modified_burden_matrix() - Code Metrics - Inspection of "fixed integer division errors for py2" - richlewis42/scikit-chem - Measure and Improve Code Quality continuously with Scrutinizer

Completed

Push — master ( 5b00a3...5fddd3 )

by Rich

created 2016-08-25 15:11 UTC

modified_burden_matrix() B

↳ Parent: Project

Complexity

Conditions

Size

Total Lines

Duplication

Lines	0
Ratio	0 %

Importance

Changes	1
Bugs	1	Features	0

Metric	Value
c	1
b	1
f	0
dl	0
loc	30
rs	8.8571
cc	1

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

"""
# skchem.features.descriptors.spectral

Spectral descriptors for scikit-chem.
"""

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

from .decorators import (requires_h_depleted, requires_bo_amat,
# .scrutinizer.yml
before_commands:
    - sudo pip install abc # Python2
    - sudo pip3 install abc # Python3
                         requires_h_filled, requires_degrees)


@requires_h_depleted
@requires_bo_amat
def original_burden_matrix(mol):

    """ The original burden matrix.


    $$ [B]_{ii} = Z_i
    [B]_{ij} = \frac{\pi^*}{10} $$

    Where $Z_i$ is the atomic number of the $i$th atom and $\pi^*_{ij}$ is the
    conventional bond order between the $i$th and $j$th atoms.

    Args:
        mol (skchem.Mol):
            The molecule for which to calculate the modified burden matrix.

    Returns:
        np.ndarray

    References:
        Molecular Descriptors for Cheminformatics p720
    """
    res = mol._bo_amat / 10
class MyParent:
    def __init__(self):
        self._x = 1;
        self.y = 2;

class MyChild(MyParent):
    def some_method(self):
        return self._x    # Ok, since accessed from a child class

class AnotherClass:
    def some_method(self, instance_of_my_child):
        return instance_of_my_child._x   # Would be flagged as AnotherClass is not
                                         # a child class of MyParent
    res[np.diag_indices_from(res)] = mol.atoms.atomic_number
    res[res == 0] = 0.001
    return res


def burden(mol, n=1):


    """ Spectral descriptors using the original burden matrix. """

    eigs = np.linalg.eigvals(original_burden_matrix(mol))
    eigs.sort()
    eigs = eigs[::-1]
    diff = n - len(eigs)
    print(diff, eigs)
    if diff > 0:
        res = np.pad(eigs, (diff, diff), 'edge')
        return np.concatenate((res[diff:], res[:diff]))
    else:
        return np.array(eigs[:n] + eigs[-n:])


@requires_h_filled
@requires_bo_amat
def burden_matrix(mol, diag='electronegativity'):

    """ The Burden matrix, with variable diagonal elements.

    Args:
        mol (skchem.Mol):
            The molecule for which to calculate the modified burden matrix.

    Returns:
        np.ndarray

    References:
        Molecular Descriptors for Cheminformatics p720"""

    diag = getattr(mol.atoms, diag)

    res = np.sqrt(mol._bo_amat)
class MyParent:
    def __init__(self):
        self._x = 1;
        self.y = 2;

class MyChild(MyParent):
    def some_method(self):
        return self._x    # Ok, since accessed from a child class

class AnotherClass:
    def some_method(self, instance_of_my_child):
        return instance_of_my_child._x   # Would be flagged as AnotherClass is not
                                         # a child class of MyParent
    res[np.diag_indices_from(res)] = diag

    return res


def bme(mol, L=15):


    """ The L highest Burden modified eigenvalues of the burden matrix.

    Args:

    """

    res = np.zeros(L)
    eigs = np.linalg.eigvals(burden_matrix(mol))
    res[:len(eigs)] = eigs
    return np.sort(eigs)[:-L-1:-1]

@requires_h_depleted
@requires_bo_amat
@requires_degrees
def modified_burden_matrix(mol):

    """ The modified burden matrix, Q.


    $$ [Q]_{ii} = Z_i + 0.1 \cdot \delta_i + 0.01 \cdot n_i^{\pi}
     [Q]_{ij} = 0.4 / d_{ij}$$

    Where Z_i is the atomic number of $i$th atom, $\delta_i$ is the vertex
    degree, $n_i^\pi$ is the number of $\pi$ electrons and d_{ij} is the
    topological distance between $i$th and $j$th atoms

    Args:
        mol (skchem.Mol):
            The molecule for which to calculate the modified burden matrix.

