Bond.props() - Code Metrics - Inspection of "Merge branch 'master' of https://github.com/richle..." - richlewis42/scikit-chem - Measure and Improve Code Quality continuously with Scrutinizer

Completed

Push — master ( 1b49d8...c3d981 )

by Rich

created 2016-08-08 14:38 UTC

Bond.props() A

↳ Parent: Project

Complexity

Conditions

Size

Total Lines

Duplication

Lines	0
Ratio	0 %

Code Coverage

Tests	1
CRAP Score	2.5

Importance

Changes	1
Bugs	0	Features	0

Metric	Value
c	1
b	0
f	0
dl	0
loc	8
ccs	1
cts	2
cp	0.5
rs	9.4285
cc	2
crap	2.5

#! /usr/bin/env python
#
# Copyright (C) 2015-2016 Rich Lewis <[email protected]>
# License: 3-clause BSD

"""
## skchem.core.bond

Defining chemical bonds in scikit-chem.
"""

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

from . import Atom
from .base import ChemicalObject, PropertyView, ChemicalObjectView

class Bond(rdkit.Chem.rdchem.Bond, ChemicalObject):

    """
    Class representing a chemical bond in scikit-chem.

    """

    @property
    def props(self):

        """ PropertyView: rdkit properties of the atom. """

        if not hasattr(self, '_props'):
            self._props = PropertyView(self)
class Foo:
    def __init__(self, x=None):
        self.x = x
        return PropertyView(self)

    @property
    def order(self):

        """ int: the order of the bond. """

        return self.GetBondTypeAsDouble()


    @property
    def atoms(self):

        """ list[Atom]: list of atoms involved in the bond. """

        return [Atom.from_super(self.GetBeginAtom()), Atom.from_super(self.GetEndAtom())]


    def draw(self):

        """ str: Draw the bond in ascii. """

        return '{}{}{}'.format(self.atoms[0].element, \
            '-' if self.order == 1 else self.GetSmarts(), \

            self.atoms[1].element)

    def to_dict(self):

        """ dict: Convert to a dictionary representation. """

        return {"b": self.GetBeginAtomIdx(), "e": self.GetEndAtomIdx(), "o": self.order}


    def __repr__(self):
        return '<{klass} type="{bond}" at {address}>'.format(klass=self.__class__.__name__, \
            bond=self.draw(), \
            address=hex(id(self)))

    def __str__(self):
        return self.draw()


class BondView(ChemicalObjectView):

    """ Bond interface wrapper """
    def __getitem__(self, index):
        from .bond import Bond
param = 5

class Foo:
    def __init__(self, param):   # "param" would be flagged here
        self.param = param
        if index >= len(self):
            raise IndexError('Index {} out of range for molecule with {} bonds.'.format(index, len(self)))

        else:
            return Bond.from_super(self.owner.GetBondWithIdx(index))


    def __len__(self):
        return self.owner.GetNumBonds()

    @property
    def order(self):
class SomeClass:
    def some_method(self):
        """Do x and return foo."""
        return pd.RangeIndex((bond.order for bond in self), index=self.index)

    @property
    def index(self):
class SomeClass:
    def some_method(self):
        """Do x and return foo."""
        return pd.RangeIndex(len(self), name='bond_idx')


