Sign upLogin

KarrLab/bpforms

View on GitHub
Star
bpforms/alphabet/protein.py

Summary

Maintainability
F
2 wks
Test Coverage
F
34%

Function build_from_pdb has a Cognitive Complexity of 96 (exceeds 5 allowed). Consider refactoring.
Open

    def build_from_pdb(self, alphabet, ph=None, major_tautomer=False, dearomatize=False):
        """ Build alphabet from `PDB Chemical Component Dictionary <http://www.wwpdb.org/data/ccd>`_

        Args:
            alphabet (:obj:`Alphabet`): alphabet
Severity: Minor
Found in bpforms/alphabet/protein.py - About 1 day 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 protein.py has 765 lines of code (exceeds 250 allowed). Consider refactoring.
Open

""" Alphabet and BpForm to represent modified proteins

:Author: Jonathan Karr <karr@mssm.edu>
:Date: 2019-02-05
:Copyright: 2019, Karr Lab
Severity: Major
Found in bpforms/alphabet/protein.py - About 1 day to fix

    Function is_c_terminus has a Cognitive Complexity of 45 (exceeds 5 allowed). Consider refactoring.
    Open

        def is_c_terminus(self, mol, atom, residue=True, convert_to_aa=False):
        """ Determine if an atom is an C-terminus

        Args:
            mol (:obj:`openbabel.OBMol`): molecule
    Severity: Minor
    Found in bpforms/alphabet/protein.py - About 6 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_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 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

    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

    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 build has 50 lines of code (exceeds 25 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 2 hrs to fix

      Function is_n_terminus has a Cognitive Complexity of 14 (exceeds 5 allowed). Consider refactoring.
      Open

          def is_n_terminus(self, mol, atom):
        """ Determine if an atom is an N-terminus

        Args:
            mol (:obj:`openbabel.OBMol`): molecule
      Severity: Minor
      Found in bpforms/alphabet/protein.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

      Avoid deeply nested control flow statements.
      Open

                              if name is not None:
                            names.append(name)
      Severity: Major
      Found in bpforms/alphabet/protein.py - About 45 mins to fix

        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
        Severity: Major
        Found in bpforms/alphabet/protein.py - About 45 mins to fix

          Function get_resid_monomer_structure has 5 arguments (exceeds 4 allowed). Consider refactoring.
          Open

              def get_resid_monomer_structure(self, name, pdb_filename, ph=None, major_tautomer=False, dearomatize=False):
          Severity: Minor
          Found in bpforms/alphabet/protein.py - About 35 mins to fix

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

                def get_resid_monomer_structure(self, name, pdb_filename, ph=None, major_tautomer=False, dearomatize=False):
        """ Get the structure of an amino acid from a PDB file

        Args:
            name (:obj:`str`): name of monomeric form
            Severity: Minor
            Found in bpforms/alphabet/protein.py - About 35 mins 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

            Avoid too many return statements within this function.
            Open

                            return False
            Severity: Major
            Found in bpforms/alphabet/protein.py - About 30 mins to fix

              Avoid too many return statements within this function.
              Open

                          return False
              Severity: Major
              Found in bpforms/alphabet/protein.py - About 30 mins to fix

                Avoid too many return statements within this function.
                Open

                        return True
                Severity: Major
                Found in bpforms/alphabet/protein.py - About 30 mins to fix

                  Avoid too many return statements within this function.
                  Open

                              return False
                  Severity: Major
                  Found in bpforms/alphabet/protein.py - About 30 mins to fix

                    Avoid too many return statements within this function.
                    Open

                            return True
                    Severity: Major
                    Found in bpforms/alphabet/protein.py - About 30 mins to fix

                      Avoid too many return statements within this function.
                      Open

                                  return False
                      Severity: Major
                      Found in bpforms/alphabet/protein.py - About 30 mins to fix

                        Avoid too many return statements within this function.
                        Open

                                            return False
                        Severity: Major
                        Found in bpforms/alphabet/protein.py - About 30 mins to fix

                          Avoid too many return statements within this function.
                          Open

                                      return False
                          Severity: Major
                          Found in bpforms/alphabet/protein.py - About 30 mins to fix

                            Avoid too many return statements within this function.
                            Open

                                        return False
                            Severity: Major
                            Found in bpforms/alphabet/protein.py - About 30 mins to fix

                              Avoid too many return statements within this function.
                              Open

                                          return False
                              Severity: Major
                              Found in bpforms/alphabet/protein.py - About 30 mins to fix

                                Avoid too many return statements within this function.
                                Open

                                                    return False
                                Severity: Major
                                Found in bpforms/alphabet/protein.py - About 30 mins to fix

                                  Avoid too many return statements within this function.
                                  Open

                                              return False
                                  Severity: Major
                                  Found in bpforms/alphabet/protein.py - About 30 mins to fix

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

                                    class CanonicalProteinForm(BpForm):
    """ Canonical protein form """

    DEFAULT_FASTA_CODE = 'X'
                                    Severity: Major
                                    Found in bpforms/alphabet/protein.py and 1 other location - About 1 day to fix
                                    bpforms/alphabet/protein.py on lines 922..942

                                    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 151.