    Returns:
        np.ndarray

    References:
        Molecular Descriptors for Cheminformatics p720
    """

    res = 0.4 / mol._bo_amat
class MyParent:
    def __init__(self):
        self._x = 1;
        self.y = 2;

class MyChild(MyParent):
    def some_method(self):
        return self._x    # Ok, since accessed from a child class

class AnotherClass:
    def some_method(self, instance_of_my_child):
        return instance_of_my_child._x   # Would be flagged as AnotherClass is not
                                         # a child class of MyParent
    diag = mol.atoms.atomic_number + 0.1 * mol._degrees + \
class MyParent:
    def __init__(self):
        self._x = 1;
        self.y = 2;

class MyChild(MyParent):
    def some_method(self):
        return self._x    # Ok, since accessed from a child class

class AnotherClass:
    def some_method(self, instance_of_my_child):
        return instance_of_my_child._x   # Would be flagged as AnotherClass is not
                                         # a child class of MyParent
           0.01 * mol.atoms.n_pi_electrons
    res[np.diag_indices_from(res)] = diag
    return res


def _bcutm(mol):

    """ BCUT descriptors for atomic masses.

    Args:
        mol (skchem.Mol):
            The molecule for which to calculate the modified burden matrix.

    Returns:
        np.ndarray

    Note:
        These memoize.

    References:
        Molecular Descriptors for Cheminformatics p720
    """

    mat = burden_matrix(mol, mol.atoms.atomic_mass)
    mat._bcutm = np.linalg.eigvals(mat)
class MyParent:
    def __init__(self):
        self._x = 1;
        self.y = 2;

class MyChild(MyParent):
    def some_method(self):
        return self._x    # Ok, since accessed from a child class

class AnotherClass:
    def some_method(self, instance_of_my_child):
        return instance_of_my_child._x   # Would be flagged as AnotherClass is not
                                         # a child class of MyParent
    return mat


def _bcutp(mol, n=1):


    """ BCUT descriptors using atomic polarizability.

    Args:
        mol (skchem.Mol):
            The molecule for which to calculate the modified burden matrix.
        n (skchem.Mol):
            The number of highest and lowest eigenvalues to use.

    Returns:
        np.ndarray

    Note:
        These memoize.

    References:
        Molecular Descriptors for Cheminformatics p720
    """

    mat = burden_matrix(mol, mol.atoms.atomic_mass)
    mat._bcutm = np.linalg.eigvals(mat)
class MyParent:
    def __init__(self):
        self._x = 1;
        self.y = 2;

class MyChild(MyParent):
    def some_method(self):
        return self._x    # Ok, since accessed from a child class

class AnotherClass:
    def some_method(self, instance_of_my_child):
        return instance_of_my_child._x   # Would be flagged as AnotherClass is not
                                         # a child class of MyParent
    return mat


