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

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by Rich

created 2016-08-30 21:24 UTC

requires_h_filled() B

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loc	27
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.
"""
import inspect
from functools import wraps
from collections import OrderedDict, defaultdict

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.
        """

        name = func.__name__

        # get the key word arguments and the default values of the function
        kwds = OrderedDict((k, v.default) for k, v in
                           inspect.signature(func).parameters.items()
                           if v.default != inspect._empty)

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


            self.setup_cache(mol)

            # get the full set of keywords to use, including defaults
            kwds.update(kwargs)
            kw_to_save = tuple(sorted(kwds.items()))

            # call function if it hasn't already been called
            # with required arguments, or if told to.
            if force or name not in self.cached.keys() or \
                    kw_to_save not in mol.cache.get(name, {}).keys():

                res = func(mol, *args, **kwargs)

                # cache the value with the args used.
                mol.cache[name].update({kw_to_save: res})

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

        self.cached[name] = inner, tuple(kwds.keys())

        return inner

    def inject(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):

            # extract the defaults for the func
            kwds = OrderedDict((k, v.default) for k, v in
                               inspect.signature(func).parameters.items()
                               if v.default != inspect._empty)

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

                # augment with the keywords from the function
                kwds.update(kwargs)

                self.setup_cache(mol)

                # look up cached values, or produce them if not.
                # inject the cached values

                args_supp = ()

                for arg in args_to_inject:
                    # lookup function to inject
                    inj_func, params = self.cached[arg.__name__]

                    # get the kwargs required
                    inj_kwargs = {param: kwds[param] for param in params
                                  if param in kwds.keys()}

                    # get a hashable representation of the kwargs
                    immut = tuple(sorted(inj_kwargs.items()))

                    # retrieve the cached result (or None if not yet cached)
                    res = mol.cache.get(arg.__name__, {}).get(immut, None)

                    # calculate and cache result
                    if res is None:
                        res = inj_func(mol, **inj_kwargs)

                    # add to injected args
                    args_supp += (res,)

                # put injected args at start of arg list
                args = args_supp + args

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

            return inner

        return outer

    @staticmethod
    def setup_cache(mol):

        """ Set up a cache on e.g. a `Mol`. """

        if not hasattr(mol, 'cache'):
            mol.cache = defaultdict(dict)

    @staticmethod
    def teardown_cache(mol):

