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// Copyright (C) 2020 Gareth Jones, Glysade LLC
// 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.
//
#include <string>
#include <vector>
#include <RDGeneral/test.h>
#include <RDGeneral/RDLog.h>
#include <RDGeneral/utils.h>
#include <GraphMol/RDKitBase.h>
#include <RDGeneral/Exceptions.h>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <GraphMol/SmilesParse/SmilesWrite.h>
#define private public
#include <GraphMol/RGroupDecomposition/RGroupDecomp.h>
#include <GraphMol/RGroupDecomposition/RGroupDecompData.h>
#include <GraphMol/RGroupDecomposition/RGroupGa.h>
using namespace RDKit;
void testCoresLabelledProperly() {
// Tests for an error in RGroupDecompositionParameters::prepareCore where
// the same unindexed label could be mistakenly given to multiple rgroups
// in different cores
// See https://github.com/rdkit/rdkit/pull/3565
BOOST_LOG(rdInfoLog)
<< "********************************************************\n";
BOOST_LOG(rdInfoLog) << "Test cores labelled properly" << std::endl;
std::vector<std::string> coreSmi = {"N1([*:1])CCN([*:2])CC1",
"C1(O[*:1])CCC(O[*:2])CC1",
"C1([*:1])CCC([*:2])CC1"};
std::vector<ROMOL_SPTR> cores;
for (const auto &s : coreSmi) {
cores.emplace_back(SmartsToMol(s));
}
RGroupDecompositionParameters params;
params.alignment = RGroupCoreAlignment::NoAlignment;
params.scoreMethod = FingerprintVariance;
RGroupDecomposition decomposition(cores, params);
auto data = decomposition.data;
std::set<int> rlabels;
for (const auto &core : data->cores) {
auto mol = core.second.core;
for (const auto atom : mol->atoms()) {
if (atom->hasProp(RLABEL)) {
int rlabel = atom->getProp<int>(RLABEL);
if (rlabel < 0) {
TEST_ASSERT(rlabels.find(rlabel) == rlabels.end());
rlabels.insert(rlabel);
}
}
}
}
}
std::pair<int, RData> makeRData(int attachment, std::vector<int> attachments,
const std::string &smiles) {
auto rData = boost::make_shared<RGroupData>();
auto mol = SmilesToMol(smiles);
auto frags = MolOps::getMolFrags(*mol);
for (auto &frag : frags) {
rData->add(frag, attachments);
}
delete mol;
std::pair<int, RData> pair(attachment, rData);
return pair;
}
std::pair<int, RData> makeRData(int attachment, const std::string &smiles) {
std::vector<int> attachments{attachment};
return makeRData(attachment, attachments, smiles);
}
void testRingMatching3Score() {
BOOST_LOG(rdInfoLog)
<< "********************************************************\n";
BOOST_LOG(rdInfoLog)
<< "Test scoring function for RingMatching3- see GitHub ##3924"
<< std::endl;
R_DECOMP decomp1Mol1 = {makeRData(-4, "*[H]"), makeRData(-2, "*[H]"),
makeRData(-1, "*[H]"), makeRData(1, "*C([H])([H])C")};
R_DECOMP decomp1Mol2 = {makeRData(-4, "*[H]"), makeRData(-3, "*[H]"),
makeRData(-2, "*[H]"), makeRData(-1, "*[H]"),
makeRData(1, "*C([H])([H])I")};
R_DECOMP decomp1Mol3 = {makeRData(-4, "*[H]"), makeRData(-2, "*[H]"),
makeRData(-1, "*[H]"), makeRData(1, "*C([H])([H])F")};
RGroupMatch match1Mol1(0, 0, decomp1Mol1, nullptr);
RGroupMatch match1Mol2(0, 0, decomp1Mol2, nullptr);
RGroupMatch match1Mol3(0, 0, decomp1Mol3, nullptr);