1			#! /usr/bin/env python
2			#
3			# Copyright (C) 2016 Rich Lewis <[email protected]>
4			# License: 3-clause BSD
5
6			"""
7			# skchem.features.descriptors.spectral
8
9			Spectral descriptors for scikit-chem.
10			"""
11
12			import numpy as np
			0 ignored issues – show Configuration introduced 2016-08-25 15:25 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...
13
14			from .decorators import (requires_h_depleted, requires_bo_amat,
			0 ignored issues – show Configuration introduced 2016-08-25 15:25 UTC by Report Bug Copy Issue Report Unable to import 'decorators' (invalid syntax (<string>, line 107)) 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			requires_h_filled, requires_degrees)
16
17
18			@requires_h_depleted
19			@requires_bo_amat
20			def original_burden_matrix(mol):
21
22			""" The original burden matrix.
			0 ignored issues – show Bug introduced 2016-08-25 15:25 UTC by Report Bug Copy Issue Report A suspicious escape sequence `\p` was found. Did you maybe forget to add an `r` prefix? Escape sequences in Python are generally interpreted according to rules similar to standard C. Only if strings are prefixed with `r` or `R` are they interpreted as regular expressions. The escape sequence that was used indicates that you might have intended to write a regular expression. Learn more about the available escape sequences. in the Python documentation. Loading history...
23
24			$$ [B]_{ii} = Z_i
25			[B]_{ij} = \frac{\pi^*}{10} $$
26
27			Where $Z_i$ is the atomic number of the $i$th atom and $\pi^*_{ij}$ is the
28			conventional bond order between the $i$th and $j$th atoms.
29
30			Args:
31			mol (skchem.Mol):
32			The molecule for which to calculate the modified burden matrix.
33
34			Returns:
35			np.ndarray
36
37			References:
38			Molecular Descriptors for Cheminformatics p720
39			"""
40			res = mol._bo_amat / 10
			0 ignored issues – show Coding Style Best Practice introduced 2016-08-25 15:25 UTC by Report Bug Copy Issue Report It seems like `_bo_amat` was declared protected and should not be accessed from this context. Prefixing a member variable `_` is usually regarded as the equivalent of declaring it with protected visibility that exists in other languages. Consequentially, such a member should only be accessed from the same class or a child class: class MyParent: def __init__(self): self._x = 1; self.y = 2; class MyChild(MyParent): def some_method(self): return self._x # Ok, since accessed from a child class class AnotherClass: def some_method(self, instance_of_my_child): return instance_of_my_child._x # Would be flagged as AnotherClass is not # a child class of MyParent Loading history...
41			res[np.diag_indices_from(res)] = mol.atoms.atomic_number
42			res[res == 0] = 0.001
43			return res
44
45
46			def burden(mol, n=1):
			0 ignored issues – show Coding Style Naming introduced 2016-08-25 15:25 UTC by Report Bug Copy Issue Report The name `n` does not conform to the argument naming conventions (`[a-z_][a-z0-9_]{2,30}$`). This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history...
47
48			""" Spectral descriptors using the original burden matrix. """
49
50			eigs = np.linalg.eigvals(original_burden_matrix(mol))
51			eigs.sort()
52			eigs = eigs[::-1]
53			diff = n - len(eigs)
54			print(diff, eigs)
55			if diff > 0:
56			res = np.pad(eigs, (diff, diff), 'edge')
57			return np.concatenate((res[diff:], res[:diff]))
58			else:
59			return np.array(eigs[:n] + eigs[-n:])
60
61
62			@requires_h_filled
63			@requires_bo_amat
64			def burden_matrix(mol, diag='electronegativity'):
65
66			""" The Burden matrix, with variable diagonal elements.
67
68			Args:
69			mol (skchem.Mol):
70			The molecule for which to calculate the modified burden matrix.
71
72			Returns:
73			np.ndarray
74
75			References:
76			Molecular Descriptors for Cheminformatics p720"""
77
78			diag = getattr(mol.atoms, diag)
79
80			res = np.sqrt(mol._bo_amat)
			0 ignored issues – show Coding Style Best Practice introduced 2016-08-25 15:25 UTC by Report Bug Copy Issue Report It seems like `_bo_amat` was declared protected and should not be accessed from this context. Prefixing a member variable `_` is usually regarded as the equivalent of declaring it with protected visibility that exists in other languages. Consequentially, such a member should only be accessed from the same class or a child class: class MyParent: def __init__(self): self._x = 1; self.y = 2; class MyChild(MyParent): def some_method(self): return self._x # Ok, since accessed from a child class class AnotherClass: def some_method(self, instance_of_my_child): return instance_of_my_child._x # Would be flagged as AnotherClass is not # a child class of MyParent Loading history...
