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#! /usr/bin/env python |
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# |
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# Copyright (C) 2016 Rich Lewis <[email protected]> |
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# License: 3-clause BSD |
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""" |
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# skchem.features.descriptors.decorators |
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Decorators for descriptors in scikit-chem. |
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""" |
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import inspect |
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from functools import wraps |
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from collections import OrderedDict, defaultdict |
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import numpy as np |
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from rdkit.Chem.rdmolops import GetDistanceMatrix, GetAdjacencyMatrix |
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def _add_cached_prop(func, prop): |
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""" Annotate a function with the cached props. """ |
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if not hasattr(func, 'caches'): |
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func.caches = [] |
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func.caches.append(prop) |
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def requires_h_depleted(func): |
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""" Decorate a function that requires an h-depleted graph. |
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This will check if the molecule argument is h-depleted, and will |
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memoize a depleted version if it is not, and pass it to the func. |
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Note: |
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This decorator should be used first if in combination with dMat etc. |
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""" |
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@wraps(func) |
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def inner(mol, *args, **kwargs): |
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# if is already h depleted |
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if (mol.atoms.atomic_number == 1).sum() == 0: |
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return func(mol, *args, **kwargs) |
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if not hasattr(mol, '_h_depleted'): |
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mol._h_depleted = mol.remove_hs() |
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return func(mol._h_depleted, *args, **kwargs) |
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_add_cached_prop(inner, '_h_depleted') |
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return inner |
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def requires_h_filled(func): |
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""" Decorate a function that requires a h-filled graph. |
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This will check if the molecule argument is h-filled, and will |
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memoize a filled version if it is not, and pass it to the func. |
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Note: |
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This decorator should be used first if in combination with dMat etc. |
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""" |
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@wraps(func) |
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def inner(mol, *args, **kwargs): |
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# if is already h enriched |
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if mol.atoms.n_total_hs.sum() == 0: |
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return func(mol, *args, **kwargs) |
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# if not, memoize the enriched one and pass it |
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if not hasattr(mol, '_h_enriched'): |
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mol._h_enriched = mol.add_hs() |
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return func(mol._h_enriched, *args, **kwargs) |
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_add_cached_prop(inner, '_h_enriched') |
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return inner |
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class Cache(object): |
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""" Function cache.""" |
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def __init__(self): |
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self.cached = {} |
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def __call__(self, func): |
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""" Create a decorator to identify a function as returning a cached |
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value. |
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This can be used for objects that are nontrivial to generate, but |
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are used by many functions. |
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""" |
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name = func.__name__ |
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# get the key word arguments and the default values of the function |
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kwds = OrderedDict((k, v.default) for k, v in |
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inspect.signature(func).parameters.items() |
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if v.default != inspect._empty) |
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@wraps(func) |
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def inner(mol, *args, force=False, **kwargs): |
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self.setup_cache(mol) |
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# get the full set of keywords to use, including defaults |
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kwds.update(kwargs) |
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kw_to_save = tuple(sorted(kwds.items())) |
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# call function if it hasn't already been called |
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# with required arguments, or if told to. |
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if force or name not in self.cached.keys() or \ |
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kw_to_save not in mol.cache.get(name, {}).keys(): |
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res = func(mol, *args, **kwargs) |
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# cache the value with the args used. |
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mol.cache[name].update({kw_to_save: res}) |
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# return the cached value |
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return mol.cache[name][kw_to_save] |
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self.cached[name] = inner, tuple(kwds.keys()) |
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return inner |
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def inject(self, *args_to_inject): |
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""" Create a decorator that will inject cached values as arguments. |
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Args: |
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args (list<str>): |
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A list of cachable requirements for this function. |
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""" |
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def outer(func): |
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# extract the defaults for the func |
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kwds = OrderedDict((k, v.default) for k, v in |
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inspect.signature(func).parameters.items() |
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if v.default != inspect._empty) |
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@wraps(func) |
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def inner(mol, *args, **kwargs): |
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# augment with the keywords from the function |
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kwds.update(kwargs) |
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self.setup_cache(mol) |
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# look up cached values, or produce them if not. |
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# inject the cached values |
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args_supp = () |
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for arg in args_to_inject: |
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# lookup function to inject |
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inj_func, params = self.cached[arg.__name__] |
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# get the kwargs required |
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inj_kwargs = {param: kwds[param] for param in params |
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if param in kwds.keys()} |
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# get a hashable representation of the kwargs |
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immut = tuple(sorted(inj_kwargs.items())) |
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# retrieve the cached result (or None if not yet cached) |
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res = mol.cache.get(arg.__name__, {}).get(immut, None) |
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# calculate and cache result |
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if res is None: |
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res = inj_func(mol, **inj_kwargs) |
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# add to injected args |
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args_supp += (res,) |
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# put injected args at start of arg list |
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args = args_supp + args |
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return func(mol, *args, **kwargs) |
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return inner |
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return outer |
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@staticmethod |
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def setup_cache(mol): |
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""" Set up a cache on e.g. a `Mol`. """ |
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if not hasattr(mol, 'cache'): |
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mol.cache = defaultdict(dict) |
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@staticmethod |
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def teardown_cache(mol): |
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""" Tear down a cache on e.g. a `Mol`. """ |
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if hasattr(mol, 'cache'): |
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del mol.cache |
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cache = Cache() |
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def requires_dmat(func): |
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""" Decorate a function that requires a distance matrix. """ |
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@wraps(func) |
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def inner(mol, *args, **kwargs): |
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if not hasattr(mol, '_dMat'): |
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dmat = GetDistanceMatrix(mol) |
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dmat[dmat > 100] = np.nan |
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mol._dMat = dmat |
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return func(mol, *args, **kwargs) |
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_add_cached_prop(inner, '_dMat') |
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return inner |
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def requires_amat(func): |
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""" Decorate a function that requires an adjacency matrix. """ |
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@wraps(func) |
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def inner(mol, *args, **kwargs): |
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if not hasattr(mol, '_adjMat'): |
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mol._adjMat = GetAdjacencyMatrix(mol) |
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return func(mol, *args, **kwargs) |
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_add_cached_prop(inner, 'amat') |
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return inner |
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def requires_bo_amat(func): |
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""" Decorate a function thate requires a bond order adjacency, matrix. """ |
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@wraps(func) |
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def inner(mol, *args, **kwargs): |
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if not hasattr(mol, '_bo_amat'): |
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mol._bo_amat = GetAdjacencyMatrix(mol, useBO=1) |
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return func(mol, *args, **kwargs) |
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_add_cached_prop(inner, '_bo_amat') |
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return inner |
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def requires_degrees(func): |
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""" Decorate a function that requires a degree vector. """ |
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@wraps(func) |
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def inner(mol, *args, **kwargs): |
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if not hasattr(mol, '_degrees'): |
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mol._degrees = np.array([atom.degree for atom in mol.atoms]) |
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return func(mol, *args, **kwargs) |
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_add_cached_prop(inner, '_degrees') |
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return inner |