Bond.stereo_symbol() - Code Metrics - Inspection of "Added a lot of functionality and tests to core." - richlewis42/scikit-chem - Measure and Improve Code Quality continuously with Scrutinizer

Completed

Push — master ( 87dea9...e88bec )

by Rich

created 2016-08-25 13:45 UTC

Bond.stereo_symbol() A

↳ Parent: Project

Complexity

Conditions

Size

Total Lines

Duplication

Lines	0
Ratio	0 %

Code Coverage

Tests	3
CRAP Score	1.0156

Importance

Changes	1
Bugs	0	Features	0

Metric	Value
c	1
b	0
f	0
dl	0
loc	6
ccs	3
cts	4
cp	0.75
rs	9.4285
cc	1
crap	1.0156

#! /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
import numpy as np
# .scrutinizer.yml
before_commands:
    - sudo pip install abc # Python2
    - sudo pip3 install abc # Python3

from .atom 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 atoms(self):

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

        return (Atom.from_super(self.GetBeginAtom()),

                Atom.from_super(self.GetEndAtom()))


    @property
    def atom_idxs(self):

        """ tuple[int]: list of atom indexes involved in the bond. """

        return (self.GetBeginAtomIdx(), self.GetEndAtomIdx())


    @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 is_aromatic(self):

        """ bool: whether the bond is aromatic. """

        return self.GetIsAromatic()


    @property
    def is_conjugated(self):

        """ bool: whether the bond is conjugated. """

        return self.GetIsConjugated()


    @property
    def owner(self):

        """ skchem.Mol: the molecule this bond is a part of. """

        from .mol import Mol
        return Mol.from_super(self.GetOwningMol())


    @property
    def stereo_symbol(self):

        """ str: the stereo label of the bond ('Z', 'E', 'ANY', 'NONE') """

        return self.GetStereo().name.lstrip('STEREO')


    @property
    def is_in_ring(self):

        """ bool: whether the bond is in a ring. """

        return self.IsInRing()


    def draw(self):

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

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

                               self.atoms[1].symbol)

    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):
        res = super(BondView, self).__getitem__(index)
        if res is None:
            if abs(index) >= len(self):
                raise IndexError('Index {} out of range for molecule with '
                                 '{} bonds.'.format(index, len(self)))

            # index is negative, so adding gives desired indexing from back
            if index < 0:
                index += len(self)

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

        else:
            return res

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

    @property
    def atom_idxs(self):

        """ The atom indices for the bonds in the view. """

        return np.array([atom.atom_idxs for atom in self])

    @property
    def order(self):

        """ np.array<int> the bond orders of the bonds in the view. """

        return np.array([bond.order for bond in self])

    @property
    def is_aromatic(self):

        """ np.array<bool> whether each of the bonds in the view are
        aromatic. """

        return np.array([bond.is_aromatic for bond in self])

    @property
    def is_conjugated(self):

        """ np.array<bool> whether each of the bonds in the view are c
        onjugated. """

        return np.array([bond.is_conjugated for bond in self])

    @property
    def is_in_ring(self):

        """ np.array<bool> whether each of the bonds in the view are in a
        ring. """

        return np.array([bond.is_in_ring for bond in self])

    @property
    def stereo_symbol(self):

        """ np.array<str> the stereo symbol of the bonds in the view. """

        return np.array([bond.stereo_symbol for bond in self])

    @property
    def index(self):

        """ A `pd.Index` of the bonds in the `BondView`. """

        return pd.RangeIndex(len(self), name='bond_idx')

__all__ = ['Atom', 'AtomView']



Push — master ( 87dea9...e88bec )

