skchem.core.Conformer - Code Metrics - Inspection of "updated pylintrc" - richlewis42/scikit-chem - Measure and Improve Code Quality continuously with Scrutinizer

Completed

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by Rich

created 2016-04-14 16:47 UTC

skchem.core.Conformer A

↳ Parent: Project

Complexity

Total Complexity

Size/Duplication

Total Lines	35
Duplicated Lines	0 %

Metric	Value
dl	0
loc	35
rs	10
wmc	6

3 Methods

Rating	Name	Size	Complexity
A	Conformer.is_three_d()	6	1
A	Conformer.__repr__()	3	1
A	Conformer.atom_positions()	6	1

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

"""
skchem.core.conformer

Defining conformers in scikit-chem.
"""

import rdkit.Chem
# .scrutinizer.yml
before_commands:
    - sudo pip install abc # Python2
    - sudo pip3 install abc # Python3
from skchem.core import Point3D
from skchem.core import ChemicalObject

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

    """ Class representing a Conformer in scikit-chem. """
    #should use a view, list for now
    @property
    def atom_positions(self):

        """ Return the atom positions in the conformer for the atoms in the molecule. """

        return [Point3D.from_super(self.GetAtomPosition(i)) for i in range(self.GetNumAtoms())]


    @atom_positions.setter
    def atom_positions(self, value):

        """ Set the atom positions in the conformer.  Not implemented. """

        raise NotImplementedError

    @property
    def is_three_d(self):

        """ Return whether the conformer is three dimensional. """

        return self.is3D()


    @is_three_d.setter
    def is_three_d(self, value):

        """ Set whether the conformer is three dimensional. """

        self.set3D(value)


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




Push — master ( 2bc047...202252 )

skchem.core.Conformer A

Complexity

Size/Duplication

3 Methods

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.core.conformer
8
9			Defining conformers in scikit-chem.
10			"""
11
12			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...
13			from skchem.core import Point3D
14			from skchem.core import ChemicalObject
15
16			class Conformer(rdkit.Chem.rdchem.Conformer, ChemicalObject):
17
18			""" Class representing a Conformer in scikit-chem. """
19			#should use a view, list for now
20			@property
21			def atom_positions(self):
22
23			""" Return the atom positions in the conformer for the atoms in the molecule. """
24
25			return [Point3D.from_super(self.GetAtomPosition(i)) for i in range(self.GetNumAtoms())]
			0 ignored issues – show Bug introduced 2016-01-19 16:21 UTC by Report Bug Copy Issue Report The Instance of `Conformer` does not seem to have a member named `GetAtomPosition`. 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 `Conformer` does not seem to have a member named `GetNumAtoms`. 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...
26
27			@atom_positions.setter
28			def atom_positions(self, value):
29
30			""" Set the atom positions in the conformer. Not implemented. """
31
32			raise NotImplementedError
33
34			@property
35			def is_three_d(self):
36
37			""" Return whether the conformer is three dimensional. """
38
39			return self.is3D()
			0 ignored issues – show Bug introduced 2016-01-19 16:21 UTC by Report Bug Copy Issue Report The Instance of `Conformer` does not seem to have a member named `is3D`. 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			@is_three_d.setter
42			def is_three_d(self, value):
43
44			""" Set whether the conformer is three dimensional. """
45
46			self.set3D(value)
			0 ignored issues – show Bug introduced 2016-01-19 16:21 UTC by Report Bug Copy Issue Report The Instance of `Conformer` does not seem to have a member named `set3D`. 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 __repr__(self):
49			return '<{klass} id="{id}" at {address}>'.format(klass=self.__class__.__name__, \
50			id=self.GetId(), address=hex(id(self)))
			0 ignored issues – show Bug introduced 2016-01-19 16:21 UTC by Report Bug Copy Issue Report The Instance of `Conformer` does not seem to have a member named `GetId`. 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...
51
52

richlewis42 / scikit-chem

Push — master ( 2bc047...202252 )

skchem.core.Conformer A

Complexity

Size/Duplication

3 Methods

1. Missing Dependencies

2. Missing __init__.py files

Duplication Side-by-Side

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2. Missing init.py files