PhysicochemicalFingerprinter - Code Metrics - Inspection of "updated descriptors for efficiency and to work wit..." - richlewis42/scikit-chem - Measure and Improve Code Quality continuously with Scrutinizer

Completed

Push — master ( c7f259...9726b9 )

by Rich

created 2016-06-02 13:35 UTC

PhysicochemicalFingerprinter A

↳ Parent: Project

Complexity

Total Complexity

Size/Duplication

Total Lines	27
Duplicated Lines	0 %

Importance

Changes	3
Bugs	0	Features	1

Metric	Value
c	3
b	0
f	1
dl	0
loc	27
rs	10
wmc	5

3 Methods

Rating	Name	Size	Complexity
A	_transform()	3	2
A	__init__()	13	2
A	index()	3	1

#! /usr/bin/env python
#
# Copyright (C) 2007-2009 Rich Lewis <[email protected]>
# License: 3-clause BSD

"""
## skchem.descriptors.physicochemical

Physicochemical descriptors and associated functions are defined.

"""

from rdkit.Chem import Descriptors
# .scrutinizer.yml
before_commands:
    - sudo pip install abc # Python2
    - sudo pip3 install abc # Python3
import pandas as pd
# .scrutinizer.yml
before_commands:
    - sudo pip install abc # Python2
    - sudo pip3 install abc # Python3
import numpy as np
# .scrutinizer.yml
before_commands:
    - sudo pip install abc # Python2
    - sudo pip3 install abc # Python3

from .fingerprints import Fingerprinter
from ..utils import camel_to_snail

DESCRIPTORS = [(camel_to_snail(s), f) for (s, f) in Descriptors.descList]

class PhysicochemicalFingerprinter(Fingerprinter):

    """ Physicochemical descriptor generator using RDKit descriptor """

    NAME = 'physchem'

    def __init__(self, descriptors='all'):
class SomeParent:
    def __init__(self):
        self.x = 1

class SomeChild(SomeParent):
    def __init__(self):
        # Initialize the super class
        SomeParent.__init__(self)

        """ Create a physicochemical descriptor generator.

        Args:
            descriptors (list<(str, func)> or 'all'):
                Descriptors to calculate, or if 'all', use all descriptors."""

        if descriptors == 'all':
            self.descriptors = DESCRIPTORS
        else:
            self.descriptors = descriptors
        self.descriptor_names, _ = zip(*self.descriptors)

    @property
    def index(self):
        return self.descriptor_names

    def _transform(self, mol):

        return np.array([f(mol) for (n, f) in self.descriptors])
param = 5

class Foo:
    def __init__(self, param):   # "param" would be flagged here
        self.param = param


Push — master ( c7f259...9726b9 )

