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

    def _find_bond_partner_types(self, atomname, final_types):
        """ Find all the atoms it is bonded to, and collect their types

        Parameters
        ----------
Severity: Minor
Found in protons/app/ligands.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

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

    def define_pools(self, dict_of_pools):
        """
        Specify named residue_pools/subgroups of residues that can be sampled from separately.

        For instance, it might be useful to separate the protein from the ligand so you can sample the
Severity: Minor
Found in protons/app/driver.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

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

    def validate(self):
        """
        Checks to see if the isomeric state is valid.

        Raises
Severity: Minor
Found in protons/app/ligands.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

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

    def _set_state_accept_attempt(
        self,
        initial_titration_states,
        final_titration_states,
        titration_group_indices,
Severity: Minor
Found in protons/app/driver.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

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

def generate_tautomer_torsion_definitions(
    isomers: dict, vacuum_file: str, isomer_index: int
):
    """
    Creates torsion entries (proper and improper) in the isomer dictionary. It does this
Severity: Minor
Found in protons/app/ligands.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

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

    def _set_state_reject_attempt(
        self,
        initial_titration_states: List[int],
        final_titration_states: List[int],
        titration_group_indices: List[int],
Severity: Minor
Found in protons/app/driver.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

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

    def from_xml(cls, xmltree: etree.Element):
        """Instantiate a COOHDummyMover class from an lxml Element."""
        obj = cls()
        if not xmltree.tag == "COOHDummyMover":
            raise ValueError(
Severity: Minor
Found in protons/app/proposals.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

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

                func_input = (
                    os.path.splitext(os.path.basename(input_file_path))[0] + ".mae"
Severity: Minor
Found in protons/app/schrodinger.py and 1 other location - About 35 mins to fix
protons/app/schrodinger.py on lines 232..236

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 33.

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

    refs = set([r.strip() for r in refnames.strip("()").split(",")])
Severity: Minor
Found in protons/_version.py and 1 other location - About 35 mins to fix
versioneer.py on lines 992..992

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 33.

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 is_output_mae:
                func_output = output_file_path
            else:
                func_output = (
                    os.path.splitext(os.path.basename(output_file_path))[0] + ".mae"
Severity: Minor
Found in protons/app/schrodinger.py and 1 other location - About 35 mins to fix
protons/app/schrodinger.py on lines 226..227

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 33.

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

    refs = set([r.strip() for r in refnames.strip("()").split(",")])
Severity: Minor
Found in versioneer.py and 1 other location - About 35 mins to fix
protons/_version.py on lines 189..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 33.

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

def setup_systems_serially():

    for solvent in ["implicit", "explicit"]:
        for aa in ["lys"]:  # ["cys", "lys", "glu", "his", "tyr", "asp"]:
            foldername = "examples/calibration-{}".format(solvent)
Severity: Minor
Found in protons/app/generate_calibration_systems.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 protons/app/driver.py - About 30 mins to fix

    Avoid too many return statements within this function.
    Open

                return False
    Severity: Major
    Found in protons/app/driver.py - About 30 mins to fix

      Avoid too many return statements within this function.
      Open

                      return False
      Severity: Major
      Found in protons/app/driver.py - About 30 mins to fix

        Avoid too many return statements within this function.
        Open

                return True
        Severity: Major
        Found in protons/app/driver.py - About 30 mins to fix

          Avoid too many return statements within this function.
          Open

                      return False
          Severity: Major
          Found in protons/app/driver.py - About 30 mins to fix

            Avoid too many return statements within this function.
            Open

                    return True
            Severity: Major
            Found in protons/app/driver.py - About 30 mins to fix

              Avoid too many return statements within this function.
              Open

                          return False
              Severity: Major
              Found in protons/app/driver.py - About 30 mins to fix

                Avoid too many return statements within this function.
                Open

                            return False
                Severity: Major
                Found in protons/app/driver.py - About 30 mins to fix
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