Bond.stereo_symbol() A

Complexity

Size

Duplication

Code Coverage

Importance

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) 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		import numpy as np
		0 ignored issues – show Configuration introduced 2016-08-25 14:00 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...
15	1
16	1	from .atom import Atom
17		from .base import ChemicalObject, PropertyView, ChemicalObjectView
18
19	1
20		class Bond(rdkit.Chem.rdchem.Bond, ChemicalObject):
21
22		"""
23		Class representing a chemical bond in scikit-chem.
24
25		"""
26	1
27		@property
28		def atoms(self):
29
30		""" tuple[Atom]: list of atoms involved in the bond. """
31
32		return (Atom.from_super(self.GetBeginAtom()),
		0 ignored issues – show Bug introduced 2016-08-25 14:00 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...
33		Atom.from_super(self.GetEndAtom()))
		0 ignored issues – show Bug introduced 2016-08-25 14:00 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...
34
35	1	@property
36		def atom_idxs(self):
37
38		""" tuple[int]: list of atom indexes involved in the bond. """
39
40	1	return (self.GetBeginAtomIdx(), self.GetEndAtomIdx())
		0 ignored issues – show Bug introduced 2016-08-25 14:00 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 2016-08-25 14:00 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...
41
42	1	@property
43		def props(self):
44
45		""" PropertyView: rdkit properties of the atom. """
46
47	1	if not hasattr(self, '_props'):
48		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...
49		return PropertyView(self)
50	1
51		@property
52		def order(self):
53
54	1	""" int: the order of the bond. """
55
56		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...
57
58	1	@property
59		def is_aromatic(self):
60
61		""" bool: whether the bond is aromatic. """
62
63		return self.GetIsAromatic()
		0 ignored issues – show Bug introduced 2016-08-25 14:00 UTC by Report Bug Copy Issue Report The Instance of `Bond` does not seem to have a member named `GetIsAromatic`. 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...
64
65		@property
66	1	def is_conjugated(self):
67
68		""" bool: whether the bond is conjugated. """
69
70		return self.GetIsConjugated()
		0 ignored issues – show Bug introduced 2016-08-25 14:00 UTC by Report Bug Copy Issue Report The Instance of `Bond` does not seem to have a member named `GetIsConjugated`. 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...
71
72	1	@property
73	1	def owner(self):
74
75		""" skchem.Mol: the molecule this bond is a part of. """
76	1
77		from .mol import Mol
78		return Mol.from_super(self.GetOwningMol())
		0 ignored issues – show Bug introduced 2016-08-25 14:00 UTC by Report Bug Copy Issue Report The Instance of `Bond` does not seem to have a member named `GetOwningMol`. 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...
79	1
80	1	@property
81	1	def stereo_symbol(self):
82	1
83		""" str: the stereo label of the bond ('Z', 'E', 'ANY', 'NONE') """
84
85		return self.GetStereo().name.lstrip('STEREO')
		0 ignored issues – show Bug introduced 2016-08-25 14:00 UTC by Report Bug Copy Issue Report The Instance of `Bond` does not seem to have a member named `GetStereo`. 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...
86	1
87		@property
88		def is_in_ring(self):
89
90	1	""" bool: whether the bond is in a ring. """
91	1
92		return self.IsInRing()
		0 ignored issues – show Bug introduced 2016-08-25 14:00 UTC by Report Bug Copy Issue Report The Instance of `Bond` does not seem to have a member named `IsInRing`. 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...
93	1
94		def draw(self):
95
96		""" str: Draw the bond in ascii. """
97
98		return '{}{}{}'.format(self.atoms[0].symbol,
99	1	'-' 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...
100		self.atoms[1].symbol)
101
102		def to_dict(self):
103
104		""" dict: Convert to a dictionary representation. """
105
106		return {"b": self.GetBeginAtomIdx(),
		0 ignored issues – show Bug introduced 2016-08-16 15:32 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...
107		"e": self.GetEndAtomIdx(),
		0 ignored issues – show Bug introduced 2016-08-16 15:32 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...
108		"o": self.order}
109
110		def __repr__(self):
111		return '<{klass} type="{bond}" at {address}>'.format(
112		klass=self.__class__.__name__,
113		bond=self.draw(),
114		address=hex(id(self)))
115
116		def __str__(self):
117		return self.draw()
118
119
120		class BondView(ChemicalObjectView):
121
122		""" Bond interface wrapper """
123		def __getitem__(self, index):
124		res = super(BondView, self).__getitem__(index)
125		if res is None:
126		if abs(index) >= len(self):
127		raise IndexError('Index {} out of range for molecule with '
128		'{} bonds.'.format(index, len(self)))
129
130		# index is negative, so adding gives desired indexing from back
131		if index < 0:
132		index += len(self)
133
134		return Bond.from_super(self.owner.GetBondWithIdx(index))
135
136		else:
137		return res
138
139		def __len__(self):
140		return self.owner.GetNumBonds()
141
142		@property
143		def atom_idxs(self):
144
145		""" The atom indices for the bonds in the view. """
146
147		return np.array([atom.atom_idxs for atom in self])
148
149		@property
150		def order(self):
151
152		""" np.array<int> the bond orders of the bonds in the view. """
153
154		return np.array([bond.order for bond in self])
155
156		@property
157		def is_aromatic(self):
158
159		""" np.array<bool> whether each of the bonds in the view are
160		aromatic. """
161
162		return np.array([bond.is_aromatic for bond in self])
163
164		@property
165		def is_conjugated(self):
166
167		""" np.array<bool> whether each of the bonds in the view are c
168		onjugated. """
169
170		return np.array([bond.is_conjugated for bond in self])
171
172		@property
173		def is_in_ring(self):
174
175		""" np.array<bool> whether each of the bonds in the view are in a
176		ring. """
177
178		return np.array([bond.is_in_ring for bond in self])
179
180		@property
181		def stereo_symbol(self):
182
183		""" np.array<str> the stereo symbol of the bonds in the view. """
184
185		return np.array([bond.stereo_symbol for bond in self])
186
187		@property
188		def index(self):
189
190		""" A `pd.Index` of the bonds in the `BondView`. """
191
192		return pd.RangeIndex(len(self), name='bond_idx')
193
194		__all__ = ['Atom', 'AtomView']
		0 ignored issues – show Bug introduced 2016-08-25 14:00 UTC by Report Bug Copy Issue Report Undefined variable name 'AtomView' in __all__ Loading history...
195

richlewis42 / scikit-chem

Push — master ( 87dea9...e88bec )

Bond.stereo_symbol() A

Complexity

Size

Duplication

Code Coverage

Importance

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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