hydrophilic_factor() - 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

hydrophilic_factor() B

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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	23
rs	8.2508
cc	5

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

"""
# skchem.features.descriptors.properties

Molecular properties for scikit-chem.
"""

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

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


def molar_refractivity(mol):

    """ The molar refractivity.

        Args:
        mol (skchem.Mol):
            The molecule for which to calculate the descriptor.

    Returns:
        float
    """

    return rdMolDescriptors.CalcCrippenDescriptors(mol)[1]


def a_log_p(mol):

    """ Ghose-Crippen octanol-water partition coefficient.

    Args:
        mol (skchem.Mol):
            The molecule for which to calculate the descriptor.

    Returns:
        float
    """
    return rdMolDescriptors.CalcCrippenDescriptors(mol)[0]


def a_log_p2(mol):
    # TODO: memoize

    """ Square of the Ghose-Crippen octanol-water partition coefficient.

    Args:
        mol (skchem.Mol):
            The molecule for which to calculate the descriptor.

    Returns:
        float
    """

    return log_p(mol) ** 2



@requires_h_depleted
def unsaturation_count(mol):

    """ Unsaturation count according to dProperties.

    Args:
        mol (skchem.Mol):
            The molecule for which to calculate the descriptor.

    Returns:
        float
    """

    return np.log2(1 + len(mol.bonds) - sum(mol.bonds.order == 1))


def unsaturation_index(mol):

    """ Unsaturation index according to dProperties.

    Args:
        mol (skchem.Mol):
            The molecule for which to calculate the descriptor.

    Returns:
        float
    """

    return np.log2(1 + sum(mol.bonds.order) - len(mol.bonds))


@requires_h_filled
def hydrophilic_factor(x):


    # TODO: memoize

    """ Hydrophilicity factor.

    Args:
        mol (skchem.Mol):
            The molecule for which to calculate the descriptor.

    Returns:
        float
    """

    n_heavy = sum(x.atoms.atomic_number != 1)
    n_carbs = sum(x.atoms.atomic_number == 6)
    n_hbonds = sum(1 for atom in x.atoms
                   for neighbor in atom.neighbours()
                   if atom.atomic_number in (7, 8, 16) and
                   neighbor.atomic_number == 1)

    return (1 + n_hbonds) * np.log2(1 + n_hbonds) + \
           n_carbs * np.log2(1/n_heavy) / n_heavy + np.sqrt(n_hbonds)/ n_heavy


def mcgowan_volume(mol):

    """ McGowan's characteristic volume.

    Args:
        mol (skchem.Mol):
            The molecule for which to calculate the descriptor.

    Returns:
        float
    """

    return mol.atoms.mcgowan.sum() - 6.56 * len(mol.bonds)


DESCRIPTORS = {
    'mol_ref': molar_refractivity,
    'a_log_p': a_log_p,
    'a_log_p2': a_log_p2,
    'unsat_count': unsaturation_count,
    'unsat': unsaturation_index,
    'hy': hydrophilic_factor,
    'mcgowan_volume': mcgowan_volume
}

__all__ = ['molar_refractivity', 'log_p', 'log_p2', 'unsaturation_count',

           'unsaturation_index', 'hydrophilic_index', 'mcgowan_volume',

           'DESCRIPTORS']


