pub_soft/rdkit
3
0
Fork 0
mirror of https://github.com/rdkit/rdkit.git synced 2026-06-04 21:54:27 +08:00
Code Issues Packages Projects Releases Wiki Activity
Files
Release_2022_09
rdkit/Code/GraphMol/SubstructLibrary/Wrap/rough_test.py
Kevin Burk f8cf31068e Support for logging via Python's logging module. (#4846) 
* Support for logging via Python's logging module.

* Avoid the Python 3.9+ PyObject_CallOneArg function.

* Move logging functions to RDBase; Python logger by default; clean up tests.

* See if removing NOGIL fixes the Windows stall.

* get tests running on windows

* Reset to using C++ logging; whiespace tweaks.

* Longer timestamp grace period; try tempfile vs Windows logging stall.

* Clean up commented code; get details for log count bug.

* SubstructLibrary: Fix c++ threads calling into python

* FilterCatalog: Fix c++ threads calling into python

* Release notes; make sure Jupyter still logs to sys.stderr.

* Always use thread-local log buffers.

* de-verbosify a test

Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
Co-authored-by: Brian Kelley <fustigator@gmail.com>
2022-01-24 04:49:27 +01:00

687 lines
28 KiB
Python
Raw Permalink Blame History

# Copyright (C) 2017-2021 Novartis Institute of BioMedical Research
# and other RDKit contributors
#
# 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 rdBase
import logging
from rdkit import RDConfig, RDLogger
from rdkit.RDLogger import logger
logger = logger()
from rdkit import Chem
from rdkit.Chem import rdSubstructLibrary
import time
import pickle
import tempfile
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 keyholderCls in [None, rdSubstructLibrary.KeyFromPropHolder]:
for fpholderCls in [None, rdSubstructLibrary.PatternHolder]:
for holder in [
rdSubstructLibrary.MolHolder(),
rdSubstructLibrary.CachedMolHolder(),
rdSubstructLibrary.CachedSmilesMolHolder()
]:
if fpholderCls:
fpholder = fpholderCls()
else:
fpholder = None
if keyholderCls:
keyholder = keyholderCls()
self.assertEqual(keyholder.GetPropName(), "_Name")
else:
keyholder = None
slib_ = rdSubstructLibrary.SubstructLibrary(holder, fpholder, keyholder)
for i in range(100):
m = Chem.MolFromSmiles("c1ccccc1")
m.SetProp("_Name", str(i))
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)
if keyholderCls:
for idx in res:
self.assertEqual(str(idx), slib.GetKeyHolder().GetKey(idx))
