In https://github.com/biopython/biopython/blob/518c4be6ae16f1e00bfd55781171da91282b340a/Bio/SeqUtils/ProtParam.py I have this importing statement:
from Bio.SeqUtils import molecular_weight
and then in a class:
class ProteinAnalysis:
.....
.....
def molecular_weight(self):
"""Calculate MW from Protein sequence."""
return molecular_weight(
self.sequence, seq_type="protein", monoisotopic=self.monoisotopic
)
......
......
What is this type of coding called? Is it normal to call imported function and class method with same name?
To my knowledge, self.molecular_weights
is not equal to molecular_weights
, but why call them the same? Is that PEP 8 compliant?
Would
a = ProteinAnalysis()
print(a.molecular_weights == molecular_weights)
give True
or False
?
What about:
print(a.molecular_weights(*args,**kwargs) == molecular_weights(*args, **kwargs))
Yes. This is normal as there is no contradiction. You cannot freely get access to any class attributes even in methods inside a class. For example, let's look at this:
var = 5
class SomeClass:
var = 6
def show(self):
print(var)
SomeClass().show()
The result is 5
. As there is only one "variable" var
in global scope.
If we unlink it via del var
, we will get NameError
:
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
Input In [38], in <cell line: 1>()
----> 1 SomeClass.show()
Input In [37], in SomeClass.show()
5 def show():
----> 6 print(var)
NameError: name 'var' is not defined
But you can get free access during the class initialisation:
class SomeClass:
var = 6
print(var)
def show():
print(var)
Hereinabove code prints 6
.
In Biopython code only the imported function is used because the calling is inside a method where there is no direct access to the class attributes. Moreover, the method even is not initialised at the moment.
a.molecular_weights == molecular_weights
gives False
because even if they do the same they are different objects: a method & a function.
molecular_weights() == a.molecular_weights()
would give True
, if the same arguments are sent.
There is no contradiction with PEP8 naming rules as both do the same but one is a function, other is a method of appropriate class and objects.