Avoid deeply nested control flow statements.

Open

                    for base in origin:
                        start_pos = seq.find(base) + 1
                        if start_pos > 0:
                            start_position = min(start_position, start_pos)

Avoid deeply nested control flow statements.

Open

                    if modification['monomer'] not in code_freq:
                        code_freq[modification['monomer']] = 0
                    canonical_code_freq[modification['residue']] += n_mods

Avoid deeply nested control flow statements.

Open

                    if start_position == 0:
                        protein['modified_errors'].append('Sequence does not contain residue {} for modification {}'.format(
                            canonical_code, modification['monomer']))
                    else:
                        monomer2.start_position = start_position

Avoid deeply nested control flow statements.

Open

                        for n in names:
                            monomer = name_to_monomer.get(n.lower(), None)
                            if monomer is not None:
                                same_names.append((id, monomer.id, n))
                                break

Avoid deeply nested control flow statements.

Open

                    if code not in code_freq:
                        code_freq[code] = 0
                    code_freq[code] += 1

Avoid deeply nested control flow statements.

Open

                    if monomer is None:
                        unsupported_codes.add(code)
                        monomer = bpforms.Monomer(id=code)
                    else:
                        monomer_codes[code] = monomer

Avoid deeply nested control flow statements.

Open

                    if numpy.isinf(start_position):
                        protein['modified_errors'].append('Sequence does not contain residues {} for modification {}'.format(
                            ', '.join(origin), modification['monomer']))
                    else:
                        monomer2.start_position = start_position

Avoid deeply nested control flow statements.

Open

                    if modification['residue'] not in canonical_code_freq:
                        canonical_code_freq[modification['residue']] = 0
                    if modification['monomer'] not in code_freq:

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

Open

    def _default(self):
        args = self.app.pargs
        type = bpforms.util.get_form(args.alphabet)

        try:

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Avoid deeply nested control flow statements.

Open

                        if identifier.ns == 'pdb-ccd':
                            monomer = None
                            break
                if monomer is not None and (

Avoid deeply nested control flow statements.

Open

                    if len(entry.org_taxid) == 1:
                        # does not include those whose taxid is 'unidentified' or 'synthetic'
                        taxid = list(entry.org_taxid)[0]
                        if taxid != 32630 and taxid != 32644:

Avoid deeply nested control flow statements.

Open

                    if key == 'comment' and value.startswith('Category=organism-modification.'):
                        proteins.append(protein)

        # save PRO in pickle format
        with open(pkl_filename, 'wb') as file:

Avoid deeply nested control flow statements.

Open

                    if position >= processing['start'] and position <= processing['end']:
                        processed_position = seq_len + position - processing['start'] + 1
                        break
                    seq_len += processing['end'] - processing['start'] + 1

Avoid deeply nested control flow statements.

Open

                        if key == 'Symbol':
                            id = child.text
                        elif key == 'Common name':
                            name = child.text
                        elif key == 'CA registry numbers' and child.text.startswith('ribonucleoside '):

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

Open

    def build(self, ph=None, major_tautomer=False, dearomatize=False):
        """ Build alphabet

        Args:
            ph (:obj:`float`, optional): pH at which to calculate the major protonation state of each monomeric form

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Avoid deeply nested control flow statements.

Open

                    if monomer is None:
                        unsupported_codes.add(code)
                        monomer = bpforms.Monomer(id=code)
                    else:
                        monomer_codes[code] = monomer

Avoid deeply nested control flow statements.

Open

                        if monomer.comments:
                            monomer.comments += ' ' + comments
                        else:
                            monomer.comments = comments

Avoid deeply nested control flow statements.

Open

                        if identifier.ns == 'pdb-ccd':
                            monomer = None
                            break
                if monomer is not None and (\

Avoid deeply nested control flow statements.

Open

                    if protein['processing'][-1]['end'] == len(form.seq):
                        seq_features[0]['positions'].pop(len(seq_features[0]['positions']) - 1)

Avoid deeply nested control flow statements.

Open

                        if name is not None:
                            names.append(name)