81			res[np.diag_indices_from(res)] = diag
82
83			return res
84
85
86			def bme(mol, L=15):
			0 ignored issues – show Coding Style Naming introduced 2016-08-25 15:25 UTC by Report Bug Copy Issue Report The name `L` does not conform to the argument naming conventions (`[a-z_][a-z0-9_]{2,30}$`). This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history...
87
88			""" The L highest Burden modified eigenvalues of the burden matrix.
89
90			Args:
91
92			"""
93
94			res = np.zeros(L)
95			eigs = np.linalg.eigvals(burden_matrix(mol))
96			res[:len(eigs)] = eigs
97			return np.sort(eigs)[:-L-1:-1]
98
99			@requires_h_depleted
100			@requires_bo_amat
101			@requires_degrees
102			def modified_burden_matrix(mol):
103
104			""" The modified burden matrix, Q.
			0 ignored issues – show Bug introduced 2016-08-25 15:25 UTC by Report Bug Copy Issue Report A suspicious escape sequence `\c` was found. Did you maybe forget to add an `r` prefix? Escape sequences in Python are generally interpreted according to rules similar to standard C. Only if strings are prefixed with `r` or `R` are they interpreted as regular expressions. The escape sequence that was used indicates that you might have intended to write a regular expression. Learn more about the available escape sequences. in the Python documentation. Loading history... Bug introduced 2016-08-25 15:25 UTC by Report Bug Copy Issue Report A suspicious escape sequence `\d` was found. Did you maybe forget to add an `r` prefix? Escape sequences in Python are generally interpreted according to rules similar to standard C. Only if strings are prefixed with `r` or `R` are they interpreted as regular expressions. The escape sequence that was used indicates that you might have intended to write a regular expression. Learn more about the available escape sequences. in the Python documentation. Loading history... Bug introduced 2016-08-25 15:25 UTC by Report Bug Copy Issue Report A suspicious escape sequence `\p` was found. Did you maybe forget to add an `r` prefix? Escape sequences in Python are generally interpreted according to rules similar to standard C. Only if strings are prefixed with `r` or `R` are they interpreted as regular expressions. The escape sequence that was used indicates that you might have intended to write a regular expression. Learn more about the available escape sequences. in the Python documentation. Loading history...
105
106			$$ [Q]_{ii} = Z_i + 0.1 \cdot \delta_i + 0.01 \cdot n_i^{\pi}
107			[Q]_{ij} = 0.4 / d_{ij}$$
108
109			Where Z_i is the atomic number of $i$th atom, $\delta_i$ is the vertex
110			degree, $n_i^\pi$ is the number of $\pi$ electrons and d_{ij} is the
111			topological distance between $i$th and $j$th atoms
112
113			Args:
114			mol (skchem.Mol):
115			The molecule for which to calculate the modified burden matrix.
116
117			Returns:
118			np.ndarray
119
120			References:
121			Molecular Descriptors for Cheminformatics p720
122			"""
123
124			res = 0.4 / mol._bo_amat
			0 ignored issues – show Coding Style Best Practice introduced 2016-08-25 15:25 UTC by Report Bug Copy Issue Report It seems like `_bo_amat` was declared protected and should not be accessed from this context. Prefixing a member variable `_` is usually regarded as the equivalent of declaring it with protected visibility that exists in other languages. Consequentially, such a member should only be accessed from the same class or a child class: class MyParent: def __init__(self): self._x = 1; self.y = 2; class MyChild(MyParent): def some_method(self): return self._x # Ok, since accessed from a child class class AnotherClass: def some_method(self, instance_of_my_child): return instance_of_my_child._x # Would be flagged as AnotherClass is not # a child class of MyParent Loading history...
125			diag = mol.atoms.atomic_number + 0.1 * mol._degrees + \
