molvs/metal.py
def disconnect(self, mol):
        """Break covalent bonds between metals and organic atoms under certain conditions.

        The algorithm works as follows:

        - Disconnect N, O, F from any metal.
        - Disconnect other non-metals from transition metals + Al (but not Hg, Ga, Ge, In, Sn, As, Tl, Pb, Bi, Po).
        - For every bond broken, adjust the charges of the begin and end atoms accordingly.

        :param mol: The input molecule.
        :type mol: rdkit.Chem.rdchem.Mol
        :return: The molecule with metals disconnected.
        :rtype: rdkit.Chem.rdchem.Mol
        """
        log.debug('Running MetalDisconnector')
        # Remove bonds that match SMARTS
        for smarts in [self._metal_nof, self._metal_non]:
            pairs = mol.GetSubstructMatches(smarts)
            rwmol = Chem.RWMol(mol)
            orders = []
            for i, j in pairs:
                # TODO: Could get the valence contributions of the bond instead of GetBondTypeAsDouble?
                orders.append(int(mol.GetBondBetweenAtoms(i, j).GetBondTypeAsDouble()))
                rwmol.RemoveBond(i, j)
            # Adjust neighbouring charges accordingly
            mol = rwmol.GetMol()
            for n, (i, j) in enumerate(pairs):
                chg = orders[n]
                atom1 = mol.GetAtomWithIdx(i)
                atom1.SetFormalCharge(atom1.GetFormalCharge() + chg)
                atom2 = mol.GetAtomWithIdx(j)
                atom2.SetFormalCharge(atom2.GetFormalCharge() - chg)
                log.info('Removed covalent bond between %s and %s', atom1.GetSymbol(), atom2.GetSymbol())
        Chem.SanitizeMol(mol)
        return mol
def disconnect(self, mol):
        log.debug('Running MetalDisconnector')
        # Remove bonds that match SMARTS
        for smarts in [self._metal_nof, self._metal_non]:
            pairs = mol.GetSubstructMatches(smarts)
            rwmol = Chem.RWMol(mol)
            orders = []
            for i, j in pairs:
                # TODO: Could get the valence contributions of the bond instead of GetBondTypeAsDouble?
                orders.append(int(mol.GetBondBetweenAtoms(i, j).GetBondTypeAsDouble()))
                rwmol.RemoveBond(i, j)
            # Adjust neighbouring charges accordingly
            mol = rwmol.GetMol()
            for n, (i, j) in enumerate(pairs):
                chg = orders[n]
                atom1 = mol.GetAtomWithIdx(i)
                atom1.SetFormalCharge(atom1.GetFormalCharge() + chg)
                atom2 = mol.GetAtomWithIdx(j)
                atom2.SetFormalCharge(atom2.GetFormalCharge() - chg)
                log.info('Removed covalent bond between %s and %s', atom1.GetSymbol(), atom2.GetSymbol())
        Chem.SanitizeMol(mol)
        return mol
def disconnect ( self , mol ) : log . debug ( 'Running MetalDisconnector' ) # Remove bonds that match SMARTS for smarts in [ self . _metal_nof , self . _metal_non ] : pairs = mol . GetSubstructMatches ( smarts ) rwmol = Chem . RWMol ( mol ) orders = [ ] for i , j in pairs : # TODO: Could get the valence contributions of the bond instead of GetBondTypeAsDouble? orders . append ( int ( mol . GetBondBetweenAtoms ( i , j ) . GetBondTypeAsDouble ( ) ) ) rwmol . RemoveBond ( i , j ) # Adjust neighbouring charges accordingly mol = rwmol . GetMol ( ) for n , ( i , j ) in enumerate ( pairs ) : chg = orders [ n ] atom1 = mol . GetAtomWithIdx ( i ) atom1 . SetFormalCharge ( atom1 . GetFormalCharge ( ) + chg ) atom2 = mol . GetAtomWithIdx ( j ) atom2 . SetFormalCharge ( atom2 . GetFormalCharge ( ) - chg ) log . info ( 'Removed covalent bond between %s and %s' , atom1 . GetSymbol ( ) , atom2 . GetSymbol ( ) ) Chem . SanitizeMol ( mol ) return mol
Break covalent bonds between metals and organic atoms under certain conditions.

        The algorithm works as follows:

        - Disconnect N, O, F from any metal.
        - Disconnect other non-metals from transition metals + Al (but not Hg, Ga, Ge, In, Sn, As, Tl, Pb, Bi, Po).
        - For every bond broken, adjust the charges of the begin and end atoms accordingly.

        :param mol: The input molecule.
        :type mol: rdkit.Chem.rdchem.Mol
        :return: The molecule with metals disconnected.
        :rtype: rdkit.Chem.rdchem.Mol
Break covalent bonds between metals and organic atoms under certain conditions .