1		#! /usr/bin/env python
2		#
3		# Copyright (C) 2015-2016 Rich Lewis <[email protected]>
4		# License: 3-clause BSD
5
6	1	"""
7		## skchem.core.bond
8
9		Defining chemical bonds in scikit-chem.
10		"""
11
12	1	import pandas as pd
		0 ignored issues – show Configuration introduced 2016-08-08 14:55 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...
13	1	import rdkit.Chem
		0 ignored issues – show Configuration introduced 2016-01-19 16:21 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	1
15		from . import Atom
16	1	from .base import ChemicalObject, PropertyView, ChemicalObjectView
17
18		class Bond(rdkit.Chem.rdchem.Bond, ChemicalObject):
19
20		"""
21		Class representing a chemical bond in scikit-chem.
22
23	1	"""
24
25		@property
26		def props(self):
27
28		""" PropertyView: rdkit properties of the atom. """
29
30	1	if not hasattr(self, '_props'):
31		self._props = PropertyView(self)
		0 ignored issues – show Coding Style introduced 2016-08-08 14:55 UTC by Report Bug Copy Issue Report The attribute `_props` was defined outside `__init__`. It is generally a good practice to initialize all attributes to default values in the `__init__` method: class Foo: def __init__(self, x=None): self.x = x Loading history...
32		return PropertyView(self)
33
34		@property
35		def order(self):
36
37	1	""" int: the order of the bond. """
38
39		return self.GetBondTypeAsDouble()
		0 ignored issues – show Bug introduced 2016-01-19 16:21 UTC by Report Bug Copy Issue Report The Instance of `Bond` does not seem to have a member named `GetBondTypeAsDouble`. This check looks for calls to members that are non-existent. These calls will fail. The member could have been renamed or removed. Loading history...
40
41		@property
42		def atoms(self):
43
44		""" list[Atom]: list of atoms involved in the bond. """
45	1
46		return [Atom.from_super(self.GetBeginAtom()), Atom.from_super(self.GetEndAtom())]
		0 ignored issues – show Bug introduced 2016-01-19 16:21 UTC by Report Bug Copy Issue Report The Instance of `Bond` does not seem to have a member named `GetBeginAtom`. This check looks for calls to members that are non-existent. These calls will fail. The member could have been renamed or removed. Loading history... Bug introduced 2016-01-19 16:21 UTC by Report Bug Copy Issue Report The Instance of `Bond` does not seem to have a member named `GetEndAtom`. This check looks for calls to members that are non-existent. These calls will fail. The member could have been renamed or removed. Loading history...
47
48		def draw(self):
49
50		""" str: Draw the bond in ascii. """
51	1
52		return '{}{}{}'.format(self.atoms[0].element, \
53		'-' if self.order == 1 else self.GetSmarts(), \
		0 ignored issues – show Bug introduced 2016-01-19 16:21 UTC by Report Bug Copy Issue Report The Instance of `Bond` does not seem to have a member named `GetSmarts`. This check looks for calls to members that are non-existent. These calls will fail. The member could have been renamed or removed. Loading history...
54		self.atoms[1].element)
55
56	1	def to_dict(self):
57
58		""" dict: Convert to a dictionary representation. """
59
60		return {"b": self.GetBeginAtomIdx(), "e": self.GetEndAtomIdx(), "o": self.order}
		0 ignored issues – show Bug introduced 2016-01-19 16:21 UTC by Report Bug Copy Issue Report The Instance of `Bond` does not seem to have a member named `GetBeginAtomIdx`. This check looks for calls to members that are non-existent. These calls will fail. The member could have been renamed or removed. Loading history... Bug introduced 2016-01-19 16:21 UTC by Report Bug Copy Issue Report The Instance of `Bond` does not seem to have a member named `GetEndAtomIdx`. This check looks for calls to members that are non-existent. These calls will fail. The member could have been renamed or removed. Loading history...
61
62		def __repr__(self):
63		return '<{klass} type="{bond}" at {address}>'.format(klass=self.__class__.__name__, \
64		bond=self.draw(), \
65		address=hex(id(self)))
66
67		def __str__(self):
68		return self.draw()
69
70
71		class BondView(ChemicalObjectView):
72
73		""" Bond interface wrapper """
74		def __getitem__(self, index):
75		from .bond import Bond
		0 ignored issues – show Comprehensibility Bug introduced 2016-08-08 14:55 UTC by Report Bug Copy Issue Report `Bond` is re-defining a name which is already available in the outer-scope (previously defined on line `18`). 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... Bug introduced 2016-08-08 14:55 UTC by Report Bug Copy Issue Report This module seems to import itself. Loading history...
76		if index >= len(self):
77		raise IndexError('Index {} out of range for molecule with {} bonds.'.format(index, len(self)))
		0 ignored issues – show Coding Style introduced 2016-08-08 14:55 UTC by Report Bug Copy Issue Report This line is too long as per the coding-style (106/100). This check looks for lines that are too long. You can specify the maximum line length. Loading history...
78		else:
79		return Bond.from_super(self.owner.GetBondWithIdx(index))
80
81
82		def __len__(self):
83		return self.owner.GetNumBonds()
84
85		@property
86		def order(self):
		0 ignored issues – show Coding Style introduced 2016-08-08 14:55 UTC by Report Bug Copy Issue Report This method should have a docstring. The coding style of this project requires that you add a docstring to this code element. Below, you find an example for methods: class SomeClass: def some_method(self): """Do x and return foo.""" If you would like to know more about docstrings, we recommend to read PEP-257: Docstring Conventions. Loading history...
87		return pd.RangeIndex((bond.order for bond in self), index=self.index)
88
89		@property
90		def index(self):
		0 ignored issues – show Coding Style introduced 2016-08-08 14:55 UTC by Report Bug Copy Issue Report This method should have a docstring. The coding style of this project requires that you add a docstring to this code element. Below, you find an example for methods: class SomeClass: def some_method(self): """Do x and return foo.""" If you would like to know more about docstrings, we recommend to read PEP-257: Docstring Conventions. Loading history...
91		return pd.RangeIndex(len(self), name='bond_idx')
92

Push — master ( 1b49d8...c3d981 )

Bond.props() A

Complexity

Size

Duplication

Code Coverage

Importance

1. Missing Dependencies

2. Missing init.py files

1. Missing Dependencies

2. Missing init.py files

richlewis42 / scikit-chem

Push — master ( 1b49d8...c3d981 )

Bond.props() A

Complexity

Size

Duplication

Code Coverage

Importance

1. Missing Dependencies

2. Missing __init__.py files

1. Missing Dependencies

2. Missing __init__.py files

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