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import sys
from rdkit import Chem
from rdkit import six
import threading
import multiprocessing
# this just tests some threading stuff to ensure it doesn't crash with python
# releasing the GIL smarts are recursive...
ref_sdf = '\n RDKit 3D\n\n 22 23 0 0 1 0 0 0 0 0999 V2000\n -6.1917 -1.9517 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -5.0664 -1.3009 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -3.9401 -1.9499 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n -2.8148 -1.2991 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -1.6885 -1.9483 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n -0.5632 -1.2973 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -0.5642 0.0027 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -1.6905 0.6517 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -1.6916 1.9517 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n -2.8158 0.0009 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -3.9422 0.6501 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -5.0685 1.2991 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n 0.5632 -1.9465 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n 1.6885 -1.2955 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 1.6874 0.0046 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n 2.8148 -1.9447 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 3.9401 -1.2936 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 3.9391 0.0064 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 5.0644 0.6572 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 6.1907 0.0082 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 6.1917 -1.2918 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 5.0664 -1.9429 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 1 2 1 0\n 2 3 1 0\n 3 4 1 0\n 4 10 2 0\n 4 5 1 0\n 5 6 2 0\n 6 7 1 0\n 6 13 1 0\n 7 8 2 0\n 8 9 1 0\n 8 10 1 0\n 10 11 1 0\n 11 12 3 0\n 13 14 1 0\n 14 15 2 0\n 14 16 1 0\n 16 17 1 0\n 17 22 1 0\n 17 18 2 0\n 18 19 1 0\n 19 20 2 0\n 20 21 1 0\n 21 22 2 0\nM END'
ref_mol = Chem.MolFromMolBlock(ref_sdf)
core_smarts = '[#6]-!@[#6]-!@[#8]-!@[#6]:1:[#6](-!@[#6]#!@[#7]):[#6](-!@[#7]):[#6]:[#6](-!@[#7]-!@[#6](-!@[#6]-!@[#6]:2:[#6]:[#6]:[#6]:[#6]:[#6]:2)=!@[#8]):[#7]:1'
if ref_mol is None:
raise ValueError('Bad ref structure')
core_mol = Chem.MolFromSmarts(core_smarts)
if core_mol is None:
raise ValueError('Bad core structure')
expected = {}
def runner(func, args):
if args:
res = getattr(ref_mol, func)(args)
else:
res = getattr(ref_mol, func)()
if func in expected:
assert res == expected[func], "Got %r expected %r" % (ers, expected[func])
return res
funcs = ["GetSubstructMatch", "GetSubstructMatches", "HasSubstructMatch"]
# get the expected results from the non-thread version
for func in funcs:
expected[func] = runner(func, core_mol)
nthreads = int(multiprocessing.cpu_count() * 100 / 4) # 100 threads per cpu
threads = []
for i in range(0, nthreads):
for func in funcs:
t = threading.Thread(target=runner, args=(func, core_mol))
t.start()
threads.append(t)
t = threading.Thread(target=runner, args=("ToBinary", None))
t.start()
threads.append(t)
for t in threads:
t.join()
def LogError():
i = 0
while 1:
if i == 10:
break
i += 1
Chem.LogErrorMsg(str(i) + ":: My dog has fleas")
def LogWarning():
i = 0
while 1:
if i == 10:
break
i += 1
Chem.LogWarningMsg(str(i) + ":: All good boys to fine")
# this spews a ton of logging info...
# that is all intermingled...
if 0:
nthreads = int(multiprocessing.cpu_count())
threads = []
for i in range(0, nthreads):
for func in funcs:
if i % 2 == 0:
t = threading.Thread(target=LogError)
else:
t = threading.Thread(target=LogWarning)
t.start()
threads.append(t)
t = threading.Thread(target=LogWarning)
t.start()
threads.append(t)
for t in threads:
t.join()
Chem.WrapLogs()
err = sys.stderr
stringio = sys.stderr = six.StringIO()
# now the errors should be synchronized...
nthreads = int(multiprocessing.cpu_count())
threads = []
for i in range(0, nthreads):
for func in funcs:
if i % 2 == 0:
t = threading.Thread(target=LogError)
else:
t = threading.Thread(target=LogWarning)
t.start()
threads.append(t)
t = threading.Thread(target=LogWarning)
t.start()
threads.append(t)
for t in threads:
t.join()
sys.stderr = err
stringio = sys.stderr = six.StringIO()
LogWarning()
LogError()
sys.stderr = err
assert "WARNING" in stringio.getvalue()
assert "ERROR" in stringio.getvalue()
assert stringio.getvalue().count("WARNING") == 10
assert stringio.getvalue().count("ERROR") == 10
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