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https://github.com/rdkit/rdkit.git
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d8722b1c64
* First entry of the SubstructLibrary module * Switch to shared_ptrs for memory safety * run clang-format and add a test * only build when threadsafe_sss is enabled, only test when test_multithreaded is enabled * Adds PRECONDITION * Adds exceptions for out of range errors * Changes getQueryBits to makeQueryBits for clarity * Adds API point to add Binary and Smiles directly * Replaces 0 with NULL for clarity. * Removes debugging code. * Makes endIdx non-inclusive * Adds substruct searching options * Adds preconditions * Small documentation cleanup and removes a line of code. * Add DataStructs library dependency * Actually uses passed in parameters * Adds TrustedSmiles/Binary inputs * Adds more api testing options/trusted smiles and binary inputs * Finalizes API adds docs and doctests * Minor copyright fixes and such
265 lines
10 KiB
Python
265 lines
10 KiB
Python
# Copyright (C) 2017 Novartis Institute of BioMedical Research
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# All Rights Reserved
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#
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# Redistribution and use in source and binary forms, with or without
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# modification, are permitted provided that the following conditions are
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# met:
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#
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# * Redistributions of source code must retain the above copyright
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# notice, this list of conditions and the following disclaimer.
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# * Redistributions in binary form must reproduce the above
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# copyright notice, this list of conditions and the following
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# disclaimer in the documentation and/or other materials provided
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# with the distribution.
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# * Neither the name of Novartis Institutes for BioMedical Research Inc.
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# nor the names of its contributors may be used to endorse or promote
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# products derived from this software without specific prior written permission.
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#
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# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
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# "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
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# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
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# A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
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# OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
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# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
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# LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
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# DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
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# THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
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# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
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# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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#
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""" This is a rough coverage test of the python wrapper for the SubstructLibrary
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it is intended to be shallow but broad.
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"""
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from __future__ import print_function
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import doctest, unittest, os, sys
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from rdkit import RDConfig
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from rdkit.RDLogger import logger
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logger = logger()
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from rdkit import Chem
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from rdkit.Chem import rdSubstructLibrary
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import time
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def load_tests(loader, tests, ignore):
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tests.addTests(doctest.DocTestSuite(rdSubstructLibrary))
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return tests
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def makeStereoExamples():
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el = "NO"
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mols = []
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for e in el:
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for e2 in el:
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if e != e2:
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smi = "C1CCO[C@@](%s)(%s)1"%(e,e2)
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m = Chem.MolFromSmiles(smi)
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if m:
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mols.append(m)
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smi = "C1CCO[C@](%s)(%s)1"%(e,e2)
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m = Chem.MolFromSmiles(smi)
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if m:
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mols.append(m)
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return mols
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class TestCase(unittest.TestCase):
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def setUp(self):
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pass
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def test0SubstructLibrary(self):
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for fpholderCls in [None, rdSubstructLibrary.PatternHolder]:
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for holder in [rdSubstructLibrary.MolHolder(), rdSubstructLibrary.CachedMolHolder(),
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rdSubstructLibrary.CachedSmilesMolHolder()]:
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if fpholderCls: fpholder = fpholderCls()
