mirror of
https://github.com/rdkit/rdkit.git
synced 2026-06-04 21:54:27 +08:00
24f1737839
* remove all of the "from __future__" imports * remove the first batch of rdkit.six imports/uses * next step of rdkit.six removal * removing xrange, range, and some maps * next round of removals * next round of cleanups * fix inchi test * last bits of "from rdkit.six" are gone * and the last of the six stuff is gone * strange importlib problem
315 lines
12 KiB
Python
315 lines
12 KiB
Python
# Copyright (C) 2017-2019 Novartis Institute of BioMedical Research
|
|
# All Rights Reserved
|
|
#
|
|
# Redistribution and use in source and binary forms, with or without
|
|
# modification, are permitted provided that the following conditions are
|
|
# met:
|
|
#
|
|
# * Redistributions of source code must retain the above copyright
|
|
# notice, this list of conditions and the following disclaimer.
|
|
# * Redistributions in binary form must reproduce the above
|
|
# copyright notice, this list of conditions and the following
|
|
# disclaimer in the documentation and/or other materials provided
|
|
# with the distribution.
|
|
# * Neither the name of Novartis Institutes for BioMedical Research Inc.
|
|
# nor the names of its contributors may be used to endorse or promote
|
|
# products derived from this software without specific prior written permission.
|
|
#
|
|
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
|
|
# "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
|
|
# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
|
|
# A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
|
|
# OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
|
|
# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
|
|
# LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
|
|
# DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
|
|
# THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
|
|
# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
|
|
# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
|
|
#
|
|
""" This is a rough coverage test of the python wrapper for the SubstructLibrary
|
|
|
|
it is intended to be shallow but broad.
|
|
"""
|
|
|
|
|
|
import doctest, unittest, os, sys
|
|
|
|
from rdkit import RDConfig
|
|
from rdkit.RDLogger import logger
|
|
logger = logger()
|
|
from rdkit import Chem
|
|
from rdkit.Chem import rdSubstructLibrary
|
|
import time
|
|
import pickle
|
|
|
|
def load_tests(loader, tests, ignore):
|
|
tests.addTests(doctest.DocTestSuite(rdSubstructLibrary))
|
|
return tests
|
|
|
|
def makeStereoExamples():
|
|
el = "NO"
|
|
mols = []
|
|
for e in el:
|
|
for e2 in el:
|
|
if e != e2:
|
|
smi = "C1CCO[C@@](%s)(%s)1"%(e,e2)
|
|
m = Chem.MolFromSmiles(smi)
|
|
if m:
|
|
mols.append(m)
|
|
smi = "C1CCO[C@](%s)(%s)1"%(e,e2)
|
|
m = Chem.MolFromSmiles(smi)
|
|
if m:
|
|
mols.append(m)
|
|
|
|
return mols
|
|
|
|
class TestCase(unittest.TestCase):
|
|
|
|
def setUp(self):
|
|
pass
|
|
|
