Function __init__ has 7 arguments (exceeds 4 allowed). Consider refactoring.

Open

    def __init__(self, l_bond_atoms=None, r_bond_atoms=None, l_displaced_atoms=None, r_displaced_atoms=None,

Function get_genomic_image has 6 arguments (exceeds 4 allowed). Consider refactoring.

Open

    def get_genomic_image(self, seq_features=None, width=1200, cols=2, nt_per_track=80, **kwargs):

Function get_details has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.

Open

    def get_details(self):
        """ Get the full details of the crosslink in a dictionary

        Returns:
            :obj:`dict`: detailed information of the crosslink

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Function __init__ has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.

Open

    def __init__(self, l_bond_atoms=None, r_bond_atoms=None, l_displaced_atoms=None, r_displaced_atoms=None,
                 order=BondOrder.single, stereo=None,
                 comments=None):
        """

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Function update_tab_name has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.

Open

function update_tab_name() {
    for (var i=0; i<num_subunits; i++) {
        if ($('#panel'+i).length) {
            name = $('#name'+i+'').val()
            if (name != null && name != '') {

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Function __init__ has 6 arguments (exceeds 4 allowed). Consider refactoring.

Open

    def __init__(self, id, stoichiometry, structure=None, formula=None, mol_wt=None, charge=None):

Function clean has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.

Open

    def clean(self):
        """ Clean up the subunits and the crosslinks

        For example, convert `1 * a + 1 * a` to `2 * a`

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Avoid deeply nested control flow statements.

Open

                        for i_atom, atom in atom_type.items():
                            atom_type[i_atom] = mol.GetAtom(atom)

        # mol.AddHydrogens()

Avoid deeply nested control flow statements.

Open

                        if encoding == 'bpforms.ProteinForm':
                            try:
                                subunit_structure = bpforms.ProteinForm().from_str(subunit['structure'])
                                sum_length += len(subunit_structure) * bc_form.get_subunit_attribute(subunit_id, 'stoichiometry')
                                bc_form.set_subunit_attribute(subunit_id, 'structure', subunit_structure)

Avoid deeply nested control flow statements.

Open

                        if 'formula' in subunit:
                            try:
                                bc_form.set_subunit_attribute(subunit_id, 'formula', subunit['formula'])
                            except Exception as error:
                                flask_restplus.abort(400, 'Unable to parse formula', errors={'formula': str(error)})

Avoid deeply nested control flow statements.

Open

                        if next(subunit for subunit in self_subunits_subunits if subunit.id == atom.subunit).stoichiometry > 1:
                            errors.append("crosslink {} contains multiple subunit '{}', so the subunit_idx of atom '{}[{}]' cannot be None".format(
                                i_crosslink + 1, atom.subunit, atom_type, i_atom))
                    elif atom.subunit_idx > next(subunit for subunit in self_subunits_subunits if subunit.id == atom.subunit).stoichiometry:

Avoid deeply nested control flow statements.

Open

                        for i_atom, atom in atom_type.items():
                            atom_type[i_atom] = atom+n_atoms[i_subunit]
            atom_maps.append(atom_map)

Function structure has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.

Open

    def structure(self, value):
        """ Set the structure of the subunit

        * setting structure will automaticall set formula, mol_wt, charge

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Function is_equal has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.

Open

    def is_equal(self, other):
        """ Check if two atoms are semantically equal (belong to the same subunit/monomer and
        have the same element, position, and charge)

        Args:

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Avoid deeply nested control flow statements.

Open

                        for i_atom, atom in atom_type.items():
                            if atom is not None:
                                atom_type[i_atom] = atom.GetIdx()

Avoid deeply nested control flow statements.

Open

                        if 'charge' in subunit:
                            try:
                                bc_form.set_subunit_attribute(subunit_id, 'charge', subunit['charge'])
                            except Exception as error:
                                flask_restplus.abort(400, 'Unable to parse charge', errors={'charge': str(error)})

Function from_set has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.

Open

    def from_set(self, subunits):
        """ Set the subunits from a list of subunits

        Note: this method does not support crosslinks

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Avoid too many return statements within this function.

Open

        return True

Avoid too many return statements within this function.

Open

                return False

Avoid too many return statements within this function.

Open

            return False