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else: fpholder = None
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slib = rdSubstructLibrary.SubstructLibrary(holder, fpholder)
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for i in range(100):
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m = Chem.MolFromSmiles("c1ccccc1")
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self.assertEqual(slib.AddMol(m), i)
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res = slib.GetMatches(m)
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t2 = time.time()
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self.assertTrue(len(res) == 100)
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res = slib.GetMatches(m)
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self.assertEqual(len(res), 100)
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self.assertTrue(set(res) == set(list(range(100))))
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res = slib.GetMatches(m, maxResults=100);
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self.assertEqual(len(res), 100)
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self.assertEqual(len(slib.GetMatches(m, startIdx=0, endIdx=100)), 100)
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self.assertTrue(slib.HasMatch(m))
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self.assertEqual(slib.CountMatches(m), 100)
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def test1SubstructLibrary(self):
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for fpholderCls in [None, rdSubstructLibrary.PatternHolder]:
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for holder in [rdSubstructLibrary.MolHolder(), rdSubstructLibrary.CachedMolHolder(),
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rdSubstructLibrary.CachedSmilesMolHolder()]:
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if fpholderCls: fpholder = fpholderCls()
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else: fpholder = None
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slib = rdSubstructLibrary.SubstructLibrary(holder, fpholder)
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mols = []
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for i in range(100):
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m = Chem.MolFromSmiles("c1ccccc1")
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self.assertEqual(slib.AddMol(m), i*2)
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mols.append(m)
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m2 = Chem.MolFromSmiles("CCCC")
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self.assertEqual(slib.AddMol(m2), i*2+1)
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mols.append(m2)
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res = slib.GetMatches(m)
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self.assertEqual(len(res), 100)
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self.assertEqual(set(res), set(list(range(0,200,2))))
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res = slib.GetMatches(m2)
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self.assertEqual(len(res), 100)
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self.assertTrue(set(res) == set(list(range(1,200,2))))
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res = slib.GetMatches(m)
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self.assertEqual(len(res), 100)
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res = slib.GetMatches(m, maxResults=100);
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self.assertEqual(len(res), 100)
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self.assertEqual(len(slib.GetMatches(m, startIdx=0, endIdx=50*2)), 50)
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self.assertEqual(len(slib.GetMatches(m2, startIdx=1, endIdx=50*2+1)), 50)
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self.assertTrue(slib.HasMatch(m))
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self.assertTrue(slib.HasMatch(m2))
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self.assertEqual(slib.CountMatches(m), 100)
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self.assertEqual(slib.CountMatches(m2), 100)
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def testOptions(self):
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mols = makeStereoExamples() * 10
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for holderCls in [
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rdSubstructLibrary.MolHolder,
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rdSubstructLibrary.CachedMolHolder,
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rdSubstructLibrary.CachedSmilesMolHolder,
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rdSubstructLibrary.CachedTrustedSmilesMolHolder,
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]:
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holder = holderCls()
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slib = rdSubstructLibrary.SubstructLibrary(holder, None)
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for mol in mols:
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slib.AddMol(mol)
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core = Chem.MolFromSmarts("C-1-C-C-O-C(-*)(-*)1")
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res = slib.GetMatches(core)
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self.assertEqual(len(res),
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len([x for x in mols if x.HasSubstructMatch(core, useChirality=True)]))
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core = Chem.MolFromSmarts("C-1-C-C-O-C(-[O])(-[N])1")
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core.SetProp("core", "core")
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res = slib.GetMatches(core, useChirality=False)
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self.assertEqual(len(res),
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len([x for x in mols if x.HasSubstructMatch(core, useChirality=False)]))
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core = Chem.MolFromSmarts("C-1-C-C-O-[C@@](-[O])(-[N])1")
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res = slib.GetMatches(core, useChirality=False)
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self.assertEqual(len(res),
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len([x for x in mols if x.HasSubstructMatch(core, useChirality=False)]))
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core = Chem.MolFromSmarts("C-1-C-C-O-[C@@](-[O])(-[N])1")
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res = slib.GetMatches(core)
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self.assertEqual(len(res),
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len([x for x in mols if x.HasSubstructMatch(core, useChirality=True)]))