self.assertEqual([str(idx) for idx in res], list(slib.GetKeyHolder().GetKeys(res)))
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 keyholderCls in [None, rdSubstructLibrary.KeyFromPropHolder]:
for fpholderCls in [None, rdSubstructLibrary.PatternHolder]:
for holder in [
rdSubstructLibrary.MolHolder(),
rdSubstructLibrary.CachedMolHolder(),
rdSubstructLibrary.CachedSmilesMolHolder()
]:
if fpholderCls:
fpholder = fpholderCls()
else:
fpholder = None
if keyholderCls:
keyholder = keyholderCls()
self.assertEqual(keyholder.GetPropName(), "_Name")
else:
keyholder = None
slib_ = rdSubstructLibrary.SubstructLibrary(holder, fpholder, keyholder)
mols = []
for i in range(100):
m = Chem.MolFromSmiles("c1ccccc1")
m.SetProp("_Name", str(i * 2))
self.assertEqual(slib_.AddMol(m), i * 2)
mols.append(m)
m2 = Chem.MolFromSmiles("CCCC")
m2.SetProp("_Name", str(i * 2 + 1))
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))))
if keyholderCls:
self.assertEqual([str(idx) for idx in res], [str(idx) for idx in range(0, 200, 2)])
res = slib.GetMatches(m2)
self.assertEqual(len(res), 100)
self.assertTrue(set(res) == set(list(range(1, 200, 2))))
if keyholderCls:
self.assertEqual([str(idx) for idx in res], [str(idx) for idx in 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)]))
def testRingSmartsWithTrustedSmiles(self):
pat = Chem.MolFromSmarts("[C&R1]")
pat2 = Chem.MolFromSmarts("C@C") # ring bond
holder = rdSubstructLibrary.CachedTrustedSmilesMolHolder()
lib = rdSubstructLibrary.SubstructLibrary(holder)
lib.AddMol(Chem.MolFromSmiles("C1CC1"))
# make sure we can get an unsanitized molecule that fails (no ring info)
print("Testing atom rings")
with self.assertRaises(RuntimeError):
holder.GetMol(0).HasSubstructMatch(pat)
print("testing bond rings")
with self.assertRaises(RuntimeError):
holder.GetMol(0).HasSubstructMatch(pat2)
# shouldn't throw
print("searching atom rings")
self.assertEqual(len(lib.GetMatches(pat)), 1)
self.assertEqual(lib.CountMatches(pat), 1)
print("searching bond rings")
self.assertEqual(len(lib.GetMatches(pat2)), 1)
self.assertEqual(lib.CountMatches(pat2), 1)
print("done")
def test_init_from_and_to_stream(self):
mols = makeStereoExamples() * 10
holder = rdSubstructLibrary.CachedSmilesMolHolder()
# one day I'll fix this, but we need to write text but read binary
# grrr.... something about the python_streambuf handler.
slib = rdSubstructLibrary.SubstructLibrary(holder, None)
