别名]
# 或者: from rdkit.Chem import CombineMols [as 别名]
def join_fragments(fragments):
    
    to_join = []
    bonds = []
    pairs = []
    del_atoms = []
    new_mol = fragments[0]
    
    j,b,r = get_join_list(fragments[0])
    to_join += j
    del_atoms += r
    bonds += b
    offset = fragments[0].GetNumAtoms()
    
    for f in fragments[1:]:
        
        j,b,r = get_join_list(f)
        p = to_join.pop()
        pb = bonds.pop()

        # Check bond types if b[:-1] == pb
        if b[:-1] != pb:
            assert("Can't connect bonds")
        
        
        
        pairs.append((p, j[-1] + offset,pb))
        
        for x in j[:-1]:
            to_join.append(x + offset)
        for x in r:
            del_atoms.append(x + offset)
        bonds += b[:-1]
        
        offset += f.GetNumAtoms()
        new_mol = Chem.CombineMols(new_mol, f)


    new_mol =  Chem.EditableMol(new_mol)
    
    for a1,a2,b in pairs:
        new_mol.AddBond(a1,a2, order=b)
    
    # Remove atom with greatest number first:
    for s in sorted(del_atoms, reverse=True):
        new_mol.RemoveAtom(s)
    return new_mol.GetMol()
    
    
    
    

# Decide the class of a fragment
#   Either R-group, Linker or Scaffold