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def testSmilesCache(self):
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mols = makeStereoExamples() * 10
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holder = rdSubstructLibrary.CachedSmilesMolHolder()
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slib = rdSubstructLibrary.SubstructLibrary(holder, None)
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for mol in mols:
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holder.AddSmiles(Chem.MolToSmiles(mol, isomericSmiles=True))
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core = Chem.MolFromSmarts("C-1-C-C-O-C(-*)(-*)1")
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res = slib.GetMatches(core)
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self.assertEqual(len(res),
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len([x for x in mols if x.HasSubstructMatch(core, useChirality=True)]))
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core = Chem.MolFromSmarts("C-1-C-C-O-C(-[O])(-[N])1")
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core.SetProp("core", "core")
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res = slib.GetMatches(core, useChirality=False)
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self.assertEqual(len(res),
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len([x for x in mols if x.HasSubstructMatch(core, useChirality=False)]))
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core = Chem.MolFromSmarts("C-1-C-C-O-[C@@](-[O])(-[N])1")
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res = slib.GetMatches(core, useChirality=False)
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self.assertEqual(len(res),
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len([x for x in mols if x.HasSubstructMatch(core, useChirality=False)]))
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core = Chem.MolFromSmarts("C-1-C-C-O-[C@@](-[O])(-[N])1")
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res = slib.GetMatches(core)
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self.assertEqual(len(res),
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len([x for x in mols if x.HasSubstructMatch(core, useChirality=True)]))
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def testTrustedSmilesCache(self):
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mols = makeStereoExamples() * 10
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holder = rdSubstructLibrary.CachedTrustedSmilesMolHolder()
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slib = rdSubstructLibrary.SubstructLibrary(holder, None)
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for mol in mols:
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holder.AddSmiles(Chem.MolToSmiles(mol, isomericSmiles=True))
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core = Chem.MolFromSmarts("C-1-C-C-O-C(-*)(-*)1")
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res = slib.GetMatches(core)
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self.assertEqual(len(res),
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len([x for x in mols if x.HasSubstructMatch(core, useChirality=True)]))
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core = Chem.MolFromSmarts("C-1-C-C-O-C(-[O])(-[N])1")
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core.SetProp("core", "core")
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res = slib.GetMatches(core, useChirality=False)
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self.assertEqual(len(res),
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len([x for x in mols if x.HasSubstructMatch(core, useChirality=False)]))
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core = Chem.MolFromSmarts("C-1-C-C-O-[C@@](-[O])(-[N])1")
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res = slib.GetMatches(core, useChirality=False)
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self.assertEqual(len(res),
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len([x for x in mols if x.HasSubstructMatch(core, useChirality=False)]))
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core = Chem.MolFromSmarts("C-1-C-C-O-[C@@](-[O])(-[N])1")
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res = slib.GetMatches(core)
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self.assertEqual(len(res),
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len([x for x in mols if x.HasSubstructMatch(core, useChirality=True)]))
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def testBinaryCache(self):
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mols = makeStereoExamples() * 10
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holder = rdSubstructLibrary.CachedMolHolder()
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slib = rdSubstructLibrary.SubstructLibrary(holder, None)
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for mol in mols:
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holder.AddBinary(mol.ToBinary())
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core = Chem.MolFromSmarts("C-1-C-C-O-C(-*)(-*)1")
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res = slib.GetMatches(core)
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self.assertEqual(len(res),
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len([x for x in mols if x.HasSubstructMatch(core, useChirality=True)]))
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core = Chem.MolFromSmarts("C-1-C-C-O-C(-[O])(-[N])1")
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core.SetProp("core", "core")
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res = slib.GetMatches(core, useChirality=False)
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self.assertEqual(len(res),
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len([x for x in mols if x.HasSubstructMatch(core, useChirality=False)]))
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core = Chem.MolFromSmarts("C-1-C-C-O-[C@@](-[O])(-[N])1")
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res = slib.GetMatches(core, useChirality=False)
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self.assertEqual(len(res),
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len([x for x in mols if x.HasSubstructMatch(core, useChirality=False)]))
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core = Chem.MolFromSmarts("C-1-C-C-O-[C@@](-[O])(-[N])1")
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res = slib.GetMatches(core)
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self.assertEqual(len(res),
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len([x for x in mols if x.HasSubstructMatch(core, useChirality=True)]))
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if __name__ == '__main__':
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unittest.main()
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