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

        with self.rethrow_zerodiv():
            return 2 * Pmax * Pmin / (P * P)
Severity: Major
Found in mordred/KappaShapeIndex.py and 2 other locations - About 45 mins to fix
mordred/KappaShapeIndex.py on lines 77..78
mordred/KappaShapeIndex.py on lines 101..102

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

Function autodoc_process_docstring has 6 arguments (exceeds 4 allowed). Consider refactoring.
Open

def autodoc_process_docstring(app, what, name, obj, options, lines):
Severity: Minor
Found in docs/conf.py - About 45 mins to fix

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

                if (V[i] == self._valence1 and V[j] == self._valence2)
    Severity: Minor
    Found in mordred/MolecularDistanceEdge.py and 1 other location - About 40 mins to fix
    mordred/MolecularDistanceEdge.py on lines 80..80

    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

                or (V[j] == self._valence1 and V[i] == self._valence2)
    Severity: Minor
    Found in mordred/MolecularDistanceEdge.py and 1 other location - About 40 mins to fix
    mordred/MolecularDistanceEdge.py on lines 79..79

    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

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

        def _serial(self, mols, nmols, quiet, ipynb, id):
    Severity: Minor
    Found in mordred/_base/calculator.py - About 35 mins to fix

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

          def __init__(self, mols, coords, n_frags, name, config):
      Severity: Minor
      Found in mordred/_base/context.py - About 35 mins to fix

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

            def __init__(
        Severity: Minor
        Found in mordred/RingCount.py - About 35 mins to fix

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

              def __str__(self):
        attrs = []

        if self._greater:
            attrs.append("G")
          Severity: Minor
          Found in mordred/RingCount.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

                  return np.sqrt((nu + nv - 2.0) / (nu * nv))
          Severity: Minor
          Found in mordred/ABCIndex.py and 1 other location - About 35 mins to fix
          mordred/ABCIndex.py on lines 53..53

          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

                  w = np.vectorize(lambda i: self.mol.GetAtomWithIdx(int(i)).GetMass())(ids)
          Severity: Minor
          Found in mordred/InformationContent.py and 1 other location - About 35 mins to fix
          mordred/InformationContent.py on lines 319..320

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

              def __new__(cls, classname, bases, dict):
        __init__ = dict.get("__init__")
        if __init__ is None:
            for base in bases:
                __init__ = getattr(base, "__init__", None)
          Severity: Minor
          Found in mordred/_base/descriptor.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

                  ps = np.array([list(conf.GetAtomPosition(i)) for i in range(mol.GetNumAtoms())])
          Severity: Minor
          Found in mordred/surface_area/_sasa.py and 1 other location - About 35 mins to fix
          mordred/_util.py on lines 21..21

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

              def calculate(self, P, chi=None):
        if self._order <= 0:
            chi = ChiBonds([], [{a.GetIdx()} for a in self.mol.GetAtoms()], [], [])

        x = 0.0
          Severity: Minor
          Found in mordred/Chi.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 __call__ has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
          Open

              def __call__(self):
        timeout_at = None if self.timeout is None else time.time() + self.timeout

        for bcc in networkx.biconnected_component_subgraphs(self.G, False):
            lsp = LongestSimplePath(bcc, self.weight, timeout_at)()
          Severity: Minor
          Found in mordred/DetourMatrix.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 calculate has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
          Open

              def calculate(self, An=None, T=None, W=None):
        if self._total:
            if self._order == 1:
                return self.mol.GetNumAtoms() + W
          Severity: Minor
          Found in mordred/WalkCount.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

                  return np.sqrt((du + dv - 2.0) / (du * dv))
          Severity: Minor
          Found in mordred/ABCIndex.py and 1 other location - About 35 mins to fix
          mordred/ABCIndex.py on lines 84..84

          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

                  w = Ags * np.vectorize(
            lambda i: self.mol.GetAtomWithIdx(int(i)).GetAtomicNum()
          Severity: Minor
          Found in mordred/InformationContent.py and 1 other location - About 35 mins to fix
          mordred/InformationContent.py on lines 298..298

          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

              return np.array([list(conf.GetAtomPosition(i)) for i in range(conf.GetNumAtoms())])
          Severity: Minor
          Found in mordred/_util.py and 1 other location - About 35 mins to fix
          mordred/surface_area/_sasa.py on lines 111..111

          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

          Avoid too many return statements within this function.
          Open

                      return np.log(An.sum() + 1)
          Severity: Major
          Found in mordred/WalkCount.py - About 30 mins to fix

            Avoid too many return statements within this function.
            Open

                                return 25.30
            Severity: Major
            Found in mordred/TopoPSA.py - About 30 mins to fix
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