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.properties
8
9			Molecular properties 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			from rdkit.Chem import rdMolDescriptors
			0 ignored issues – show Configuration introduced 2016-08-25 15:25 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
15			from .decorators import requires_h_filled, requires_h_depleted
			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...
16
17
18			def molar_refractivity(mol):
19
20			""" The molar refractivity.
21
22			Args:
23			mol (skchem.Mol):
24			The molecule for which to calculate the descriptor.
25
26			Returns:
27			float
28			"""
29
30			return rdMolDescriptors.CalcCrippenDescriptors(mol)[1]
31
32
33			def a_log_p(mol):
34
35			""" Ghose-Crippen octanol-water partition coefficient.
36
37			Args:
38			mol (skchem.Mol):
39			The molecule for which to calculate the descriptor.
40
41			Returns:
42			float
43			"""
44			return rdMolDescriptors.CalcCrippenDescriptors(mol)[0]
45
46
47			def a_log_p2(mol):
48			# TODO: memoize
			0 ignored issues – show Coding Style introduced 2016-08-25 15:25 UTC by Report Bug Copy Issue Report `TODO` and `FIXME` comments should generally be avoided. Loading history...
49			""" Square of the Ghose-Crippen octanol-water partition coefficient.
50
51			Args:
52			mol (skchem.Mol):
53			The molecule for which to calculate the descriptor.
54
55			Returns:
56			float
57			"""
58
59			return log_p(mol) ** 2
			0 ignored issues – show Comprehensibility Best Practice introduced 2016-08-25 15:25 UTC by Report Bug Copy Issue Report Undefined variable 'log_p' Loading history...
60
61
62			@requires_h_depleted
63			def unsaturation_count(mol):
64
65			""" Unsaturation count according to dProperties.
66
67			Args:
68			mol (skchem.Mol):
69			The molecule for which to calculate the descriptor.
70
71			Returns:
72			float
73			"""
74
75			return np.log2(1 + len(mol.bonds) - sum(mol.bonds.order == 1))
76
77
78			def unsaturation_index(mol):
79
80			""" Unsaturation index according to dProperties.
81
82			Args:
83			mol (skchem.Mol):
84			The molecule for which to calculate the descriptor.
85
86			Returns:
87			float
88			"""
89
90			return np.log2(1 + sum(mol.bonds.order) - len(mol.bonds))
91
92
93			@requires_h_filled
94			def hydrophilic_factor(x):
			0 ignored issues – show Coding Style Naming introduced 2016-08-25 15:25 UTC by Report Bug Copy Issue Report The name `x` 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...
95
96			# TODO: memoize
			0 ignored issues – show Coding Style introduced 2016-08-25 15:25 UTC by Report Bug Copy Issue Report `TODO` and `FIXME` comments should generally be avoided. Loading history...
97			""" Hydrophilicity factor.
98
99			Args:
100			mol (skchem.Mol):
101			The molecule for which to calculate the descriptor.
102
103			Returns:
104			float
105			"""
106
107			n_heavy = sum(x.atoms.atomic_number != 1)
108			n_carbs = sum(x.atoms.atomic_number == 6)
109			n_hbonds = sum(1 for atom in x.atoms
110			for neighbor in atom.neighbours()
111			if atom.atomic_number in (7, 8, 16) and
112			neighbor.atomic_number == 1)
113
114			return (1 + n_hbonds) * np.log2(1 + n_hbonds) + \
115			n_carbs * np.log2(1/n_heavy) / n_heavy + np.sqrt(n_hbonds)/ n_heavy
116
117
118			def mcgowan_volume(mol):
119
120			""" McGowan's characteristic volume.
121
122			Args:
123			mol (skchem.Mol):
124			The molecule for which to calculate the descriptor.
125
126			Returns:
127			float
128			"""
129
130			return mol.atoms.mcgowan.sum() - 6.56 * len(mol.bonds)
131
132
133			DESCRIPTORS = {
134			'mol_ref': molar_refractivity,
135			'a_log_p': a_log_p,
136			'a_log_p2': a_log_p2,
137			'unsat_count': unsaturation_count,
138			'unsat': unsaturation_index,
139			'hy': hydrophilic_factor,
140			'mcgowan_volume': mcgowan_volume
141			}
142
143			__all__ = ['molar_refractivity', 'log_p', 'log_p2', 'unsaturation_count',
			0 ignored issues – show Bug introduced 2016-08-25 15:25 UTC by Report Bug Copy Issue Report Undefined variable name 'log_p' in __all__ Loading history... Bug introduced 2016-08-25 15:25 UTC by Report Bug Copy Issue Report Undefined variable name 'log_p2' in __all__ Loading history...
144			'unsaturation_index', 'hydrophilic_index', 'mcgowan_volume',
			0 ignored issues – show Bug introduced 2016-08-25 15:25 UTC by Report Bug Copy Issue Report Undefined variable name 'hydrophilic_index' in __all__ Loading history...
145			'DESCRIPTORS']
			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 )

hydrophilic_factor() B

Complexity

Size

Duplication

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

richlewis42 / scikit-chem

Push — master ( 5b00a3...5fddd3 )

hydrophilic_factor() B

Complexity

Size

Duplication

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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