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mordred/ExtendedTopochemicalAtom.py

Summary

Maintainability
D
3 days
Test Coverage

File ExtendedTopochemicalAtom.py has 577 lines of code (exceeds 250 allowed). Consider refactoring.
Open

r"""Extended Topochemical Atom(ETA) descriptor.

References
    * :doi:`10.1021/ci0342066`
    * :doi:`10.1016/j.jhazmat.2013.03.023`
Severity: Major
Found in mordred/ExtendedTopochemicalAtom.py - About 1 day to fix

    Function calculate has a Cognitive Complexity of 23 (exceeds 5 allowed). Consider refactoring.
    Open

        def calculate(self):
        new = Chem.RWMol(Chem.Mol())
        ids = {}
        for a in self.mol.GetAtoms():
            if a.GetAtomicNum() == 1:
    Severity: Minor
    Found in mordred/ExtendedTopochemicalAtom.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

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

        def __str__(self):
        loc = "L" if self._local else ""
        ave = "A" if self._averaged else ""

        return "{}ETA_eta_F{}".format(ave, loc)
    Severity: Major
    Found in mordred/ExtendedTopochemicalAtom.py and 3 other locations - About 1 hr to fix
    mordred/ExtendedTopochemicalAtom.py on lines 47..51
    mordred/ExtendedTopochemicalAtom.py on lines 145..149
    mordred/ExtendedTopochemicalAtom.py on lines 515..519

    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 4 locations. Consider refactoring.
    Open

        def __str__(self):
        suffix = "_R" if self._reference else ""
        ave = "A" if self._averaged else ""

        return "{}ETA_alpha{}".format(ave, suffix)
    Severity: Major
    Found in mordred/ExtendedTopochemicalAtom.py and 3 other locations - About 1 hr to fix
    mordred/ExtendedTopochemicalAtom.py on lines 47..51
    mordred/ExtendedTopochemicalAtom.py on lines 457..461
    mordred/ExtendedTopochemicalAtom.py on lines 515..519

    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 4 locations. Consider refactoring.
    Open

        def __str__(self):
        ring = "R" if self._ring else ""
        ave = "A" if self._averaged else ""

        return "{}ETA_eta_B{}".format(ave, ring)
    Severity: Major
    Found in mordred/ExtendedTopochemicalAtom.py and 3 other locations - About 1 hr to fix
    mordred/ExtendedTopochemicalAtom.py on lines 47..51
    mordred/ExtendedTopochemicalAtom.py on lines 145..149
    mordred/ExtendedTopochemicalAtom.py on lines 457..461

    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 4 locations. Consider refactoring.
    Open

        def __str__(self):
        b = "Saturated" if self._saturated else "Reference"
        H = "H" if self.explicit_hydrogens else ""

        return "{}Mol{}".format(b, H)
    Severity: Major
    Found in mordred/ExtendedTopochemicalAtom.py and 3 other locations - About 1 hr to fix
    mordred/ExtendedTopochemicalAtom.py on lines 145..149
    mordred/ExtendedTopochemicalAtom.py on lines 457..461
    mordred/ExtendedTopochemicalAtom.py on lines 515..519

    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

        def calculate(self, eta, eta_R):
        v = eta_R - eta
        if self._averaged:
            v /= self.mol.GetNumAtoms()
    Severity: Major
    Found in mordred/ExtendedTopochemicalAtom.py and 1 other location - About 1 hr to fix
    mordred/ExtendedTopochemicalAtom.py on lines 750..756

    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 41.

    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

        def calculate(self, ns, s):
        v = ns - s

        if self._averaged:
            v /= self.mol.GetNumAtoms()
    Severity: Major
    Found in mordred/ExtendedTopochemicalAtom.py and 1 other location - About 1 hr to fix
    mordred/ExtendedTopochemicalAtom.py on lines 476..481

    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 41.

    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

        @classmethod
    def preset(cls, version):
        return (cls(r, a) for r in [False, True] for a in [False, True])
    Severity: Major
    Found in mordred/ExtendedTopochemicalAtom.py and 2 other locations - About 50 mins to fix
    mordred/ExtendedTopochemicalAtom.py on lines 453..455
    mordred/GravitationalIndex.py on lines 19..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 36.

    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

        @classmethod
    def preset(cls, version):
        return (cls(l, a) for l in [False, True] for a in [False, True])
    Severity: Major
    Found in mordred/ExtendedTopochemicalAtom.py and 2 other locations - About 50 mins to fix
    mordred/ExtendedTopochemicalAtom.py on lines 511..513
    mordred/GravitationalIndex.py on lines 19..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 36.

    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 7 locations. Consider refactoring.
    Open

        def description(self):
        return "{}ETA core count{}".format(
            "averaged " if self._averaged else "",
            " for reference graph" if self._reference else "",
    Severity: Major
    Found in mordred/ExtendedTopochemicalAtom.py and 6 other locations - About 30 mins to fix
    mordred/ExtendedTopochemicalAtom.py on lines 448..450
    mordred/ExtendedTopochemicalAtom.py on lines 505..508
    mordred/GravitationalIndex.py on lines 14..16
    mordred/GravitationalIndex.py on lines 29..30
    mordred/Weight.py on lines 15..17
    mordred/Weight.py on lines 29..31

    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

    Similar blocks of code found in 7 locations. Consider refactoring.
    Open

        def description(self):
        return "{}ETA branching index{}".format(
            "averaged " if self._averaged else "",
            " (use ring count)" if self._ring else "",
    Severity: Major
    Found in mordred/ExtendedTopochemicalAtom.py and 6 other locations - About 30 mins to fix
    mordred/ExtendedTopochemicalAtom.py on lines 135..138
    mordred/ExtendedTopochemicalAtom.py on lines 448..450
    mordred/GravitationalIndex.py on lines 14..16
    mordred/GravitationalIndex.py on lines 29..30
    mordred/Weight.py on lines 15..17
    mordred/Weight.py on lines 29..31

    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

    Similar blocks of code found in 7 locations. Consider refactoring.
    Open

        def description(self):
        return "{}{}ETA functionality index".format(
            "averaged " if self._averaged else "", "local " if self._local else ""
    Severity: Major
    Found in mordred/ExtendedTopochemicalAtom.py and 6 other locations - About 30 mins to fix
    mordred/ExtendedTopochemicalAtom.py on lines 135..138
    mordred/ExtendedTopochemicalAtom.py on lines 505..508
    mordred/GravitationalIndex.py on lines 14..16
    mordred/GravitationalIndex.py on lines 29..30
    mordred/Weight.py on lines 15..17
    mordred/Weight.py on lines 29..31

    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

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