PhysicochemicalFingerprinter A

Complexity

Size/Duplication

Importance

3 Methods

1. Missing Dependencies

2. Missing init.py files

1. Missing Dependencies

2. Missing init.py files

1. Missing Dependencies

2. Missing init.py files

1			#! /usr/bin/env python
2			#
3			# Copyright (C) 2007-2009 Rich Lewis <[email protected]>
4			# License: 3-clause BSD
5
6			"""
7			## skchem.descriptors.physicochemical
8
9			Physicochemical descriptors and associated functions are defined.
10
11			"""
12
13			from rdkit.Chem import Descriptors
			0 ignored issues – show Configuration introduced 2016-04-14 16:48 UTC by Report Bug Copy Issue Report The import `rdkit.Chem` could not be resolved. This can be caused by one of the following: 1. Missing Dependencies This error could indicate a configuration issue of Pylint. Make sure that your libraries are available by adding the necessary commands. # .scrutinizer.yml before_commands: - sudo pip install abc # Python2 - sudo pip3 install abc # Python3 Tip: We are currently not using virtualenv to run pylint, when installing your modules make sure to use the command for the correct version. 2. Missing __init__.py files This error could also result from missing `__init__.py` files in your module folders. Make sure that you place one file in each sub-folder. Loading history...
14			import pandas as pd
			0 ignored issues – show Configuration introduced 2016-04-14 16:48 UTC by Report Bug Copy Issue Report The import `pandas` could not be resolved. This can be caused by one of the following: 1. Missing Dependencies This error could indicate a configuration issue of Pylint. Make sure that your libraries are available by adding the necessary commands. # .scrutinizer.yml before_commands: - sudo pip install abc # Python2 - sudo pip3 install abc # Python3 Tip: We are currently not using virtualenv to run pylint, when installing your modules make sure to use the command for the correct version. 2. Missing __init__.py files This error could also result from missing `__init__.py` files in your module folders. Make sure that you place one file in each sub-folder. Loading history... Unused Code introduced 2016-06-02 13:37 UTC by Report Bug Copy Issue Report Unused pandas imported as pd Loading history...
15			import numpy as np
			0 ignored issues – show Configuration introduced 2016-06-02 13:37 UTC by Report Bug Copy Issue Report The import `numpy` could not be resolved. This can be caused by one of the following: 1. Missing Dependencies This error could indicate a configuration issue of Pylint. Make sure that your libraries are available by adding the necessary commands. # .scrutinizer.yml before_commands: - sudo pip install abc # Python2 - sudo pip3 install abc # Python3 Tip: We are currently not using virtualenv to run pylint, when installing your modules make sure to use the command for the correct version. 2. Missing __init__.py files This error could also result from missing `__init__.py` files in your module folders. Make sure that you place one file in each sub-folder. Loading history...
16
17			from .fingerprints import Fingerprinter
18			from ..utils import camel_to_snail
19
20			DESCRIPTORS = [(camel_to_snail(s), f) for (s, f) in Descriptors.descList]
21
22			class PhysicochemicalFingerprinter(Fingerprinter):
23
24			""" Physicochemical descriptor generator using RDKit descriptor """
25
26			NAME = 'physchem'
27
28			def __init__(self, descriptors='all'):
			0 ignored issues – show Bug introduced 2016-04-14 16:48 UTC by Report Bug Copy Issue Report The `__init__` method of the super-class `Fingerprinter` is not called. It is generally advisable to initialize the super-class by calling its `__init__` method: class SomeParent: def __init__(self): self.x = 1 class SomeChild(SomeParent): def __init__(self): # Initialize the super class SomeParent.__init__(self) Loading history...
29
30			""" Create a physicochemical descriptor generator.
31
32			Args:
33			descriptors (list<(str, func)> or 'all'):
34			Descriptors to calculate, or if 'all', use all descriptors."""
35
36			if descriptors == 'all':
37			self.descriptors = DESCRIPTORS
38			else:
39			self.descriptors = descriptors
40			self.descriptor_names, _ = zip(*self.descriptors)
41
42			@property
43			def index(self):
44			return self.descriptor_names
45
46			def _transform(self, mol):
47
48			return np.array([f(mol) for (n, f) in self.descriptors])
			0 ignored issues – show Comprehensibility Bug introduced 2016-06-02 13:37 UTC by Report Bug Copy Issue Report `f` is re-defining a name which is already available in the outer-scope (previously defined on line `20`). It is generally a bad practice to shadow variables from the outer-scope. In most cases, this is done unintentionally and might lead to unexpected behavior: param = 5 class Foo: def __init__(self, param): # "param" would be flagged here self.param = param Loading history... Unused Code introduced 2016-06-02 13:37 UTC by Report Bug Copy Issue Report The variable `n` seems to be unused. Loading history...
49

richlewis42 / scikit-chem

Push — master ( c7f259...9726b9 )

PhysicochemicalFingerprinter A

Complexity

Size/Duplication

Importance

3 Methods

1. Missing Dependencies

2. Missing __init__.py files

1. Missing Dependencies

2. Missing __init__.py files

1. Missing Dependencies

2. Missing __init__.py files

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