b44dc788d6eaf6fe53cb6468763b46a0c4c74a12,src/biotite/structure/charges.py,,partial_charges,#Any#Any#Any#,293

Before Change

    if 5 in nitrogen_bond_types:
        for i, element in enumerate(elements):
            if element != "C" and 5 in types[i]:
                types[i].sort()
                // Aromaticity implies molecular cyclicality, i. e. an
                // atom involved in an aromatic system has at least two
                // bonds with the aromatic bond type and at most
                second_max = types[i][-3]

After Change

    // single bonds or a double bond as well
    nitrogen_bond_types = types[elements == "N"]
    if 5 in nitrogen_bond_types:
        nitrogen_indices = np.unique(
            np.where(elements == "N")[0]
        )
        for i in nitrogen_indices:
            if 5 in types[i]:
                considered_row = types[i]
                considered_row.sort()
                // Aromaticity implies molecular cyclicality, i. e. an
                // atom involved in an aromatic system has at least two
                // bonds with the aromatic bond type
                // Nitrogen has at most three bonds if involved in an
                // aromatic system, where the third bond type is `single`
                // Therefore, the presence of a third bond type indicates
                // a sp3 hybridisation, whereas the absence of a third
                // bond type can be either due to sp2 hybridisation or
                // deprotonation
                // In order to account for this ambiguity, the charge is
                // considered in case that a third bond type is not
                // present
                try:
                    considered_row[-3]
                    bond_types[i] = 1
                except IndexError:
                    nitrogen_charge = charges[i]
                    if nitrogen_charge == -1:
                        bond_types[i] = 1
                    else:
                        bond_types[i] = 2
    damping = 1.0
    parameters = _get_parameters(
        elements, bond_types, amount_of_binding_partners
    )

Instances