std::set<int> labels{-4, -3, -2, -1, 1};
std::vector<RGroupMatch> matches1Mol1{match1Mol1};
std::vector<RGroupMatch> matches1Mol2{match1Mol2};
std::vector<RGroupMatch> matches1Mol3{match1Mol3};
std::vector<std::vector<RGroupMatch>> allMatches1 = {
matches1Mol1, matches1Mol2, matches1Mol3};
std::vector<size_t> permutation{0, 0, 0};
R_DECOMP decomp2Mol1 = {makeRData(-4, "*[H]"), makeRData(-3, "*C([H])([H])C"),
makeRData(-2, "*[H]"), makeRData(-1, "*[H]")};
R_DECOMP decomp2Mol2 = {makeRData(-4, "*[H]"), makeRData(-3, "*[H]"),
makeRData(-2, "*[H]"), makeRData(-1, "*[H]"),
makeRData(1, "*C([H])([H])I")};
R_DECOMP decomp2Mol3 = {makeRData(-4, "*[H]"), makeRData(-2, "*[H]"),
makeRData(-1, "*[H]"), makeRData(1, "*C([H])([H])F")};
RGroupMatch match2Mol1(0, 1, decomp2Mol1, nullptr);
RGroupMatch match2Mol2(0, 0, decomp2Mol2, nullptr);
RGroupMatch match2Mol3(0, 0, decomp2Mol3, nullptr);
std::vector<RGroupMatch> matches2Mol1{match2Mol1};
std::vector<RGroupMatch> matches2Mol2{match2Mol2};
std::vector<RGroupMatch> matches2Mol3{match2Mol3};
std::vector<std::vector<RGroupMatch>> allMatches2 = {
matches2Mol1, matches2Mol2, matches2Mol3};
RGroupScorer scorer;
auto test1 = scorer.matchScore(permutation, allMatches1, labels);
auto test2 = scorer.matchScore(permutation, allMatches2, labels);
// expect test1 to have better score than test2 since all halogens are on R1
TEST_ASSERT(test1 > test2);
auto testFp1 = fingerprintVarianceScore(permutation, allMatches1, labels);
auto testFp2 = fingerprintVarianceScore(permutation, allMatches2, labels);
TEST_ASSERT(testFp1 > testFp2);
}
void testGithub3746() {
BOOST_LOG(rdInfoLog)
<< "********************************************************\n";
BOOST_LOG(rdInfoLog) << "Test GA falls over to exhaustive on simple system"
<< std::endl;
const std::vector<ROMOL_SPTR> cores{"c1([*:1])c([*:2])c([*:3])ccc1"_smiles,
"c1([*:1])c([*:2])c([*:3])cnc1"_smiles};
const std::vector<const char *> smilesData{"c1(CO)cc(CN)ccc1",
"c1(CO)cc(CN)cnc1"};
RGroupDecompositionParameters params;
params.onlyMatchAtRGroups = true;
params.removeHydrogensPostMatch = true;
params.matchingStrategy = GA;
params.removeHydrogensPostMatch = true;
RGroupDecomposition decomposition(cores, params);
size_t i = 0;
for (const auto &smi : smilesData) {
ROMOL_SPTR mol(static_cast<ROMol *>(SmilesToMol(smi)));
TEST_ASSERT(decomposition.add(*mol) == static_cast<int>(i++));
}
auto data = decomposition.data;
RGroupGa ga(*data);
auto numberPermutations = ga.numberPermutations();
TEST_ASSERT(numberPermutations == 4);
// criteria for exhaustive search instead of GA
TEST_ASSERT(numberPermutations < ga.getPopsize() * 100);
}
int main() {
RDLog::InitLogs();
boost::logging::disable_logs("rdApp.debug");
BOOST_LOG(rdInfoLog)
<< "********************************************************\n";
BOOST_LOG(rdInfoLog) << "Testing R-Group Decomposition Internals\n";
testRingMatching3Score();
testGithub3746();
testCoresLabelledProperly();
BOOST_LOG(rdInfoLog)
<< "********************************************************\n";
return 0;
}
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