adjacency_matrix() - Code Metrics - Inspection of "started the descriptors package with the caching f..." - richlewis42/scikit-chem - Measure and Improve Code Quality continuously with Scrutinizer

Completed

Branch — master (360284)

by Rich

created 2016-08-31 12:37 UTC

adjacency_matrix() A

↳ Parent: Project

Complexity

Conditions

Size

Total Lines

Duplication

Lines	0
Ratio	0 %

Code Coverage

Tests	1
CRAP Score	1.125

Importance

Changes	1
Bugs	0	Features	0

Metric	Value
c	1
b	0
f	0
dl	0
loc	6
ccs	1
cts	2
cp	0.5
rs	9.4285
cc	1
crap	1.125

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

"""
# skchem.features.descriptors.fundamentals

Fundamental representations for descriptors.
"""


from rdkit.Chem import rdmolops
# .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 .caching import cache
from ...core import Mol


@cache
def atom_props(mol, prop_name='unweighted', c_scaled=False):

    """ Atom based properties."""

    if prop_name == 'unweighted':
        return np.ones(len(mol.atoms))
    else:
        props = getattr(mol.atoms, prop_name)
        if c_scaled:
            props /= getattr(Mol.from_smiles('CC').atoms[0], prop_name)

        return props




@cache
def distance_matrix(mol):

    """ The topological distance matrix. """

    return rdmolops.GetDistanceMatrix(mol)


@cache
def adjacency_matrix(mol):

    """ The topological adjacency matrix. """

    return rdmolops.GetAdjacencyMatrix(mol)


@cache
def bond_order_adjacency_matrix(mol):

    """ The bond order scaled topological adjacency matrix. """
    return rdmolops.GetAdjacencyMatrix(mol, useBO=1)


# probably this anymore (props, degrees)
@cache
def degrees(mol):
class SomeClass:
    def some_method(self):
        """Do x and return foo."""

    return mol.atoms.degree


@cache
def geometric_matrix(mol, conformer=-1):
class SomeClass:
    def some_method(self):
        """Do x and return foo."""
    return rdmolops.Get3DDistanceMatrix(mol, confId=conformer)


@cache
def molecular_matrix(mol, conformer=-1):
class SomeClass:
    def some_method(self):
        """Do x and return foo."""
    return mol.conformers[conformer].positions


__all__ = ['distance_matrix', 'adjacency_matrix',
           'bond_order_adjacency_matrix', 'degrees', 'geometric_matrix',
           'molecular_matrix']


1		#! /usr/bin/env python
2		#
3		# Copyright (C) 2016 Rich Lewis <[email protected]>
4		# License: 3-clause BSD
5
6	1	"""
7		# skchem.features.descriptors.fundamentals
8
9		Fundamental representations for descriptors.
10		"""
11
12
13	1	from rdkit.Chem import rdmolops
		0 ignored issues – show Configuration introduced 2016-08-30 22:12 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	import numpy as np
		0 ignored issues – show Configuration introduced 2016-08-30 22:12 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
16	1	from .caching import cache
17	1	from ...core import Mol
18
19
20	1	@cache
21	1	def atom_props(mol, prop_name='unweighted', c_scaled=False):
22
23		""" Atom based properties."""
24
25	1	if prop_name == 'unweighted':
26		return np.ones(len(mol.atoms))
27		else:
28	1	props = getattr(mol.atoms, prop_name)
29	1	if c_scaled:
30	1	props /= getattr(Mol.from_smiles('CC').atoms[0], prop_name)
		0 ignored issues – show Bug introduced 2016-08-30 22:12 UTC by Report Bug Copy Issue Report The Class `Mol` does not seem to have a member named `from_smiles`. 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...
31	1	return props
32
33
34
35
36	1	@cache
37		def distance_matrix(mol):
38
39		""" The topological distance matrix. """
40
41	1	return rdmolops.GetDistanceMatrix(mol)
42
43
44	1	@cache
45		def adjacency_matrix(mol):
46
47		""" The topological adjacency matrix. """
48
49		return rdmolops.GetAdjacencyMatrix(mol)
50
51
52	1	@cache
53		def bond_order_adjacency_matrix(mol):
54
55		""" The bond order scaled topological adjacency matrix. """
56		return rdmolops.GetAdjacencyMatrix(mol, useBO=1)
57
58
59		# probably this anymore (props, degrees)
60	1	@cache
61		def degrees(mol):
		0 ignored issues – show Coding Style introduced 2016-08-30 22:12 UTC by Report Bug Copy Issue Report This function 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...
62
63		return mol.atoms.degree
64
65
66	1	@cache
67	1	def geometric_matrix(mol, conformer=-1):
		0 ignored issues – show Coding Style introduced 2016-08-30 22:12 UTC by Report Bug Copy Issue Report This function 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...
68		return rdmolops.Get3DDistanceMatrix(mol, confId=conformer)
69
70
71	1	@cache
72	1	def molecular_matrix(mol, conformer=-1):
		0 ignored issues – show Coding Style introduced 2016-08-30 22:12 UTC by Report Bug Copy Issue Report This function 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...
73		return mol.conformers[conformer].positions
74
75
76	1	__all__ = ['distance_matrix', 'adjacency_matrix',
77		'bond_order_adjacency_matrix', 'degrees', 'geometric_matrix',
78		'molecular_matrix']
		0 ignored issues – show Coding Style introduced 2016-08-30 22:12 UTC by Report Bug Copy Issue Report Final newline missing Loading history...

Branch — master (360284)

adjacency_matrix() 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

Branch — master (360284)

adjacency_matrix() 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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