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pytim/writepdb.py

Summary

Maintainability
A
2 hrs
Test Coverage

Cyclomatic complexity is too high in function _writepdb. (9)
Open

def _writepdb(interface,
              filename='layers.pdb',
              centered='no',
              group='all',
              multiframe=True,
Severity: Minor
Found in pytim/writepdb.py by radon

Cyclomatic Complexity

Cyclomatic Complexity corresponds to the number of decisions a block of code contains plus 1. This number (also called McCabe number) is equal to the number of linearly independent paths through the code. This number can be used as a guide when testing conditional logic in blocks.

Radon analyzes the AST tree of a Python program to compute Cyclomatic Complexity. Statements have the following effects on Cyclomatic Complexity:

Construct Effect on CC Reasoning
if +1 An if statement is a single decision.
elif +1 The elif statement adds another decision.
else +0 The else statement does not cause a new decision. The decision is at the if.
for +1 There is a decision at the start of the loop.
while +1 There is a decision at the while statement.
except +1 Each except branch adds a new conditional path of execution.
finally +0 The finally block is unconditionally executed.
with +1 The with statement roughly corresponds to a try/except block (see PEP 343 for details).
assert +1 The assert statement internally roughly equals a conditional statement.
Comprehension +1 A list/set/dict comprehension of generator expression is equivalent to a for loop.
Boolean Operator +1 Every boolean operator (and, or) adds a decision point.

Source: http://radon.readthedocs.org/en/latest/intro.html

Function _writepdb has a Cognitive Complexity of 13 (exceeds 5 allowed). Consider refactoring.
Open

def _writepdb(interface,
              filename='layers.pdb',
              centered='no',
              group='all',
              multiframe=True,
Severity: Minor
Found in pytim/writepdb.py - About 1 hr 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 _writepdb has 6 arguments (exceeds 4 allowed). Consider refactoring.
Open

def _writepdb(interface,
Severity: Minor
Found in pytim/writepdb.py - About 45 mins to fix

Do not use bare 'except'
Open

    except:
Severity: Minor
Found in pytim/writepdb.py by pep8

When catching exceptions, mention specific exceptions when possible.

Okay: except Exception:
Okay: except BaseException:
E722: except:

Do not use bare 'except'
Open

            except:
Severity: Minor
Found in pytim/writepdb.py by pep8

When catching exceptions, mention specific exceptions when possible.

Okay: except Exception:
Okay: except BaseException:
E722: except:

Line too long (81 > 79 characters)
Open

                interface.universe.atoms.positions = interface.original_positions
Severity: Minor
Found in pytim/writepdb.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Comparison to false should be 'if cond is false:' or 'if not cond:'
Open

        if interface.do_center == False:  # we need to center
Severity: Minor
Found in pytim/writepdb.py by pep8

Comparison to singletons should use "is" or "is not".

Comparisons to singletons like None should always be done
with "is" or "is not", never the equality operators.

Okay: if arg is not None:
E711: if arg != None:
E711: if None == arg:
E712: if arg == True:
E712: if False == arg:

Also, beware of writing if x when you really mean if x is not None
-- e.g. when testing whether a variable or argument that defaults to
None was set to some other value.  The other value might have a type
(such as a container) that could be false in a boolean context!

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