|
def test0SubstructLibrary(self):
|
|
for fpholderCls in [None, rdSubstructLibrary.PatternHolder]:
|
|
for holder in [rdSubstructLibrary.MolHolder(), rdSubstructLibrary.CachedMolHolder(),
|
|
rdSubstructLibrary.CachedSmilesMolHolder()]:
|
|
if fpholderCls: fpholder = fpholderCls()
|
|
else: fpholder = None
|
|
slib_ = rdSubstructLibrary.SubstructLibrary(holder, fpholder)
|
|
for i in range(100):
|
|
m = Chem.MolFromSmiles("c1ccccc1")
|
|
self.assertEqual(slib_.AddMol(m), i)
|
|
|
|
libs = [slib_]
|
|
if rdSubstructLibrary.SubstructLibraryCanSerialize():
|
|
serialized1 = pickle.loads(pickle.dumps(slib_))
|
|
serialized2 = rdSubstructLibrary.SubstructLibrary(slib_.Serialize())
|
|
libs.append(serialized1)
|
|
libs.append(serialized2)
|
|
|
|
for slib in libs:
|
|
res = slib.GetMatches(m)
|
|
t2 = time.time()
|
|
self.assertTrue(len(res) == 100)
|
|
|
|
res = slib.GetMatches(m)
|
|
|
|
self.assertEqual(len(res), 100)
|
|
self.assertTrue(set(res) == set(list(range(100))))
|
|
|
|
res = slib.GetMatches(m, maxResults=100);
|
|
self.assertEqual(len(res), 100)
|
|
self.assertEqual(len(slib.GetMatches(m, startIdx=0, endIdx=100)), 100)
|
|
|
|
self.assertTrue(slib.HasMatch(m))
|
|
self.assertEqual(slib.CountMatches(m), 100)
|
|
|
|
def test1SubstructLibrary(self):
|
|
for fpholderCls in [None, rdSubstructLibrary.PatternHolder]:
|
|
for holder in [rdSubstructLibrary.MolHolder(), rdSubstructLibrary.CachedMolHolder(),
|
|
rdSubstructLibrary.CachedSmilesMolHolder()]:
|
|
if fpholderCls: fpholder = fpholderCls()
|
|
else: fpholder = None
|
|
|
|
slib_ = rdSubstructLibrary.SubstructLibrary(holder, fpholder)
|
|
mols = []
|
|
for i in range(100):
|
|
m = Chem.MolFromSmiles("c1ccccc1")
|
|
self.assertEqual(slib_.AddMol(m), i*2)
|
|
mols.append(m)
|
|
m2 = Chem.MolFromSmiles("CCCC")
|
|
self.assertEqual(slib_.AddMol(m2), i*2+1)
|
|
mols.append(m2)
|
|
|
|
libs = [slib_]
|
|
if rdSubstructLibrary.SubstructLibraryCanSerialize():
|
|
serialized1 = pickle.loads(pickle.dumps(slib_))
|
|
serialized2 = rdSubstructLibrary.SubstructLibrary(slib_.Serialize())
|
|
libs.append(serialized1)
|
|
libs.append(serialized2)
|
|
|
|
for slib in libs:
|
|
res = slib.GetMatches(m)
|
|
self.assertEqual(len(res), 100)
|
|
self.assertEqual(set(res), set(list(range(0,200,2))))
|
|
|
|
res = slib.GetMatches(m2)
|
|
self.assertEqual(len(res), 100)
|
|
self.assertTrue(set(res) == set(list(range(1,200,2))))
|
|
|
|
res = slib.GetMatches(m)
|
|
self.assertEqual(len(res), 100)
|
|
|
|
res = slib.GetMatches(m, maxResults=100);
|
|
self.assertEqual(len(res), 100)
|
|
|
|
self.assertEqual(len(slib.GetMatches(m, startIdx=0, endIdx=50*2)), 50)
|
|
self.assertEqual(len(slib.GetMatches(m2, startIdx=1, endIdx=50*2+1)), 50)
|
|
|
|
self.assertTrue(slib.HasMatch(m))
|
|
self.assertTrue(slib.HasMatch(m2))
|
|
self.assertEqual(slib.CountMatches(m), 100)
|
|
self.assertEqual(slib.CountMatches(m2), 100)
|
|
|
|
def testOptions(self):
|
|
mols = makeStereoExamples() * 10
