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Function get_resid_monomer_details has a Cognitive Complexity of 35 (exceeds 5 allowed). Consider refactoring.
Open

    def get_resid_monomer_details(self, id, session):
        """ Get the CHEBI ID and synonyms of an amino acid from its RESID webpage

        Args:
            input_pdb (:obj:`str`): id of RESID entry
Severity: Minor
Found in bpforms/alphabet/protein.py - About 5 hrs 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 build has a Cognitive Complexity of 35 (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
Severity: Minor
Found in bpforms/alphabet/rna.py - About 5 hrs 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 is_l_atom has a Cognitive Complexity of 34 (exceeds 5 allowed). Consider refactoring.
Open

    def is_l_atom(self, l_atom):
        """ Determine if an atom is a valid left bonding site

        Args:
            l_atom (:obj:`openbabel.OBAtom`): potential left atom
Severity: Minor
Found in bpforms/alphabet/rna.py - About 5 hrs 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 build has a Cognitive Complexity of 33 (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 calculate major protonation state of each monomeric form
Severity: Minor
Found in bpforms/alphabet/protein.py - About 4 hrs 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 match.group(1) == '?':
                start = None
                errors.append('Unknown processing start position')
            else:
                start = int(float(match.group(1)))
Severity: Major
Found in examples/pro.py and 1 other location - About 4 hrs to fix
examples/pro.py on lines 468..474

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 84.

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 match.group(2) == '?':
                end = None
                errors.append('Unknown processing end position')
            else:
                end = int(float(match.group(2)))
Severity: Major
Found in examples/pro.py and 1 other location - About 4 hrs to fix
examples/pro.py on lines 461..467

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 84.

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 run_rrna has a Cognitive Complexity of 31 (exceeds 5 allowed). Consider refactoring.
Open

def run_rrna(session, modomics_short_code_to_monomer, monomer_codes, out_filename):
    response = session.get(URL, params={
        'RNA_type': 'rRNA',
        'RNA_subtype': 'all',
        'organism': 'all species',
Severity: Minor
Found in examples/modomics.py - About 4 hrs 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 load_full_pdb_hets_by_entry_from_local has a Cognitive Complexity of 30 (exceeds 5 allowed). Consider refactoring.
Open

def load_full_pdb_hets_by_entry_from_local(max_entries):
    """ read the PDB database and get heterogen sets for all entries from local directory

    """
    # get amino acid set (canonical and non-canonical) from bpforms
Severity: Minor
Found in examples/pdb_analysis.py - About 4 hrs 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_pro_from_obo has a Cognitive Complexity of 30 (exceeds 5 allowed). Consider refactoring.
Open

def get_pro_from_obo(obo_filename=IN_OBO_FILENAME, pkl_filename=IN_PKL_FILENAME, max_num_proteins=None):
    """ Get the PRO ontology and extract the modified proteins from the ontology

    Args:
        obo_filename (:obj:`str`, optional): filename to save PRO in OBO format
Severity: Minor
Found in examples/pro.py - About 4 hrs 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

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

                if monomer is None:
                    unsupported_codes.add(code)
                    monomer = bpforms.Monomer(id=code)
                else:
                    monomer_codes[code] = monomer
Severity: Major
Found in examples/modomics.py and 1 other location - About 4 hrs to fix
examples/modomics.py on lines 182..189

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 78.

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

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

                    if monomer is None:
                        unsupported_codes.add(code)
                        monomer = bpforms.Monomer(id=code)
                    else:
                        monomer_codes[code] = monomer
Severity: Major
Found in examples/modomics.py and 1 other location - About 4 hrs to fix
examples/modomics.py on lines 194..201

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 78.

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 build_from_resid has a Cognitive Complexity of 29 (exceeds 5 allowed). Consider refactoring.
Open

    def build_from_resid(self, alphabet, ph=None, major_tautomer=False, dearomatize=False):
        """ Build alphabet from RESID

        Args:
            alphabet (:obj:`Alphabet`): alphabet
Severity: Minor
Found in bpforms/alphabet/protein.py - About 4 hrs 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 set_termini has a Cognitive Complexity of 29 (exceeds 5 allowed). Consider refactoring.
Open

    def set_termini(self, mol, monomer, i_n, i_c):
        """ Set the C and N terminal bond atoms of a monomer

        Args:
            mol (:obj:`openbabel.OBMol`): molecule
Severity: Minor
Found in bpforms/alphabet/protein.py - About 4 hrs 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

Bond has 33 functions (exceeds 20 allowed). Consider refactoring.
Open

class Bond(BondBase):
    """ Bond between monomeric forms (inter-residue bond or crosslink)

    Attributes:
        id (:obj:`str`): id
Severity: Minor
Found in bpforms/core.py - About 4 hrs to fix

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

        with open(os.path.join('examples', 'modomics.trna.canonical-code-freq.tsv'), 'w') as file:
        writer = csv.DictWriter(file, fieldnames=['Code', 'Frequency'], dialect='excel-tab')
        writer.writeheader()
        for code, freq in canonical_code_freq.items():
            writer.writerow({'Code': code, 'Frequency': freq})
    Severity: Major
    Found in examples/modomics.py and 1 other location - About 4 hrs to fix
    examples/modomics.py on lines 237..241

    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 76.

    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

        with open(os.path.join('examples', 'modomics.trna.code-freq.tsv'), 'w') as file:
        writer = csv.DictWriter(file, fieldnames=['Code', 'Frequency'], dialect='excel-tab')
        writer.writeheader()
        for code, freq in code_freq.items():
            writer.writerow({'Code': code, 'Frequency': freq})
    Severity: Major
    Found in examples/modomics.py and 1 other location - About 4 hrs to fix
    examples/modomics.py on lines 231..235

    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 76.

    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 get_charge has a Cognitive Complexity of 27 (exceeds 5 allowed). Consider refactoring.
    Open

        def get_charge(self):
        """ Get the charge

        Returns:
            :obj:`int`: charge
    Severity: Minor
    Found in bpforms/core.py - About 3 hrs 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

    File modomics.py has 325 lines of code (exceeds 250 allowed). Consider refactoring.
    Open

    """ Generate BpForms for all of the tRNA in MODOMICS, verify
them, and calculate their properties

:Author: Jonathan Karr <karr@mssm.edu>
:Date: 2019-06-20
    Severity: Minor
    Found in examples/modomics.py - About 3 hrs to fix

      Function get_termini has a Cognitive Complexity of 26 (exceeds 5 allowed). Consider refactoring.
      Open

          def get_termini(self, mol, residue=True):
        """ Get indices of atoms of N and C termini

        Args:
            mol (:obj:`openbabel.OBMol`): molecule
      Severity: Minor
      Found in bpforms/alphabet/protein.py - About 3 hrs 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 form has a Cognitive Complexity of 25 (exceeds 5 allowed). Consider refactoring.
      Open

          def form(self, value):
        """ Set the biopolymer form

        Args:
            value (:obj:`BpForm`): biopolymer form
      Severity: Minor
      Found in bpforms/core.py - About 3 hrs 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

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