def explicit_hydrogen_keys(xgr):
""" explicit hydrogen keys (H types: explicit, implicit, backbone)
"""
hyd_keys = dict_.keys_by_value(atom_symbols(xgr), lambda x: x == 'H')
atm_ngb_keys_dct = atom_neighbor_keys(xgr)
def _is_backbone(hyd_key):
return all(ngb_key in hyd_keys and hyd_key < ngb_key
for ngb_key in atm_ngb_keys_dct[hyd_key])
exp_hyd_keys = frozenset(fmit.filterfalse(_is_backbone, hyd_keys))
return exp_hyd_keys
def difference(orig, new):
'''
Calculate difference between two iterables.
Will return two iterables, one with added elements and one with
removed elements.
Arguments: orig - original iterable
new - new iterable
Returns: added, removed
'''
try:
added = set(new).difference(orig)
except TypeError:
added = filterfalse(orig.__contains__, new)
try:
removed = set(orig).difference(new)
except TypeError:
removed = filterfalse(new.__contains__, orig)
return added, removed
def explicit_hydrogen_keys(gra):
""" explicit hydrogen keys (H types: explicit, implicit, backbone)
"""
hyd_keys = dict_.keys_by_value(atom_symbols(gra), lambda x: x == 'H')
atm_ngb_keys_dct = atoms_neighbor_atom_keys(gra)
def _is_backbone(hyd_key):
is_h2 = all(ngb_key in hyd_keys and hyd_key < ngb_key
for ngb_key in atm_ngb_keys_dct[hyd_key])
is_multivalent = len(atm_ngb_keys_dct[hyd_key]) > 1
return is_h2 or is_multivalent
exp_hyd_keys = frozenset(fmit.filterfalse(_is_backbone, hyd_keys))
return exp_hyd_keys
def unique_everseen(iterable, key=None):
"List unique elements, preserving order. Remember all elements ever seen."
# unique_everseen('AAAABBBCCDAABBB') --> A B C D
# unique_everseen('ABBCcAD', str.lower) --> A B C D
from future.moves.itertools import filterfalse
seen = set()
seen_add = seen.add
if key is None:
for element in filterfalse(seen.__contains__, iterable):
seen_add(element)
yield element
else:
for element in iterable:
k = key(element)
if k not in seen:
seen_add(k)
yield element
def _ref_key(self, key):
"""Record a reference to the argument key."""
queue = self.queue
refcount = self.refcount
queue.append(key)
refcount[key] = refcount[key] + 1
# periodically compact the queue by eliminating duplicate keys
# while preserving order of most recent access. Note that this
# is only required when the cache does not exceed its maximum
# size
if len(queue) > self.max_queue:
refcount.clear()
queue_appendleft = queue.appendleft
queue_appendleft(self.sentinel)
for k in filterfalse(refcount.__contains__,
iter(queue.pop, self.sentinel)):
queue_appendleft(k)
refcount[k] = 1
def _ref_key(self, key):
"""Record a reference to the argument key."""
queue = self.queue
refcount = self.refcount
queue.append(key)
refcount[key] = refcount[key] + 1
# periodically compact the queue by eliminating duplicate keys
# while preserving order of most recent access. Note that this
# is only required when the cache does not exceed its maximum
# size
if len(queue) > self.max_queue:
refcount.clear()
queue_appendleft = queue.appendleft
queue_appendleft(self.sentinel)
for k in filterfalse(refcount.__contains__,
iter(queue.pop, self.sentinel)):
queue_appendleft(k)
refcount[k] = 1
def combinatorial_difference(input):
'''Gets the sequence of differences. This corresponds to the upper
triangular portion of a difference matrix.'''
combos = combinations_with_replacement(input, 2)
diffs = map(lambda x: abs(x[0] - x[1]), combos)
return list(filterfalse(lambda x: x == 0, diffs))
def partition(pred, iterable):
"""From itertools documentation"""
t1, t2 = tee(iterable)
return list(filterfalse(pred, t1)), list(filter(pred, t2))
def makedirs(*paths):
"""
None is a path with abspath None and not filesystem counterpart
"""
for path in filterfalse(testpaths, paths):
os.makedirs(path)