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mordred-descriptor/mordred

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

    def __str__(self):
        return "GRAV{}{}".format("" if self._heavy else "H", "p" if self._pair else "")
Severity: Major
Found in mordred/GravitationalIndex.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/ExtendedTopochemicalAtom.py on lines 505..508
mordred/GravitationalIndex.py on lines 14..16
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 __str__(self):
        return "{}{}MW".format(
            "A" if self._averaged else "", "" if self._exact else "a"
Severity: Major
Found in mordred/Weight.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/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

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 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 2 locations. Consider refactoring.
Open

    all_functions = (getattr(mdl, name) for name in __all__ if name[:1] != "_")
Severity: Minor
Found in mordred/_base/calculator.py and 1 other location - About 30 mins to fix
mordred/_base/calculator.py on lines 453..453

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 2 locations. Consider refactoring.
Open

        self.bonds = [
            (b.GetBeginAtomIdx(), b.GetEndAtomIdx()) for b in self.mol.GetBonds()
Severity: Minor
Found in mordred/Chi.py and 1 other location - About 30 mins to fix
mordred/PathCount.py on lines 25..27

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 "{}{}molecular weight".format(
            "averaged " if self._averaged else "", "exact " if self._exact else ""
Severity: Major
Found in mordred/Weight.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/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 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 2 locations. Consider refactoring.
Open

        for i, j in ((i, j) for i in range(L) for j in range(i + 1, L)):
Severity: Minor
Found in mordred/RingCount.py and 1 other location - About 30 mins to fix
mordred/Framework.py on lines 36..36

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

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

    def description(self):
        return "{}{}gravitational index".format(
            "heavy atom " if self._heavy else "", "pair " if self._pair else ""
Severity: Major
Found in mordred/GravitationalIndex.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/ExtendedTopochemicalAtom.py on lines 505..508
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 2 locations. Consider refactoring.
Open

    all_values = (getattr(mdl, name) for name in __all__ if name[:1] != "_")
Severity: Minor
Found in mordred/_base/calculator.py and 1 other location - About 30 mins to fix
mordred/_base/calculator.py on lines 419..419

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 2 locations. Consider refactoring.
Open

    def _gen_bonds(self):
        self._bonds = [
            (b.GetBeginAtomIdx(), b.GetEndAtomIdx()) for b in self.mol.GetBonds()
Severity: Minor
Found in mordred/PathCount.py and 1 other location - About 30 mins to fix
mordred/Chi.py on lines 67..68

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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