for mol in mols:
holder.AddSmiles(Chem.MolToSmiles(mol, isomericSmiles=True))
if rdSubstructLibrary.SubstructLibraryCanSerialize():
fd, path = tempfile.mkstemp()
with open(path, 'w') as file:
slib.ToStream(file)
with open(path, 'rb') as file:
slib2 = rdSubstructLibrary.SubstructLibrary()
slib2.InitFromStream(file)
self.assertEqual(len(slib), len(slib2))
from io import StringIO, BytesIO
s = StringIO()
slib.ToStream(s)
sb = BytesIO(s.getvalue().encode("ascii"))
self.assertTrue(len(sb.getvalue()) > 0)
slib3 = rdSubstructLibrary.SubstructLibrary()
slib3.InitFromStream(sb)
self.assertEqual(len(slib), len(slib2))
def test_addpatterns(self):
pdb_ligands = [
"CCS(=O)(=O)c1ccc(OC)c(Nc2ncc(-c3cccc(-c4ccccn4)c3)o2)c1",
"COc1ccc(S(=O)(=O)NCC2CC2)cc1Nc1ncc(-c2cccc(-c3cccnc3)c2)o1",
"COc1ccc(-c2oc3ncnc(N)c3c2-c2ccc(NC(=O)Nc3cc(C(F)(F)F)ccc3F)cc2)cc1",
"COC(=O)Nc1nc2ccc(Oc3ccc(NC(=O)Nc4cc(C(F)(F)F)ccc4F)cc3)cc2[nH]1",
"COc1cc(Nc2ncnc(-c3cccnc3Nc3ccccc3)n2)cc(OC)c1OC",
"O=C(Nc1ccc(Oc2ccccc2)cc1)c1cccnc1NCc1ccncc1", "O=C(Nc1ccc(Oc2ccccc2)cc1)c1cccnc1NCc1ccncc1",
"CNC(=O)c1cc(Oc2ccc3[nH]c(Nc4ccc(Cl)c(C(F)(F)F)c4)nc3c2)ccn1",
"CNC(=O)c1cc(Oc2ccc3oc(Nc4ccc(Cl)c(OCC5CCC[NH+]5C)c4)nc3c2)ccn1",
"CNC(=O)c1cc(Oc2ccc3oc(Nc4ccc(Cl)c(OCC5CCC[NH+]5C)c4)nc3c2)ccn1",
"COc1cc2nccc(Oc3ccc4c(c3)OCCN4C(=O)Nc3ccc(Cl)cc3)c2cc1OC",
"CNC(=O)c1c(C)oc2cc(Oc3cc[nH+]c4cc(OCCN5CCOCC5)ccc34)ccc12",
"COc1cc2[nH+]ccc(Oc3ccc4c(C(=O)Nc5ccc(Cl)cc5)cccc4c3)c2cc1OC",
"COc1cc2[nH+]ccc(Oc3ccc4c(C(=O)Nc5ccc(Cl)cc5)cccc4c3)c2cc1OC",
"COc1cc2[nH+]ccc(Oc3ccc4c(C(=O)NC5CC5)cccc4c3)c2cc1OC",
"COc1cc2[nH+]ccc(Oc3ccc4c(C(=O)NC5CC5)cccc4c3)c2cc1OC",
"Cc1ccc(C(=O)Nc2cc(CCC[NH+](C)C)cc(C(F)(F)F)c2)cc1Nc1ncccc1-c1ccncn1",
"COc1cc(Nc2nccc(Nc3ccc4c(C)n[nH]c4c3)n2)cc(OC)c1OC",
"COc1cc(Nc2nccc(N(C)c3ccc4c(C)n[nH]c4c3)n2)cc(OC)c1OC",
"Cc1ccn(-c2ccc3c(c2)NCC3(C)C)c(=O)c1-c1ccc2nc(N)ncc2c1",
"Cc1ccn(-c2ccc3c(c2)NCC3(C)C)c(=O)c1-c1ccc2nc(N)ncc2c1",
"Cc1ccc(C(=O)NCCC2CCCC2)cc1C(=O)Nc1ccc(N)nc1", "Cc1ccc(C(=O)NCCC2CCCC2)cc1C(=O)Nc1ccc(N)nc1",
"Cc1ccn(-c2cccc(C(F)(F)F)c2)c(=O)c1-c1ccc2nc(N)ncc2c1",
"Cc1ccn(-c2cccc(C(F)(F)F)c2)c(=O)c1-c1ccc2nc(N)ncc2c1",
"O=C(Nc1cncnc1)c1c(Cl)ccc2c(Nc3cccc(C(F)(F)F)c3)noc12",
"O=C(Nc1cncnc1)c1c(Cl)ccc2c(Nc3cccc(C(F)(F)F)c3)noc12",
"CC1(C)CNc2cc(NC(=O)c3cccnc3NCc3ccncc3)ccc21", "CC1(C)CNc2cc(NC(=O)c3cccnc3NCc3ccncc3)ccc21"
]
for patterns in [
rdSubstructLibrary.PatternHolder(),