                                    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

                                    class ProteinForm(BpForm):
    """ Protein form """

    DEFAULT_FASTA_CODE = 'X'
                                    Severity: Major
                                    Found in bpforms/alphabet/protein.py and 1 other location - About 1 day to fix
                                    bpforms/alphabet/protein.py on lines 946..966

                                    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 151.

                                    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 'GO' in l2:
                    identifiers.add(Identifier('go', 'GO:' + l2[l2.index('GO')+1]))
                                    Severity: Major
                                    Found in bpforms/alphabet/protein.py and 2 other locations - About 1 hr to fix
                                    bpforms/alphabet/protein.py on lines 887..888
                                    bpforms/alphabet/protein.py on lines 893..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 48.

                                    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 'ChEBI' in l2:
                    identifiers.add(Identifier('chebi', 'CHEBI:' + l2[l2.index('ChEBI')+1]))
                                    Severity: Major
                                    Found in bpforms/alphabet/protein.py and 2 other locations - About 1 hr to fix
                                    bpforms/alphabet/protein.py on lines 893..894
                                    bpforms/alphabet/protein.py on lines 896..897

                                    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 48.

                                    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 'PSI-MOD' in l2:
                    identifiers.add(Identifier('mod', 'MOD:' + l2[l2.index('PSI-MOD')+1]))
                                    Severity: Major
                                    Found in bpforms/alphabet/protein.py and 2 other locations - About 1 hr to fix
                                    bpforms/alphabet/protein.py on lines 887..888
                                    bpforms/alphabet/protein.py on lines 896..897

                                    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 48.

                                    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

                                                file.write(('{} monomers were merged into the alphabet because they have the same names:\n'
                        '  PDB-CCD ID\tRESID ID\tName\n'
                        '  {}\n\n').format(
                len(same_names), '\n  '.join(sorted('\t'.join(n) for n in same_names))))
                                    Severity: Major
                                    Found in bpforms/alphabet/protein.py and 3 other locations - About 1 hr to fix
                                    bpforms/alphabet/protein.py on lines 528..531
                                    bpforms/alphabet/protein.py on lines 533..537
                                    bpforms/alphabet/protein.py on lines 544..547

                                    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 44.

                                    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

                                                file.write(('{} monomers were merged into the alphabet because they have the same PDB ids (ligand / CCD), '
                        'but different structures (e.g., different stereochemistry or bond order):\n'
                        '  PDB-CCD ID\tPDB-CCD SMILES\tRESID SMILES\n'
                        '  {}\n\n').format(
                len(same_pdb_ids), '\n  '.join(sorted('\t'.join(n) for n in same_pdb_ids))))
                                    Severity: Major
                                    Found in bpforms/alphabet/protein.py and 3 other locations - About 1 hr to fix
                                    bpforms/alphabet/protein.py on lines 528..531
                                    bpforms/alphabet/protein.py on lines 539..542
                                    bpforms/alphabet/protein.py on lines 544..547

                                    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 44.

                                    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

                                                file.write(('{} monomers were potentially merged incorrectly:\n'
                        '  PDB-CCD ID-1\tPDB-CCD ID-2\n'
                        '  {}\n\n').format(
                len(potential_incorrect_merges), '\n  '.join(sorted('\t'.join(n) for n in potential_incorrect_merges))))
                                    Severity: Major
                                    Found in bpforms/alphabet/protein.py and 3 other locations - About 1 hr to fix
                                    bpforms/alphabet/protein.py on lines 528..531
                                    bpforms/alphabet/protein.py on lines 533..537
                                    bpforms/alphabet/protein.py on lines 539..542

                                    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 44.

                                    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

                                                file.write(('{} monomers were merged into the alphabet because they have the same structures (SMILES):\n'
                        '  PDB-CCD ID\tRESID ID\tPDB Ligand RESID ID\n'
                        '  {}\n\n').format(
                len(same_structures), '\n  '.join(sorted('\t'.join(n) for n in same_structures))))
                                    Severity: Major
                                    Found in bpforms/alphabet/protein.py and 3 other locations - About 1 hr to fix
                                    bpforms/alphabet/protein.py on lines 533..537
                                    bpforms/alphabet/protein.py on lines 539..542
                                    bpforms/alphabet/protein.py on lines 544..547

                                    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 44.