|
|
|
|
for holderCls in [
|
|
rdSubstructLibrary.MolHolder,
|
|
rdSubstructLibrary.CachedMolHolder,
|
|
rdSubstructLibrary.CachedSmilesMolHolder,
|
|
rdSubstructLibrary.CachedTrustedSmilesMolHolder,
|
|
]:
|
|
holder = holderCls()
|
|
slib_ = rdSubstructLibrary.SubstructLibrary(holder, None)
|
|
|
|
for mol in mols:
|
|
slib_.AddMol(mol)
|
|
|
|
libs = [slib_]
|
|
if rdSubstructLibrary.SubstructLibraryCanSerialize():
|
|
serialized1 = pickle.loads(pickle.dumps(slib_))
|
|
serialized2 = rdSubstructLibrary.SubstructLibrary(slib_.Serialize())
|
|
libs.append(serialized1)
|
|
libs.append(serialized2)
|
|
|
|
for slib in libs:
|
|
core = Chem.MolFromSmarts("C-1-C-C-O-C(-*)(-*)1")
|
|
res = slib.GetMatches(core)
|
|
self.assertEqual(len(res),
|
|
len([x for x in mols if x.HasSubstructMatch(core, useChirality=True)]))
|
|
|
|
core = Chem.MolFromSmarts("C-1-C-C-O-C(-[O])(-[N])1")
|
|
core.SetProp("core", "core")
|
|
res = slib.GetMatches(core, useChirality=False)
|
|
self.assertEqual(len(res),
|
|
len([x for x in mols if x.HasSubstructMatch(core, useChirality=False)]))
|
|
|
|
core = Chem.MolFromSmarts("C-1-C-C-O-[C@@](-[O])(-[N])1")
|
|
res = slib.GetMatches(core, useChirality=False)
|
|
self.assertEqual(len(res),
|
|
len([x for x in mols if x.HasSubstructMatch(core, useChirality=False)]))
|
|
|
|
core = Chem.MolFromSmarts("C-1-C-C-O-[C@@](-[O])(-[N])1")
|
|
res = slib.GetMatches(core)
|
|
self.assertEqual(len(res),
|
|
len([x for x in mols if x.HasSubstructMatch(core, useChirality=True)]))
|
|
|
|
def testSmilesCache(self):
|
|
mols = makeStereoExamples() * 10
|
|
holder = rdSubstructLibrary.CachedSmilesMolHolder()
|
|
|
|
slib_ = rdSubstructLibrary.SubstructLibrary(holder, None)
|
|
|
|
for mol in mols:
|
|
holder.AddSmiles(Chem.MolToSmiles(mol, isomericSmiles=True))
|
|
|
|
libs = [slib_]
|
|
if rdSubstructLibrary.SubstructLibraryCanSerialize():
|
|
serialized1 = pickle.loads(pickle.dumps(slib_))
|
|
serialized2 = rdSubstructLibrary.SubstructLibrary(slib_.Serialize())
|
|
libs.append(serialized1)
|
|
libs.append(serialized2)
|
|
|
|
for slib in libs:
|
|
core = Chem.MolFromSmarts("C-1-C-C-O-C(-*)(-*)1")
|
|
res = slib.GetMatches(core)
|
|
self.assertEqual(len(res),
|
|
len([x for x in mols if x.HasSubstructMatch(core, useChirality=True)]))
|
|
|
|
core = Chem.MolFromSmarts("C-1-C-C-O-C(-[O])(-[N])1")
|
|
core.SetProp("core", "core")
|
|
res = slib.GetMatches(core, useChirality=False)
|
|
self.assertEqual(len(res),
|
|
len([x for x in mols if x.HasSubstructMatch(core, useChirality=False)]))
|
|
|
|
core = Chem.MolFromSmarts("C-1-C-C-O-[C@@](-[O])(-[N])1")
|
|
res = slib.GetMatches(core, useChirality=False)
|
|
self.assertEqual(len(res),
|
|
len([x for x in mols if x.HasSubstructMatch(core, useChirality=False)]))
|
|
|
|
core = Chem.MolFromSmarts("C-1-C-C-O-[C@@](-[O])(-[N])1")
|
|
res = slib.GetMatches(core)
|
|
self.assertEqual(len(res),
|
|
len([x for x in mols if x.HasSubstructMatch(core, useChirality=True)]))
