joaomcteixeira/taurenmd

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src/taurenmd/libs/libcalc.py

Summary

Maintainability
A
50 mins
Test Coverage

Use of assert detected. The enclosed code will be removed when compiling to optimised byte code.
Open

    assert coords.shape[0] > 3
Severity: Info
Found in src/taurenmd/libs/libcalc.py by bandit

Use of assert detected. The enclosed code will be removed when compiling to optimised byte code.
Open

    assert p4_vecs.shape[1] == 3
Severity: Info
Found in src/taurenmd/libs/libcalc.py by bandit

Use of assert detected. The enclosed code will be removed when compiling to optimised byte code.
Open

    assert coords.shape[1] == 3

Severity: Info
Found in src/taurenmd/libs/libcalc.py by bandit

Use of assert detected. The enclosed code will be removed when compiling to optimised byte code.
Open

    assert n1.shape == (3,)
Severity: Info
Found in src/taurenmd/libs/libcalc.py by bandit

Use of assert detected. The enclosed code will be removed when compiling to optimised byte code.
Open

    assert n2.shape == p4_vecs.shape, f'{n2.shape}, {p4_vecs.shape}'

Severity: Info
Found in src/taurenmd/libs/libcalc.py by bandit

Use of assert detected. The enclosed code will be removed when compiling to optimised byte code.
Open

    assert u2.shape == p4_vecs.shape

Severity: Info
Found in src/taurenmd/libs/libcalc.py by bandit

Use of assert detected. The enclosed code will be removed when compiling to optimised byte code.
Open

    assert q1x2.shape == (3,)
Severity: Info
Found in src/taurenmd/libs/libcalc.py by bandit

Use of assert detected. The enclosed code will be removed when compiling to optimised byte code.
Open

    assert theta.size == p4_vecs.shape[0]
Severity: Info
Found in src/taurenmd/libs/libcalc.py by bandit

Use of assert detected. The enclosed code will be removed when compiling to optimised byte code.
Open

    assert q2x3s.shape == q3s.shape

Severity: Info
Found in src/taurenmd/libs/libcalc.py by bandit

Use of assert detected. The enclosed code will be removed when compiling to optimised byte code.
Open

    assert q3s.shape == p4_vecs.shape

Severity: Info
Found in src/taurenmd/libs/libcalc.py by bandit

Function calc_planes_angle has 7 arguments (exceeds 4 allowed). Consider refactoring.
Open

def calc_planes_angle(a1, b1, c1, a2, b2, c2, aunit='radians'):
Severity: Major
Found in src/taurenmd/libs/libcalc.py - About 50 mins to fix

    Remove this commented out code.
    Open

        # rmsds[:, ii] = R.rmsd[:, 2][self._fslicer]
    Severity: Major
    Found in src/taurenmd/libs/libcalc.py by sonar-python

    Programmers should not comment out code as it bloats programs and reduces readability.

    Unused code should be deleted and can be retrieved from source control history if required.

    See

    • MISRA C:2004, 2.4 - Sections of code should not be "commented out".
    • MISRA C++:2008, 2-7-2 - Sections of code shall not be "commented out" using C-style comments.
    • MISRA C++:2008, 2-7-3 - Sections of code should not be "commented out" using C++ comments.
    • MISRA C:2012, Dir. 4.4 - Sections of code should not be "commented out"

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