rdSubstructLibrary.TautomerPatternHolder()
]:
mols = [Chem.MolFromSmiles(smi) for smi in pdb_ligands]
holder = rdSubstructLibrary.CachedMolHolder()
slib_with_patterns = rdSubstructLibrary.SubstructLibrary(holder, patterns)
for mol in mols:
slib_with_patterns.AddMol(mol)
for nthreads in [1, 2, 0]:
slib_without_patterns = rdSubstructLibrary.SubstructLibrary(holder, None)
rdSubstructLibrary.AddPatterns(slib_without_patterns, nthreads)
# check for seg fault
# were the fingerprints really created
slib_without_patterns.GetFpHolder().GetFingerprint(0)
for mol in mols:
l1 = slib_with_patterns.CountMatches(mol)
l2 = slib_without_patterns.CountMatches(mol)
self.assertTrue(l1)
self.assertEqual(l1, l2)
def test_basic_addpatterns(self):
# add mols
pdb_ligands = [
"CCS(=O)(=O)c1ccc(OC)c(Nc2ncc(-c3cccc(-c4ccccn4)c3)o2)c1",
"COc1ccc(S(=O)(=O)NCC2CC2)cc1Nc1ncc(-c2cccc(-c3cccnc3)c2)o1",
"COc1ccc(-c2oc3ncnc(N)c3c2-c2ccc(NC(=O)Nc3cc(C(F)(F)F)ccc3F)cc2)cc1",
"COC(=O)Nc1nc2ccc(Oc3ccc(NC(=O)Nc4cc(C(F)(F)F)ccc4F)cc3)cc2[nH]1",
"COc1cc(Nc2ncnc(-c3cccnc3Nc3ccccc3)n2)cc(OC)c1OC",
"O=C(Nc1ccc(Oc2ccccc2)cc1)c1cccnc1NCc1ccncc1", "O=C(Nc1ccc(Oc2ccccc2)cc1)c1cccnc1NCc1ccncc1",
"CNC(=O)c1cc(Oc2ccc3[nH]c(Nc4ccc(Cl)c(C(F)(F)F)c4)nc3c2)ccn1",
"CNC(=O)c1cc(Oc2ccc3oc(Nc4ccc(Cl)c(OCC5CCC[NH+]5C)c4)nc3c2)ccn1",
"CNC(=O)c1cc(Oc2ccc3oc(Nc4ccc(Cl)c(OCC5CCC[NH+]5C)c4)nc3c2)ccn1",
"COc1cc2nccc(Oc3ccc4c(c3)OCCN4C(=O)Nc3ccc(Cl)cc3)c2cc1OC",
"CNC(=O)c1c(C)oc2cc(Oc3cc[nH+]c4cc(OCCN5CCOCC5)ccc34)ccc12",
"COc1cc2[nH+]ccc(Oc3ccc4c(C(=O)Nc5ccc(Cl)cc5)cccc4c3)c2cc1OC",
"COc1cc2[nH+]ccc(Oc3ccc4c(C(=O)Nc5ccc(Cl)cc5)cccc4c3)c2cc1OC",
"COc1cc2[nH+]ccc(Oc3ccc4c(C(=O)NC5CC5)cccc4c3)c2cc1OC",
"COc1cc2[nH+]ccc(Oc3ccc4c(C(=O)NC5CC5)cccc4c3)c2cc1OC",
"Cc1ccc(C(=O)Nc2cc(CCC[NH+](C)C)cc(C(F)(F)F)c2)cc1Nc1ncccc1-c1ccncn1",
"COc1cc(Nc2nccc(Nc3ccc4c(C)n[nH]c4c3)n2)cc(OC)c1OC",
"COc1cc(Nc2nccc(N(C)c3ccc4c(C)n[nH]c4c3)n2)cc(OC)c1OC",
"Cc1ccn(-c2ccc3c(c2)NCC3(C)C)c(=O)c1-c1ccc2nc(N)ncc2c1",
"Cc1ccn(-c2ccc3c(c2)NCC3(C)C)c(=O)c1-c1ccc2nc(N)ncc2c1",
"Cc1ccc(C(=O)NCCC2CCCC2)cc1C(=O)Nc1ccc(N)nc1", "Cc1ccc(C(=O)NCCC2CCCC2)cc1C(=O)Nc1ccc(N)nc1",
"Cc1ccn(-c2cccc(C(F)(F)F)c2)c(=O)c1-c1ccc2nc(N)ncc2c1",
"Cc1ccn(-c2cccc(C(F)(F)F)c2)c(=O)c1-c1ccc2nc(N)ncc2c1",
"O=C(Nc1cncnc1)c1c(Cl)ccc2c(Nc3cccc(C(F)(F)F)c3)noc12",
"O=C(Nc1cncnc1)c1c(Cl)ccc2c(Nc3cccc(C(F)(F)F)c3)noc12",
"CC1(C)CNc2cc(NC(=O)c3cccnc3NCc3ccncc3)ccc21", "CC1(C)CNc2cc(NC(=O)c3cccnc3NCc3ccncc3)ccc21"