			0 ignored issues – show Coding Style Best Practice introduced 2016-08-25 15:25 UTC by Report Bug Copy Issue Report It seems like `_degrees` was declared protected and should not be accessed from this context. Prefixing a member variable `_` is usually regarded as the equivalent of declaring it with protected visibility that exists in other languages. Consequentially, such a member should only be accessed from the same class or a child class: class MyParent: def __init__(self): self._x = 1; self.y = 2; class MyChild(MyParent): def some_method(self): return self._x # Ok, since accessed from a child class class AnotherClass: def some_method(self, instance_of_my_child): return instance_of_my_child._x # Would be flagged as AnotherClass is not # a child class of MyParent Loading history...
126			0.01 * mol.atoms.n_pi_electrons
127			res[np.diag_indices_from(res)] = diag
128			return res
129
130
131			def _bcutm(mol):
132
133			""" BCUT descriptors for atomic masses.
134
135			Args:
136			mol (skchem.Mol):
137			The molecule for which to calculate the modified burden matrix.
138
139			Returns:
140			np.ndarray
141
142			Note:
143			These memoize.
144
145			References:
146			Molecular Descriptors for Cheminformatics p720
147			"""
148
149			mat = burden_matrix(mol, mol.atoms.atomic_mass)
150			mat._bcutm = np.linalg.eigvals(mat)
			0 ignored issues – show Coding Style Best Practice introduced 2016-08-25 15:25 UTC by Report Bug Copy Issue Report It seems like `_bcutm` was declared protected and should not be accessed from this context. Prefixing a member variable `_` is usually regarded as the equivalent of declaring it with protected visibility that exists in other languages. Consequentially, such a member should only be accessed from the same class or a child class: class MyParent: def __init__(self): self._x = 1; self.y = 2; class MyChild(MyParent): def some_method(self): return self._x # Ok, since accessed from a child class class AnotherClass: def some_method(self, instance_of_my_child): return instance_of_my_child._x # Would be flagged as AnotherClass is not # a child class of MyParent Loading history...
151			return mat
152
153
154			def _bcutp(mol, n=1):
			0 ignored issues – show Coding Style Naming introduced 2016-08-25 15:25 UTC by Report Bug Copy Issue Report The name `n` does not conform to the argument naming conventions (`[a-z_][a-z0-9_]{2,30}$`). This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history... Unused Code introduced 2016-08-25 15:25 UTC by Report Bug Copy Issue Report The argument `n` seems to be unused. Loading history...
155
156			""" BCUT descriptors using atomic polarizability.
157
158			Args:
159			mol (skchem.Mol):
160			The molecule for which to calculate the modified burden matrix.
161			n (skchem.Mol):
162			The number of highest and lowest eigenvalues to use.
163
164			Returns:
165			np.ndarray
166
167			Note:
168			These memoize.
169
170			References:
171			Molecular Descriptors for Cheminformatics p720
172			"""
173
174			mat = burden_matrix(mol, mol.atoms.atomic_mass)
175			mat._bcutm = np.linalg.eigvals(mat)
			0 ignored issues – show Coding Style Best Practice introduced 2016-08-25 15:25 UTC by Report Bug Copy Issue Report It seems like `_bcutm` was declared protected and should not be accessed from this context. Prefixing a member variable `_` is usually regarded as the equivalent of declaring it with protected visibility that exists in other languages. Consequentially, such a member should only be accessed from the same class or a child class: class MyParent: def __init__(self): self._x = 1; self.y = 2; class MyChild(MyParent): def some_method(self): return self._x # Ok, since accessed from a child class class AnotherClass: def some_method(self, instance_of_my_child): return instance_of_my_child._x # Would be flagged as AnotherClass is not # a child class of MyParent Loading history...
176			return mat
			0 ignored issues – show Coding Style introduced 2016-08-25 15:25 UTC by Report Bug Copy Issue Report Final newline missing Loading history...

Push — master ( 5b00a3...5fddd3 )

modified_burden_matrix() B

Complexity

Size

Duplication

Importance

1. Missing Dependencies

2. Missing init.py files

1. Missing Dependencies

2. Missing init.py files

richlewis42 / scikit-chem

Push — master ( 5b00a3...5fddd3 )

modified_burden_matrix() B

Complexity

Size

Duplication

Importance

1. Missing Dependencies

2. Missing __init__.py files

1. Missing Dependencies

2. Missing __init__.py files

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