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

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by Rich

created 2016-08-25 15:11 UTC

requires_h_depleted() B

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c	1
b	1
f	0
dl	0
loc	26
rs	8.5806
cc	4

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

"""
# skchem.features.descriptors.decorators

Decorators for descriptors in scikit-chem.
"""

from functools import wraps

import numpy as np
from rdkit.Chem.rdmolops import GetDistanceMatrix, GetAdjacencyMatrix


def _add_cached_prop(func, prop):

    """ Annotate a function with the cached props. """

    if not hasattr(func, 'caches'):
        func.caches = []
    func.caches.append(prop)


def requires_h_depleted(func):

    """ Decorate a function that requires an h-depleted graph.

    This will check if the molecule argument is h-depleted, and will
    memoize a depleted version if it is not, and pass it to the func.

    Note:
        This decorator should be used first if in combination with dMat etc.
    """

    @wraps(func)
    def inner(mol, *args, **kwargs):

        # if is already h depleted
        if (mol.atoms.atomic_number == 1).sum() == 0:
            return func(mol, *args, **kwargs)

        if not hasattr(mol, '_h_depleted'):
            mol._h_depleted = mol.remove_hs()

        return func(mol._h_depleted, *args, **kwargs)

    _add_cached_prop(inner, '_h_depleted')

    return inner


def requires_h_filled(func):

    """ Decorate a function that requires a h-filled graph.

    This will check if the molecule argument is h-filled, and will
    memoize a filled version if it is not, and pass it to the func.

     Note:
        This decorator should be used first if in combination with dMat etc.

     """

    @wraps(func)
    def inner(mol, *args, **kwargs):
        # if is already h enriched
        if mol.atoms.n_total_hs.sum() == 0:
            return func(mol, *args, **kwargs)

        # if not, memoize the enriched one and pass it
        if not hasattr(mol, '_h_enriched'):
            mol._h_enriched = mol.add_hs()

        return func(mol._h_enriched, *args, **kwargs)

    _add_cached_prop(inner, '_h_enriched')

    return inner


class Cache(object):

    """ Function cache."""

    def __init__(self):
        self.cached = {}

    def __call__(self, func):

        """ Create a decorator to identify a function as returning a cached
        value.

        This can be used for objects  that are nontrivial to generate, but
        are used by many functions.

        Args:
            name (str):
                The name to cache the values under
        """

        name = func.__name__

        @wraps(func)
        def inner(mol, *args, force=False, **kwargs):


            self.setup_cache(mol)

            # call function if it hasn't already been called.
            if force or name not in mol.cache.keys():
                res = func(mol, *args, **kwargs)
                mol.cache[name] = res

            # return the cached value
            return mol.cache[name]

        self.cached[name] = inner
        return inner

    def retrieve(self, *args_to_inject):

        """ Create a decorator that will inject cached values as arguments.

        Args:
            args (list<str>):
                A list of cachable requirements for this function.
        """

        def outer(func):

            @wraps(func)
            def inner(mol, *args, **kwargs):

                self.setup_cache(mol)

                # look up cached values, or produce them if not.
                # inject the cached values
                args = tuple(mol.cache.get(arg.__name__,
                                           self.cached[arg.__name__](mol))
                             for arg in args_to_inject) + args

                return func(mol, *args, **kwargs)
            return inner
        return outer

    @staticmethod
    def setup_cache(mol):
        if not hasattr(mol, 'cache'):
            mol.cache = {}

    @staticmethod
    def teardown_cache(mol):
        if hasattr(mol, 'cache'):
            del mol.cache

cache = Cache()


def requires_dmat(func):
    """ Decorate a function that requires a distance matrix. """
    @wraps(func)
    def inner(mol, *args, **kwargs):
        if not hasattr(mol, '_dMat'):
            dmat = GetDistanceMatrix(mol)
            dmat[dmat > 100] = np.nan
            mol._dMat = dmat
        return func(mol, *args, **kwargs)

    _add_cached_prop(inner, '_dMat')

    return inner


def requires_amat(func):
    """ Decorate a function that requires an adjacency matrix. """
    @wraps(func)
    def inner(mol, *args, **kwargs):
        if not hasattr(mol, '_adjMat'):
            mol._adjMat = GetAdjacencyMatrix(mol)
        return func(mol, *args, **kwargs)

    _add_cached_prop(inner, 'amat')

    return inner


def requires_bo_amat(func):
    """ Decorate a function thate requires a bond order adjacency, matrix. """
    @wraps(func)
    def inner(mol, *args, **kwargs):
        if not hasattr(mol, '_bo_amat'):
            mol._bo_amat = GetAdjacencyMatrix(mol, useBO=1)
        return func(mol, *args, **kwargs)

    _add_cached_prop(inner, '_bo_amat')

    return inner


def requires_degrees(func):
    """ Decorate a function that requires a degree vector. """
    @wraps(func)
    def inner(mol, *args, **kwargs):
        if not hasattr(mol, '_degrees'):
            mol._degrees = np.array([atom.degree for atom in mol.atoms])
        return func(mol, *args, **kwargs)