]
for holder in [
rdSubstructLibrary.CachedSmilesMolHolder(),
rdSubstructLibrary.CachedTrustedSmilesMolHolder()
]:
for smi in pdb_ligands:
holder.AddSmiles(smi)
for patttern in [
None,
rdSubstructLibrary.PatternHolder(),
rdSubstructLibrary.TautomerPatternHolder()
]:
lib = rdSubstructLibrary.SubstructLibrary(holder)
rdSubstructLibrary.AddPatterns(lib, numThreads=-1)
self.assertEqual(len(lib.GetMolHolder()), len(lib.GetFpHolder()))
for smi in pdb_ligands:
self.assertTrue(lib.CountMatches(Chem.MolFromSmiles(smi)))
def test_PatternHolder(self):
for holder in [rdSubstructLibrary.PatternHolder, rdSubstructLibrary.TautomerPatternHolder]:
fname = os.path.join(os.environ["RDBASE"], "Data", "NCI", "first_5K.smi")
suppl = Chem.SmilesMolSupplier(fname, delimiter="\t", titleLine=False)
mols1 = rdSubstructLibrary.CachedTrustedSmilesMolHolder()
fps1 = holder(2048)
ssslib1 = rdSubstructLibrary.SubstructLibrary(mols1, fps1)
mols2 = rdSubstructLibrary.CachedTrustedSmilesMolHolder()
fps2 = holder()
ssslib2 = rdSubstructLibrary.SubstructLibrary(mols2, fps2)
RDLogger.DisableLog('rdApp.error')
for i in range(0, 1000, 10):
try:
mol = suppl[i]
except Exception:
continue
if (not mol):
continue
mols1.AddSmiles(Chem.MolToSmiles(mol))
fps1.AddFingerprint(fps1.MakeFingerprint(mol))
ssslib2.AddMol(mol)
RDLogger.EnableLog('rdApp.error')
query = Chem.MolFromSmarts("N")
self.assertIsNotNone(query)
matches1 = sorted(ssslib1.GetMatches(query))
matches2 = sorted(ssslib2.GetMatches(query))
self.assertEqual(len(matches1), len(matches2))
self.assertTrue(all([m1 == matches2[i] for i, m1 in enumerate(matches1)]))
def testMolBundles(self):
ssl = rdSubstructLibrary.SubstructLibrary()
for smi in ('CCOC', 'CCNC', 'COOCOO', 'CCNC', 'CCCC'):
ssl.AddMol(Chem.MolFromSmiles(smi))
bndl = Chem.MolBundle()
for smi in ('COC', 'CCC'):
bndl.AddMol(Chem.MolFromSmiles(smi))
self.assertEqual(list(ssl.GetMatches(bndl)), [0, 4])
bndl.AddMol(Chem.MolFromSmiles('CN'))
self.assertEqual(list(sorted(ssl.GetMatches(bndl))), [0, 1, 3, 4])
def testSubstructParameters(self):
ssl = rdSubstructLibrary.SubstructLibrary()
for smi in ('C[C@H](F)Cl', 'C[C@@H](F)Cl', 'CC(F)Cl'):
ssl.AddMol(Chem.MolFromSmiles(smi))
bndl = Chem.MolBundle()
for smi in ('C[C@H](F)Cl', ):
bndl.AddMol(Chem.MolFromSmiles(smi))
params = Chem.SubstructMatchParameters()
self.assertEqual(list(sorted(ssl.GetMatches(bndl, params))), [0, 1, 2])
