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examples/adress/fadress_protein/ubiquitin.py

Summary

Maintainability
F
3 days
Test Coverage

File ubiquitin.py has 316 lines of code (exceeds 250 allowed). Consider refactoring.
Open

#!/usr/bin/env python3
#  Copyright (C) 2016-2017(H)
#      Max Planck Institute for Polymer Research
#
#  This file is part of ESPResSo++.
Severity: Minor
Found in examples/adress/fadress_protein/ubiquitin.py - About 3 hrs to fix

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

            allParticles.append([particlePID[aaindex],
                          particleTypes[aaindex],
                          Real3D(particleX[aaindex],particleY[aaindex],particleZ[aaindex]),
                          Real3D(particleVX[aaindex],particleVY[aaindex],particleVZ[aaindex]),
                          particleMasses[aaindex],particleCharges[aaindex],1])
    Severity: Major
    Found in examples/adress/fadress_protein/ubiquitin.py and 2 other locations - About 5 hrs to fix
    examples/adress/fadress_protein/ubiquitin.py on lines 271..275
    examples/adress/fadress_protein/ubiquitin.py on lines 294..297

    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 89.

    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

        allParticles.append([particlePID[cgindex],
                        particleTypes[cgindex],
                        Real3D(particleX[cgindex],particleY[cgindex],particleZ[cgindex]),
                        Real3D(particleVX[cgindex],particleVY[cgindex],particleVZ[cgindex]),
                        particleMasses[cgindex],particleCharges[cgindex],0])
    Severity: Major
    Found in examples/adress/fadress_protein/ubiquitin.py and 2 other locations - About 5 hrs to fix
    examples/adress/fadress_protein/ubiquitin.py on lines 280..284
    examples/adress/fadress_protein/ubiquitin.py on lines 294..297

    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 89.

    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

        allParticles.append([particlePID[i],particleTypes[i],
                        Real3D(particleX[i],particleY[i],particleZ[i]),
                        Real3D(particleVX[i],particleVY[i],particleVZ[i]),
                        particleMasses[i],particleCharges[i],1])
    Severity: Major
    Found in examples/adress/fadress_protein/ubiquitin.py and 2 other locations - About 5 hrs to fix
    examples/adress/fadress_protein/ubiquitin.py on lines 271..275
    examples/adress/fadress_protein/ubiquitin.py on lines 280..284

    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 89.

    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 atkey in list(atDihedraltypes.keys()):
    newDihedraltypes=[]
    for (a1,a2,a3,a4) in atDihedraltypes[atkey]:
        newDihedraltypes.append((mapAtToCgIndex[a1],mapAtToCgIndex[a2],mapAtToCgIndex[a3],mapAtToCgIndex[a4]))
    cgDihedraltypes[atkey]=newDihedraltypes
    Severity: Major
    Found in examples/adress/fadress_protein/ubiquitin.py and 1 other location - About 4 hrs to fix
    examples/adress/fadress_protein/ubiquitin.py on lines 423..427

    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 85.

    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 atkey in list(atImpropertypes.keys()):
    newImpropertypes=[]
    for (a1,a2,a3,a4) in atImpropertypes[atkey]:
        newImpropertypes.append((mapAtToCgIndex[a1],mapAtToCgIndex[a2],mapAtToCgIndex[a3],mapAtToCgIndex[a4]))
    cgImpropertypes[atkey]=newImpropertypes
    Severity: Major
    Found in examples/adress/fadress_protein/ubiquitin.py and 1 other location - About 4 hrs to fix
    examples/adress/fadress_protein/ubiquitin.py on lines 414..418

    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 85.

    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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