                                    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 ((i_n_2 is not None) + (i_c_2 is not None)) > ((i_n is not None) + (i_c is not None)):
                                    Severity: Major
                                    Found in bpforms/alphabet/protein.py and 1 other location - About 1 hr to fix
                                    bpforms/alphabet/protein.py on lines 431..431

                                    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 43.

                                    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 ((i_n_2 is not None) + (i_c_2 is not None)) > ((i_n is not None) + (i_c is not None)):
                                    Severity: Major
                                    Found in bpforms/alphabet/protein.py and 1 other location - About 1 hr to fix
                                    bpforms/alphabet/protein.py on lines 345..345

                                    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 43.

                                    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

                                        def run(self, ph=None, major_tautomer=False, dearomatize=False, path=filename):
        """ Build alphabet and, optionally, save to YAML file

        Args:
            ph (:obj:`float`, optional): pH at which calculate major protonation state of each monomeric form
                                    Severity: Major
                                    Found in bpforms/alphabet/protein.py and 2 other locations - About 1 hr to fix
                                    bpforms/alphabet/dna.py on lines 103..115
                                    bpforms/alphabet/rna.py on lines 46..58

                                    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 43.

                                    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 'CAS' in l2:
                    identifiers.add(Identifier('cas', l2[l2.index('CAS')+1]))
                                    Severity: Major
                                    Found in bpforms/alphabet/protein.py and 1 other location - About 1 hr to fix
                                    bpforms/alphabet/protein.py on lines 890..891

                                    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 42.

                                    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 'PDBHET' in l2:
                    identifiers.add(Identifier('pdb.ligand', l2[l2.index('PDBHET')+1]))
                                    Severity: Major
                                    Found in bpforms/alphabet/protein.py and 1 other location - About 1 hr to fix
                                    bpforms/alphabet/protein.py on lines 884..885

                                    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 42.

                                    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 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 3 locations. Consider refactoring.
                                    Open

                                                file.write(('{} monomers only have C termini:\n'
                        '  Code\tSMILES\n'
                        '  {}\n\n').format(
                len(c_only), '\n  '.join('\t'.join(txt) for txt in c_only)))
                                    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 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 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 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

                                            for atom_n in atom_ns:
            for atom_c in atom_cs:
                if self.is_terminus(atom_n, atom_c):
                    termini.append((atom_n, atom_c))
                                    Severity: Minor
                                    Found in bpforms/alphabet/protein.py and 1 other location - About 45 mins to fix
                                    bpforms/alphabet/rna.py on lines 897..900

                                    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 35.

                                    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

                                            for monomer in alphabet.monomers.values():
            if monomer in monomer.base_monomers:
                monomer.base_monomers.remove(monomer)
                                    Severity: Minor
                                    Found in bpforms/alphabet/protein.py and 1 other location - About 45 mins to fix
                                    bpforms/alphabet/protein.py on lines 141..143

                                    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 35.

                                    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

                                                    for o_monomer in alphabet.monomers.values():
                    if monomer in o_monomer.base_monomers:
                        o_monomer.base_monomers.remove(monomer)
                                    Severity: Minor
                                    Found in bpforms/alphabet/protein.py and 1 other location - About 45 mins to fix
                                    bpforms/alphabet/protein.py on lines 131..133

                                    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 35.

                                    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

                                            atom_n_neighbors = set((atom.GetIdx(), atom.GetAtomicNum()) for atom in openbabel.OBAtomAtomIter(atom_n))
                                    Severity: Minor
                                    Found in bpforms/alphabet/protein.py and 1 other location - About 40 mins to fix
                                    bpforms/alphabet/protein.py on lines 826..826

                                    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 34.

                                    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

                                            atom_c_neighbors = set((atom.GetIdx(), atom.GetAtomicNum()) for atom in openbabel.OBAtomAtomIter(atom_c))
                                    Severity: Minor
                                    Found in bpforms/alphabet/protein.py and 1 other location - About 40 mins to fix
                                    bpforms/alphabet/protein.py on lines 825..825

                                    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 34.

                                    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

                                                for other_atom in openbabel.OBAtomAtomIter(atom):
                if other_atom.GetAtomicNum() == 1:
                    h_atom = other_atom
                    break
                                    Severity: Minor
                                    Found in bpforms/alphabet/protein.py and 2 other locations - About 30 mins to fix
                                    bpforms/alphabet/rna.py on lines 128..131
                                    bpforms/alphabet/rna.py on lines 1063..1066

                                    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 32.

                                    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

                                    There are no issues that match your filters.

                                    Category
                                    Status