params.useChirality = True
self.assertEqual(list(sorted(ssl.GetMatches(bndl, params))), [0])
def testSearchOrder(self):
for keyholder in [None, rdSubstructLibrary.KeyFromPropHolder()]:
ssl = rdSubstructLibrary.SubstructLibrary(rdSubstructLibrary.MolHolder(), keyholder)
for idx, smi in enumerate(("CCCOC", "CCCCOCC", "CCOC", "COC", "CCCCCOC")):
m = Chem.MolFromSmiles(smi)
m.SetProp("_Name", str(idx))
ssl.AddMol(m)
ssl.SetSearchOrder((3, 2, 0, 1, 4))
self.assertEqual(ssl.GetSearchOrder(), (3, 2, 0, 1, 4))
qm = Chem.MolFromSmiles('COC')
self.assertEqual(list(ssl.GetMatches(qm, maxResults=2)), [3, 2])
self.assertEqual(list(ssl.GetMatches(qm, maxResults=2)), [3, 2])
if keyholder:
self.assertEqual(keyholder.GetPropName(), "_Name")
self.assertEqual(list(ssl.GetKeyHolder().GetKeys(ssl.GetMatches(qm, maxResults=2))),
['3', '2'])
# make sure we can clear the search order:
ssl.SetSearchOrder(None)
self.assertEqual(ssl.GetSearchOrder(), ())
ssl.SetSearchOrder((3, 2, 0, 1, 4))
self.assertEqual(ssl.GetSearchOrder(), (3, 2, 0, 1, 4))
ssl.SetSearchOrder([])
self.assertEqual(ssl.GetSearchOrder(), ())
def testSearchOrder2(self):
ssl = rdSubstructLibrary.SubstructLibrary()
for smi in ("CCCOC", "CCCCOCC", "CCOC", "COC", "CCCCCOC"):
ssl.AddMol(Chem.MolFromSmiles(smi))
def setSearchSmallestFirst(sslib):
searchOrder = list(range(len(sslib)))
holder = sslib.GetMolHolder()
searchOrder.sort(key=lambda x, holder=holder: holder.GetMol(x).GetNumAtoms())
sslib.SetSearchOrder(searchOrder)
setSearchSmallestFirst(ssl)
qm = Chem.MolFromSmiles('COC')
self.assertEqual(list(ssl.GetMatches(qm)), [3, 2, 0, 1, 4])
def testPropHolder(self):
for propname in [None, 'foo']:
if propname is None:
keyholder = rdSubstructLibrary.KeyFromPropHolder()
else:
keyholder = rdSubstructLibrary.KeyFromPropHolder(propname)
library = rdSubstructLibrary.SubstructLibrary(rdSubstructLibrary.MolHolder(), keyholder)
m = Chem.MolFromSmiles('CCC')
if propname is None:
self.assertEqual(keyholder.GetPropName(), "_Name")
else:
self.assertEqual(keyholder.GetPropName(), propname)
if propname:
m.SetProp(propname, 'Z11234')
else:
m.SetProp("_Name", 'Z11234')
library.AddMol(m)
indices = library.GetMatches(m)
self.assertEqual(['Z11234'], list(library.GetKeyHolder().GetKeys(indices)))
def test_bad_smiles(self):
# add mols
pdb_ligands = [
"&CCS(=O)(=O)c1ccc(OC)c(Nc2ncc(-c3cccc(-c4ccccn4)c3)o2)c1",
