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Similar blocks of code found in 6 locations. Consider refactoring.
Open

        doc += '          <td>{}</td>\n'.format(', '.join('{}{}'.format(atom.element, atom.position)
                                                          for atom in monomer.backbone_bond_atoms))
Severity: Major
Found in bpforms/util.py and 5 other locations - About 1 hr to fix
bpforms/util.py on lines 162..163
bpforms/util.py on lines 164..164
bpforms/util.py on lines 165..166
bpforms/util.py on lines 167..167
bpforms/util.py on lines 168..169

Duplicated Code

Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

Tuning

This issue has a mass of 40.

We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

Refactorings

Further Reading

Similar blocks of code found in 3 locations. Consider refactoring.
Open

            file.write(('{} monomers only have N termini:\n'
                        '  Code\tSMILES\n'
                        '  {}\n\n').format(
                len(n_only), '\n  '.join('\t'.join(txt) for txt in n_only)))
Severity: Major
Found in bpforms/alphabet/protein.py and 2 other locations - About 1 hr to fix
bpforms/alphabet/protein.py on lines 167..170
bpforms/alphabet/protein.py on lines 172..175

Duplicated Code

Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

Tuning

This issue has a mass of 40.

We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

Refactorings

Further Reading

Similar blocks of code found in 6 locations. Consider refactoring.
Open

        doc += '          <td>{}</td>\n'.format(', '.join('{}{}'.format(atom.element, atom.position) for atom in monomer.r_bond_atoms))
Severity: Major
Found in bpforms/util.py and 5 other locations - About 1 hr to fix
bpforms/util.py on lines 160..161
bpforms/util.py on lines 162..163
bpforms/util.py on lines 165..166
bpforms/util.py on lines 167..167
bpforms/util.py on lines 168..169

Duplicated Code

Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

Tuning

This issue has a mass of 40.

We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

Refactorings

Further Reading

Similar blocks of code found in 4 locations. Consider refactoring.
Open

        print('{} entries with similar ids potentially should be joined:\n  {}\t{}\n  {}'.format(
            len(same_ids_case_insensitive), 'PDB CCD id', 'Alphabet code',
            '\n  '.join(sorted('\t'.join(ids) for ids in same_ids_case_insensitive))))
Severity: Major
Found in bpforms/alphabet/rna.py and 3 other locations - About 1 hr to fix
bpforms/alphabet/dna.py on lines 715..717
bpforms/alphabet/dna.py on lines 720..722
bpforms/alphabet/rna.py on lines 865..867

Duplicated Code

Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

Tuning

This issue has a mass of 40.

We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

Refactorings

Further Reading

Similar blocks of code found in 6 locations. Consider refactoring.
Open

        doc += '          <td>{}</td>\n'.format(', '.join('{}{}'.format(atom.element, atom.position) for atom in monomer.l_bond_atoms))
Severity: Major
Found in bpforms/util.py and 5 other locations - About 1 hr to fix
bpforms/util.py on lines 160..161
bpforms/util.py on lines 162..163
bpforms/util.py on lines 164..164
bpforms/util.py on lines 165..166
bpforms/util.py on lines 168..169

Duplicated Code

Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

Tuning

This issue has a mass of 40.

We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

Refactorings

Further Reading

Similar blocks of code found in 3 locations. Consider refactoring.
Open

            file.write(('{} monomers have no termini:\n'
                        '  Code\tSMILES\n'
                        '  {}\n\n').format(
                len(no_termini), '\n  '.join('\t'.join(txt) for txt in no_termini)))
Severity: Major
Found in bpforms/alphabet/protein.py and 2 other locations - About 1 hr to fix
bpforms/alphabet/protein.py on lines 162..165
bpforms/alphabet/protein.py on lines 167..170

Duplicated Code

Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

Tuning

This issue has a mass of 40.

We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

Refactorings

Further Reading

Similar blocks of code found in 4 locations. Consider refactoring.
Open

        print('{} entries with the similar structures were joined:\n  {}\t{}\n  {}'.format(
            len(same_structures), 'PDB CCD id', 'Alphabet code',
            '\n  '.join(sorted('\t'.join(ids) for ids in same_structures))))
Severity: Major
Found in bpforms/alphabet/rna.py and 3 other locations - About 1 hr to fix
bpforms/alphabet/dna.py on lines 715..717
bpforms/alphabet/dna.py on lines 720..722
bpforms/alphabet/rna.py on lines 870..872

Duplicated Code

Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

Tuning

This issue has a mass of 40.

We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

Refactorings

Further Reading

Function _add_bonds_to_set has 9 arguments (exceeds 4 allowed). Consider refactoring.
Open

    def _add_bonds_to_set(self, mol, r_bond_atoms, l_bond_atoms, atom_map, bond_set, el_table,
Severity: Major
Found in bpforms/core.py - About 1 hr to fix

    Function is_backbone_atom has 28 lines of code (exceeds 25 allowed). Consider refactoring.
    Open

        def is_backbone_atom(self, b_atom):
        """ Determine if an atom is a valid backbone bonding site

        Args:
            b_atom (:obj:`openbabel.OBAtom`): potential backbone atom
    Severity: Minor
    Found in bpforms/alphabet/rna.py - About 1 hr to fix

      Function from_dict has 28 lines of code (exceeds 25 allowed). Consider refactoring.
      Open

          def from_dict(self, dict, alphabet=None):
        """ Get a dictionary representation of the monomeric form