    _add_cached_prop(inner, '_degrees')

    return inner

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.decorators
8
9			Decorators for descriptors in scikit-chem.
10			"""
11
12			from functools import wraps
13
14			import numpy as np
15			from rdkit.Chem.rdmolops import GetDistanceMatrix, GetAdjacencyMatrix
16
17
18			def _add_cached_prop(func, prop):
19
20			""" Annotate a function with the cached props. """
21
22			if not hasattr(func, 'caches'):
23			func.caches = []
24			func.caches.append(prop)
25
26
27			def requires_h_depleted(func):
28
29			""" Decorate a function that requires an h-depleted graph.
30
31			This will check if the molecule argument is h-depleted, and will
32			memoize a depleted version if it is not, and pass it to the func.
33
34			Note:
35			This decorator should be used first if in combination with dMat etc.
36			"""
37
38			@wraps(func)
39			def inner(mol, args, *kwargs):
40
41			# if is already h depleted
42			if (mol.atoms.atomic_number == 1).sum() == 0:
43			return func(mol, args, *kwargs)
44
45			if not hasattr(mol, '_h_depleted'):
46			mol._h_depleted = mol.remove_hs()
47
48			return func(mol._h_depleted, args, *kwargs)
49
50			_add_cached_prop(inner, '_h_depleted')
51
52			return inner
53
54
55			def requires_h_filled(func):
56
57			""" Decorate a function that requires a h-filled graph.
58
59			This will check if the molecule argument is h-filled, and will
60			memoize a filled version if it is not, and pass it to the func.
61
62			Note:
63			This decorator should be used first if in combination with dMat etc.
64
65			"""
66
67			@wraps(func)
68			def inner(mol, args, *kwargs):
69			# if is already h enriched
70			if mol.atoms.n_total_hs.sum() == 0:
71			return func(mol, args, *kwargs)
72
73			# if not, memoize the enriched one and pass it
74			if not hasattr(mol, '_h_enriched'):
75			mol._h_enriched = mol.add_hs()
76
77			return func(mol._h_enriched, args, *kwargs)
78
79			_add_cached_prop(inner, '_h_enriched')
80
81			return inner
82
83
84			class Cache(object):
85
86			""" Function cache."""
87
88			def __init__(self):
89			self.cached = {}
90
91			def __call__(self, func):
92
93			""" Create a decorator to identify a function as returning a cached
94			value.
95
96			This can be used for objects that are nontrivial to generate, but
97			are used by many functions.
98
99			Args:
100			name (str):
101			The name to cache the values under
102			"""
103
104			name = func.__name__
105
106			@wraps(func)
107			def inner(mol, args, force=False, *kwargs):
			0 ignored issues – show introduced 2016-08-25 15:25 UTC by Report Bug Copy Issue Report invalid syntax Loading history...
108
109			self.setup_cache(mol)
110
111			# call function if it hasn't already been called.
112			if force or name not in mol.cache.keys():
113			res = func(mol, args, *kwargs)
114			mol.cache[name] = res
115
116			# return the cached value
117			return mol.cache[name]
118
119			self.cached[name] = inner
120			return inner
121
122			def retrieve(self, *args_to_inject):
123
124			""" Create a decorator that will inject cached values as arguments.
125
126			Args:
127			args (list<str>):
128			A list of cachable requirements for this function.
129			"""
130
131			def outer(func):
132
133			@wraps(func)
134			def inner(mol, args, *kwargs):
135
136			self.setup_cache(mol)
137
138			# look up cached values, or produce them if not.
139			# inject the cached values
140			args = tuple(mol.cache.get(arg.__name__,
141			self.cached[arg.__name__](mol))
142			for arg in args_to_inject) + args
143
144			return func(mol, args, *kwargs)
145			return inner
146			return outer
147
148			@staticmethod
149			def setup_cache(mol):
150			if not hasattr(mol, 'cache'):
151			mol.cache = {}
152
153			@staticmethod
154			def teardown_cache(mol):
155			if hasattr(mol, 'cache'):
156			del mol.cache
157
158			cache = Cache()
159
160
161			def requires_dmat(func):
162			""" Decorate a function that requires a distance matrix. """
163			@wraps(func)
164			def inner(mol, args, *kwargs):
165			if not hasattr(mol, '_dMat'):
166			dmat = GetDistanceMatrix(mol)
167			dmat[dmat > 100] = np.nan
168			mol._dMat = dmat
169			return func(mol, args, *kwargs)
170
171			_add_cached_prop(inner, '_dMat')
172
173			return inner
174
175
176			def requires_amat(func):
177			""" Decorate a function that requires an adjacency matrix. """
178			@wraps(func)
179			def inner(mol, args, *kwargs):
180			if not hasattr(mol, '_adjMat'):
181			mol._adjMat = GetAdjacencyMatrix(mol)
182			return func(mol, args, *kwargs)
183
184			_add_cached_prop(inner, 'amat')
185
186			return inner
187
188
189			def requires_bo_amat(func):
190			""" Decorate a function thate requires a bond order adjacency, matrix. """
191			@wraps(func)
192			def inner(mol, args, *kwargs):
193			if not hasattr(mol, '_bo_amat'):
194			mol._bo_amat = GetAdjacencyMatrix(mol, useBO=1)
195			return func(mol, args, *kwargs)
196
197			_add_cached_prop(inner, '_bo_amat')
198
199			return inner
200
201
202			def requires_degrees(func):
203			""" Decorate a function that requires a degree vector. """
204			@wraps(func)
205			def inner(mol, args, *kwargs):
206			if not hasattr(mol, '_degrees'):
207			mol._degrees = np.array([atom.degree for atom in mol.atoms])
208			return func(mol, args, *kwargs)
209
210			_add_cached_prop(inner, '_degrees')
211
212			return inner

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