"&COc1ccc(S(=O)(=O)NCC2CC2)cc1Nc1ncc(-c2cccc(-c3cccnc3)c2)o1",
"&COc1ccc(-c2oc3ncnc(N)c3c2-c2ccc(NC(=O)Nc3cc(C(F)(F)F)ccc3F)cc2)cc1",
"&COC(=O)Nc1nc2ccc(Oc3ccc(NC(=O)Nc4cc(C(F)(F)F)ccc4F)cc3)cc2[nH]1",
"&COc1cc(Nc2ncnc(-c3cccnc3Nc3ccccc3)n2)cc(OC)c1OC",
"&O=C(Nc1ccc(Oc2ccccc2)cc1)c1cccnc1NCc1ccncc1",
"&O=C(Nc1ccc(Oc2ccccc2)cc1)c1cccnc1NCc1ccncc1",
"&CNC(=O)c1cc(Oc2ccc3[nH]c(Nc4ccc(Cl)c(C(F)(F)F)c4)nc3c2)ccn1",
"&CNC(=O)c1cc(Oc2ccc3oc(Nc4ccc(Cl)c(OCC5CCC[NH+]5C)c4)nc3c2)ccn1",
"&CNC(=O)c1cc(Oc2ccc3oc(Nc4ccc(Cl)c(OCC5CCC[NH+]5C)c4)nc3c2)ccn1",
"&COc1cc2nccc(Oc3ccc4c(c3)OCCN4C(=O)Nc3ccc(Cl)cc3)c2cc1OC",
"&CNC(=O)c1c(C)oc2cc(Oc3cc[nH+]c4cc(OCCN5CCOCC5)ccc34)ccc12",
"&COc1cc2[nH+]ccc(Oc3ccc4c(C(=O)Nc5ccc(Cl)cc5)cccc4c3)c2cc1OC",
"&COc1cc2[nH+]ccc(Oc3ccc4c(C(=O)Nc5ccc(Cl)cc5)cccc4c3)c2cc1OC",
"&COc1cc2[nH+]ccc(Oc3ccc4c(C(=O)NC5CC5)cccc4c3)c2cc1OC",
"&COc1cc2[nH+]ccc(Oc3ccc4c(C(=O)NC5CC5)cccc4c3)c2cc1OC",
"&Cc1ccc(C(=O)Nc2cc(CCC[NH+](C)C)cc(C(F)(F)F)c2)cc1Nc1ncccc1-c1ccncn1",
"&COc1cc(Nc2nccc(Nc3ccc4c(C)n[nH]c4c3)n2)cc(OC)c1OC",
"&COc1cc(Nc2nccc(N(C)c3ccc4c(C)n[nH]c4c3)n2)cc(OC)c1OC",
"&Cc1ccn(-c2ccc3c(c2)NCC3(C)C)c(=O)c1-c1ccc2nc(N)ncc2c1",
"&Cc1ccn(-c2ccc3c(c2)NCC3(C)C)c(=O)c1-c1ccc2nc(N)ncc2c1",
"&Cc1ccc(C(=O)NCCC2CCCC2)cc1C(=O)Nc1ccc(N)nc1",
"&Cc1ccc(C(=O)NCCC2CCCC2)cc1C(=O)Nc1ccc(N)nc1",
"&Cc1ccn(-c2cccc(C(F)(F)F)c2)c(=O)c1-c1ccc2nc(N)ncc2c1",
"&Cc1ccn(-c2cccc(C(F)(F)F)c2)c(=O)c1-c1ccc2nc(N)ncc2c1",
"&O=C(Nc1cncnc1)c1c(Cl)ccc2c(Nc3cccc(C(F)(F)F)c3)noc12",
"&O=C(Nc1cncnc1)c1c(Cl)ccc2c(Nc3cccc(C(F)(F)F)c3)noc12",
"&CC1(C)CNc2cc(NC(=O)c3cccnc3NCc3ccncc3)ccc21", "&CC1(C)CNc2cc(NC(=O)c3cccnc3NCc3ccncc3)ccc21"
]
# this test is really verbose, so disable the actual output without
# disabling that logging happens.
rdBase.LogToPythonLogger()
pylog = logging.getLogger("rdkit")
pylog.setLevel(logging.CRITICAL)
for holder in [
rdSubstructLibrary.CachedSmilesMolHolder(),
rdSubstructLibrary.CachedTrustedSmilesMolHolder()
]:
for smi in pdb_ligands:
holder.AddSmiles(smi)
lib = rdSubstructLibrary.SubstructLibrary(holder)
# this should excercise the logger
smi = "CCS(=O)(=O)c1ccc(OC)c(Nc2ncc(-c3cccc(-c4ccccn4)c3)o2)c1"
self.assertEqual(0, lib.CountMatches(Chem.MolFromSmiles(smi)))
# test add patterns
rdSubstructLibrary.AddPatterns(lib, -1)
pylog.setLevel(logging.WARN)
rdBase.LogToCppStreams()
if __name__ == '__main__':
unittest.main()
Reference in New Issue View Git Blame Copy Permalink