        Args:
            dict (:obj:`dict`): dictionary representation of the monomeric form
      Severity: Minor
      Found in bpforms/core.py - About 1 hr to fix

        Function parse_pdb_ccd has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.
        Open

        def parse_pdb_ccd(filename, valid_types, max_monomers):
    """ Parse entries out of the PDB CCD

    Args:
        filename (:obj:`str`): path to tar.gz file for PDB CCD
        Severity: Minor
        Found in bpforms/alphabet/core.py - About 1 hr to fix

        Cognitive Complexity

        Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

        A method's cognitive complexity is based on a few simple rules:

        • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
        • Code is considered more complex for each "break in the linear flow of the code"
        • Code is considered more complex when "flow breaking structures are nested"

        Further reading

        Function get_nucleoside_details_from_modomics has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.
        Open

            def get_nucleoside_details_from_modomics(self, id, session):
        """ Get the structure of a nucleoside in the MODOMICS database

        Args:
            id (:obj:`str`): id of nucleoside in MODOMICS database
        Severity: Minor
        Found in bpforms/alphabet/rna.py - About 1 hr to fix

        Cognitive Complexity

        Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

        A method's cognitive complexity is based on a few simple rules:

        • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
        • Code is considered more complex for each "break in the linear flow of the code"
        • Code is considered more complex when "flow breaking structures are nested"

        Further reading

        Similar blocks of code found in 2 locations. Consider refactoring.
        Open

                            if re.match(r"^COMPND    ", line):
                        part1 = str(line[10:].strip())
                        names.append(part1)
        Severity: Major
        Found in bpforms/alphabet/protein.py and 1 other location - About 1 hr to fix
        bpforms/alphabet/protein.py on lines 237..239

        Duplicated Code

        Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

        Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

        When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

        Tuning

        This issue has a mass of 39.

        We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

        The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

        If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

        See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

        Refactorings

        Further Reading

        Similar blocks of code found in 2 locations. Consider refactoring.
        Open

                            if re.match(r"^COMPND   1", line):
                        part2 = str(line[10:].strip())
                        names.append(part2)
        Severity: Major
        Found in bpforms/alphabet/protein.py and 1 other location - About 1 hr to fix
        bpforms/alphabet/protein.py on lines 232..234

        Duplicated Code

        Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

        Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

        When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

        Tuning

        This issue has a mass of 39.

        We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

        The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

        If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

        See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

        Refactorings

        Further Reading

        Similar blocks of code found in 3 locations. Consider refactoring.
        Open

                            if form.seq[position - 1] == monomers[seq[position - 1]]:
        Severity: Major
        Found in examples/pro.py and 2 other locations - About 1 hr to fix
        examples/pro.py on lines 688..688
        examples/pro.py on lines 748..748

        Duplicated Code

        Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

        Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

        When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

        Tuning

        This issue has a mass of 39.

        We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

        The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

        If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

        See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

        Refactorings

        Further Reading

        Similar blocks of code found in 2 locations. Consider refactoring.
        Open

                    if self.is_backbone_atom(atom):
                atom_bs.append(atom)
            elif self.is_r_bond_atom(atom):
                atom_rs.append(atom)
        Severity: Major
        Found in bpforms/alphabet/rna.py and 1 other location - About 1 hr to fix
        bpforms/alphabet/rna.py on lines 165..168

        Duplicated Code

        Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

        Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

        When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

        Tuning

        This issue has a mass of 39.

        We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

        The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

        If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

        See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

        Refactorings

        Further Reading

        Similar blocks of code found in 3 locations. Consider refactoring.
        Open

                                if form.seq[i_monomer - 1] == monomers[seq[i_monomer - 1]]:
        Severity: Major
        Found in examples/pro.py and 2 other locations - About 1 hr to fix
        examples/pro.py on lines 660..660
        examples/pro.py on lines 688..688

        Duplicated Code

        Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

        Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

        When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

        Tuning

        This issue has a mass of 39.

        We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

        The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

        If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

        See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

        Refactorings

        Further Reading

        Similar blocks of code found in 2 locations. Consider refactoring.
        Open

                        if self.is_l_atom(atom):
                    atom_ls.append(atom)
                elif self.is_r_bond_atom(atom):
                    atom_rs.append(atom)
        Severity: Major
        Found in bpforms/alphabet/rna.py and 1 other location - About 1 hr to fix
        bpforms/alphabet/rna.py on lines 891..894

        Duplicated Code

        Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

        Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

        When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

        Tuning

        This issue has a mass of 39.

        We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

        The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

        If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

        See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

        Refactorings

        Further Reading

        Similar blocks of code found in 3 locations. Consider refactoring.
        Open

                            if form.seq[i_monomer - 1] == monomers[seq[i_monomer - 1]]:
        Severity: Major
        Found in examples/pro.py and 2 other locations - About 1 hr to fix
        examples/pro.py on lines 660..660
        examples/pro.py on lines 748..748

        Duplicated Code

        Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

        Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

        When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

        Tuning

        This issue has a mass of 39.

        We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

        The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

        If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

        See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

        Refactorings

        Further Reading

        Function draw_monomer has 8 arguments (exceeds 4 allowed). Consider refactoring.
        Open

        def draw_monomer(Form, monomer, dirname, filename, show_atom_nums=False,
        Severity: Major
        Found in docs/build_examples.py - About 1 hr to fix
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