|
|
|
|
|
|
def testTrustedSmilesCache(self):
|
|
mols = makeStereoExamples() * 10
|
|
holder = rdSubstructLibrary.CachedTrustedSmilesMolHolder()
|
|
|
|
slib_ = rdSubstructLibrary.SubstructLibrary(holder, None)
|
|
|
|
for mol in mols:
|
|
holder.AddSmiles(Chem.MolToSmiles(mol, isomericSmiles=True))
|
|
|
|
libs = [slib_]
|
|
if rdSubstructLibrary.SubstructLibraryCanSerialize():
|
|
serialized1 = pickle.loads(pickle.dumps(slib_))
|
|
serialized2 = rdSubstructLibrary.SubstructLibrary(slib_.Serialize())
|
|
libs.append(serialized1)
|
|
libs.append(serialized2)
|
|
|
|
for slib in libs:
|
|
core = Chem.MolFromSmarts("C-1-C-C-O-C(-*)(-*)1")
|
|
res = slib.GetMatches(core)
|
|
self.assertEqual(len(res),
|
|
len([x for x in mols if x.HasSubstructMatch(core, useChirality=True)]))
|
|
|
|
core = Chem.MolFromSmarts("C-1-C-C-O-C(-[O])(-[N])1")
|
|
core.SetProp("core", "core")
|
|
res = slib.GetMatches(core, useChirality=False)
|
|
self.assertEqual(len(res),
|
|
len([x for x in mols if x.HasSubstructMatch(core, useChirality=False)]))
|
|
|
|
core = Chem.MolFromSmarts("C-1-C-C-O-[C@@](-[O])(-[N])1")
|
|
res = slib.GetMatches(core, useChirality=False)
|
|
self.assertEqual(len(res),
|
|
len([x for x in mols if x.HasSubstructMatch(core, useChirality=False)]))
|
|
|
|
core = Chem.MolFromSmarts("C-1-C-C-O-[C@@](-[O])(-[N])1")
|
|
res = slib.GetMatches(core)
|
|
self.assertEqual(len(res),
|
|
len([x for x in mols if x.HasSubstructMatch(core, useChirality=True)]))
|
|
|
|
def testBinaryCache(self):
|
|
mols = makeStereoExamples() * 10
|
|
holder = rdSubstructLibrary.CachedMolHolder()
|
|
|
|
slib_ = rdSubstructLibrary.SubstructLibrary(holder, None)
|
|
|
|
for mol in mols:
|
|
holder.AddBinary(mol.ToBinary())
|
|
|
|
libs = [slib_]
|
|
if rdSubstructLibrary.SubstructLibraryCanSerialize():
|
|
serialized1 = pickle.loads(pickle.dumps(slib_))
|
|
serialized2 = rdSubstructLibrary.SubstructLibrary(slib_.Serialize())
|
|
libs.append(serialized1)
|
|
libs.append(serialized2)
|
|
|
|
for slib in libs:
|
|
core = Chem.MolFromSmarts("C-1-C-C-O-C(-*)(-*)1")
|
|
res = slib.GetMatches(core)
|
|
self.assertEqual(len(res),
|
|
len([x for x in mols if x.HasSubstructMatch(core, useChirality=True)]))
|
|
|
|
core = Chem.MolFromSmarts("C-1-C-C-O-C(-[O])(-[N])1")
|
|
core.SetProp("core", "core")
|
|
res = slib.GetMatches(core, useChirality=False)
|
|
self.assertEqual(len(res),
|
|
len([x for x in mols if x.HasSubstructMatch(core, useChirality=False)]))
|
|
|
|
core = Chem.MolFromSmarts("C-1-C-C-O-[C@@](-[O])(-[N])1")
|
|
res = slib.GetMatches(core, useChirality=False)
|
|
self.assertEqual(len(res),
|
|
len([x for x in mols if x.HasSubstructMatch(core, useChirality=False)]))
|
|
|
|
core = Chem.MolFromSmarts("C-1-C-C-O-[C@@](-[O])(-[N])1")
|
|
res = slib.GetMatches(core)
|
|
self.assertEqual(len(res),
|
|
len([x for x in mols if x.HasSubstructMatch(core, useChirality=True)]))
|
|
|
|
if __name__ == '__main__':
|
|
unittest.main()
|