        """ Tear down a cache on e.g. a `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			import inspect
12			from functools import wraps
13			from collections import OrderedDict, defaultdict
14
15			import numpy as np
16			from rdkit.Chem.rdmolops import GetDistanceMatrix, GetAdjacencyMatrix
17
18
19			def _add_cached_prop(func, prop):
20
21			""" Annotate a function with the cached props. """
22
23			if not hasattr(func, 'caches'):
24			func.caches = []
25			func.caches.append(prop)
26
27
28			def requires_h_depleted(func):
29
30			""" Decorate a function that requires an h-depleted graph.
31
32			This will check if the molecule argument is h-depleted, and will
33			memoize a depleted version if it is not, and pass it to the func.
34
35			Note:
36			This decorator should be used first if in combination with dMat etc.
37			"""
38
39			@wraps(func)
40			def inner(mol, args, *kwargs):
41
42			# if is already h depleted
43			if (mol.atoms.atomic_number == 1).sum() == 0:
44			return func(mol, args, *kwargs)
45
46			if not hasattr(mol, '_h_depleted'):
47			mol._h_depleted = mol.remove_hs()
48
49			return func(mol._h_depleted, args, *kwargs)
50
51			_add_cached_prop(inner, '_h_depleted')
52
53			return inner
54
55
56			def requires_h_filled(func):
57
58			""" Decorate a function that requires a h-filled graph.
59
60			This will check if the molecule argument is h-filled, and will
61			memoize a filled version if it is not, and pass it to the func.
62
63			Note:
64			This decorator should be used first if in combination with dMat etc.
65
66			"""
67
68			@wraps(func)
69			def inner(mol, args, *kwargs):
70			# if is already h enriched
71			if mol.atoms.n_total_hs.sum() == 0:
72			return func(mol, args, *kwargs)
73
74			# if not, memoize the enriched one and pass it
75			if not hasattr(mol, '_h_enriched'):
76			mol._h_enriched = mol.add_hs()
77
78			return func(mol._h_enriched, args, *kwargs)
79
80			_add_cached_prop(inner, '_h_enriched')
81
82			return inner
83
84
85			class Cache(object):
86
87			""" Function cache."""
88
89			def __init__(self):
90			self.cached = {}
91
92			def __call__(self, func):
93
94			""" Create a decorator to identify a function as returning a cached
95			value.
96
97			This can be used for objects that are nontrivial to generate, but
98			are used by many functions.
99			"""
100
101			name = func.__name__
102
103			# get the key word arguments and the default values of the function
104			kwds = OrderedDict((k, v.default) for k, v in
105			inspect.signature(func).parameters.items()
106			if v.default != inspect._empty)
107
108			@wraps(func)
109			def inner(mol, args, force=False, *kwargs):
			0 ignored issues – show introduced 2016-08-30 21:40 UTC by Report Bug Copy Issue Report invalid syntax Loading history...
110
111			self.setup_cache(mol)
112
113			# get the full set of keywords to use, including defaults
114			kwds.update(kwargs)
115			kw_to_save = tuple(sorted(kwds.items()))
116
117			# call function if it hasn't already been called
118			# with required arguments, or if told to.
119			if force or name not in self.cached.keys() or \
120			kw_to_save not in mol.cache.get(name, {}).keys():
121
122			res = func(mol, args, *kwargs)
123
124			# cache the value with the args used.
125			mol.cache[name].update({kw_to_save: res})
126
127			# return the cached value
128			return mol.cache[name][kw_to_save]
129
130			self.cached[name] = inner, tuple(kwds.keys())
131
132			return inner
133
134			def inject(self, *args_to_inject):
135
136			""" Create a decorator that will inject cached values as arguments.
137
138			Args:
139			args (list<str>):
140			A list of cachable requirements for this function.
141			"""
142
143			def outer(func):
144
145			# extract the defaults for the func
146			kwds = OrderedDict((k, v.default) for k, v in
147			inspect.signature(func).parameters.items()
148			if v.default != inspect._empty)
149
150			@wraps(func)
151			def inner(mol, args, *kwargs):
152
153			# augment with the keywords from the function
154			kwds.update(kwargs)
155
156			self.setup_cache(mol)
157
158			# look up cached values, or produce them if not.
159			# inject the cached values
160
161			args_supp = ()
162
163			for arg in args_to_inject:
164			# lookup function to inject
165			inj_func, params = self.cached[arg.__name__]
166
167			# get the kwargs required
168			inj_kwargs = {param: kwds[param] for param in params
169			if param in kwds.keys()}
170
171			# get a hashable representation of the kwargs
172			immut = tuple(sorted(inj_kwargs.items()))
173
174			# retrieve the cached result (or None if not yet cached)
175			res = mol.cache.get(arg.__name__, {}).get(immut, None)
176
177			# calculate and cache result
178			if res is None:
179			res = inj_func(mol, **inj_kwargs)
180
181			# add to injected args
182			args_supp += (res,)
183
184			# put injected args at start of arg list
185			args = args_supp + args
186
187			return func(mol, args, *kwargs)
188
189			return inner
190
191			return outer
192
193			@staticmethod
194			def setup_cache(mol):
195
196			""" Set up a cache on e.g. a `Mol`. """
197
198			if not hasattr(mol, 'cache'):
199			mol.cache = defaultdict(dict)
200
201			@staticmethod
202			def teardown_cache(mol):
203
204			""" Tear down a cache on e.g. a `Mol`. """
205
206			if hasattr(mol, 'cache'):
207			del mol.cache
208
209			cache = Cache()
210
211
212			def requires_dmat(func):
213			""" Decorate a function that requires a distance matrix. """
214			@wraps(func)
215			def inner(mol, args, *kwargs):
216			if not hasattr(mol, '_dMat'):
217			dmat = GetDistanceMatrix(mol)
218			dmat[dmat > 100] = np.nan
219			mol._dMat = dmat
220			return func(mol, args, *kwargs)
221
222			_add_cached_prop(inner, '_dMat')
223
224			return inner
225
226
227			def requires_amat(func):
228			""" Decorate a function that requires an adjacency matrix. """
229			@wraps(func)
230			def inner(mol, args, *kwargs):
231			if not hasattr(mol, '_adjMat'):
232			mol._adjMat = GetAdjacencyMatrix(mol)
233			return func(mol, args, *kwargs)
234
235			_add_cached_prop(inner, 'amat')
236
237			return inner
238
239
240			def requires_bo_amat(func):
241			""" Decorate a function thate requires a bond order adjacency, matrix. """
242			@wraps(func)
243			def inner(mol, args, *kwargs):
244			if not hasattr(mol, '_bo_amat'):
245			mol._bo_amat = GetAdjacencyMatrix(mol, useBO=1)
246			return func(mol, args, *kwargs)
247
248			_add_cached_prop(inner, '_bo_amat')
249
250			return inner
251
252
253			def requires_degrees(func):
254			""" Decorate a function that requires a degree vector. """
255			@wraps(func)
256			def inner(mol, args, *kwargs):
257			if not hasattr(mol, '_degrees'):
258			mol._degrees = np.array([atom.degree for atom in mol.atoms])
259			return func(mol, args, *kwargs)
260
261			_add_cached_prop(inner, '_degrees')
262
263			return inner

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