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98237b8ade
* Fixes #3924 The scoring function was not taking into account empty rgroups which biased certain arrangements of rgroups that didn't have an rgroup at every position. * Change in response to review * Rigger the no_rgroup into EMPTY_RGROUP * Remove Fix Me label from the geminal rgroup test * add testUserMatchTypesDefaultScore to test default score on user types * Fix scoring RGroups with split attachments [*:1]O.[*:1]N. * Test both scoring functions for testMutipleCoreRelabellingIssues and testUnprocessedMapping * Update testRGroupInternals.cpp remove a couple obsolete comments as suggested in review Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
319 lines
11 KiB
C++
319 lines
11 KiB
C++
// Copyright (C) 2020 Gareth Jones, Glysade LLC
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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
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// 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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#include <string>
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#include <vector>
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#include <RDGeneral/test.h>
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#include <RDGeneral/RDLog.h>
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#include <RDGeneral/utils.h>
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#include <GraphMol/RDKitBase.h>
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#include <RDGeneral/Exceptions.h>
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#include <GraphMol/SmilesParse/SmilesParse.h>
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#include <GraphMol/SmilesParse/SmilesWrite.h>
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#define private public
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#include <GraphMol/RGroupDecomposition/RGroupDecomp.h>
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#include <GraphMol/RGroupDecomposition/RGroupDecompData.h>
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using namespace RDKit;
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void testCoresLabelledProperly() {
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// Tests for an error in RGroupDecompositionParameters::prepareCore where
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// the same unindexed label could be mistakenly given to multiple rgroups
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// in different cores
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// See https://github.com/rdkit/rdkit/pull/3565
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BOOST_LOG(rdInfoLog)
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<< "********************************************************\n";
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BOOST_LOG(rdInfoLog) << "Test cores labelled properly" << std::endl;
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std::vector<std::string> coreSmi = {"N1([*:1])CCN([*:2])CC1",
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"C1(O[*:1])CCC(O[*:2])CC1",
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"C1([*:1])CCC([*:2])CC1"};
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std::vector<ROMOL_SPTR> cores;
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for (const auto &s : coreSmi) {
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cores.emplace_back(SmartsToMol(s));
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}
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RGroupDecompositionParameters params;
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params.alignment = RGroupCoreAlignment::None;
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params.scoreMethod = FingerprintVariance;
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RGroupDecomposition decomposition(cores, params);
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auto data = decomposition.data;
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std::set<int> rlabels;
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for (const auto &core : data->cores) {
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auto mol = core.second.core;
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for (const auto atom : mol->atoms()) {
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if (atom->hasProp(RLABEL)) {
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int rlabel = atom->getProp<int>(RLABEL);
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if (rlabel < 0) {
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TEST_ASSERT(rlabels.find(rlabel) == rlabels.end());
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rlabels.insert(rlabel);
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}
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}
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}
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}
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}
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std::pair<int, RData> makeRData(int attachment, std::vector<int> attachments, const std::string &smiles) {
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auto rData = boost::make_shared<RGroupData>();
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auto mol = SmilesToMol(smiles);
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auto frags = MolOps::getMolFrags(*mol);
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for (auto &frag : frags) {
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rData->add(frag, attachments);
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}
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delete mol;
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std::pair<int, RData> pair(attachment, rData);
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return pair;
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}
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std::pair<int, RData> makeRData(int attachment, const std::string &smiles) {
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std::vector<int> attachments{attachment};
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return makeRData(attachment, attachments, smiles) ;
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}
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void testRingMatching3Score() {
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BOOST_LOG(rdInfoLog)
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<< "********************************************************\n";
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BOOST_LOG(rdInfoLog) << "Test scoring function for RingMatching3- see GitHub ##3924" << std::endl;
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R_DECOMP decomp1Mol1 = {
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makeRData(-4, "*[H]"),
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makeRData(-2, "*[H]"),
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makeRData(-1, "*[H]"),
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makeRData(1, "*C([H])([H])C")
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};
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R_DECOMP decomp1Mol2 = {
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makeRData(-4, "*[H]"),
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makeRData(-3, "*[H]"),
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makeRData(-2, "*[H]"),
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makeRData(-1, "*[H]"),
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makeRData(1, "*C([H])([H])I")
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};
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R_DECOMP decomp1Mol3 = {
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makeRData(-4, "*[H]"),
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makeRData(-2, "*[H]"),
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makeRData(-1, "*[H]"),
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makeRData(1, "*C([H])([H])F")
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};
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RGroupMatch match1Mol1(0, 0, decomp1Mol1, nullptr);
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RGroupMatch match1Mol2(0, 0, decomp1Mol2, nullptr);
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RGroupMatch match1Mol3(0, 0, decomp1Mol3, nullptr);
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std::set<int> labels{-4, -3, -2, -1, 1};
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std::vector<RGroupMatch> matches1Mol1{match1Mol1};
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std::vector<RGroupMatch> matches1Mol2{match1Mol2};
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std::vector<RGroupMatch> matches1Mol3{match1Mol3};
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std::vector<std::vector<RGroupMatch>> allMatches1 = {
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matches1Mol1, matches1Mol2, matches1Mol3};
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std::vector<size_t> permutation{0, 0, 0};
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R_DECOMP decomp2Mol1 = {
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makeRData(-4, "*[H]"),
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makeRData(-3, "*C([H])([H])C"),
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makeRData(-2, "*[H]"),
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makeRData(-1, "*[H]")
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};
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R_DECOMP decomp2Mol2 = {
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makeRData(-4, "*[H]"),
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makeRData(-3, "*[H]"),
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makeRData(-2, "*[H]"),
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makeRData(-1, "*[H]"),
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makeRData(1, "*C([H])([H])I")
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};
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R_DECOMP decomp2Mol3 = {makeRData(-4, "*[H]"), makeRData(-2, "*[H]"),
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makeRData(-1, "*[H]"), makeRData(1, "*C([H])([H])F")};
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RGroupMatch match2Mol1(0, 1, decomp2Mol1, nullptr);
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RGroupMatch match2Mol2(0, 0, decomp2Mol2, nullptr);
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RGroupMatch match2Mol3(0, 0, decomp2Mol3, nullptr);
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std::vector<RGroupMatch> matches2Mol1{match2Mol1};
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std::vector<RGroupMatch> matches2Mol2{match2Mol2};
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std::vector<RGroupMatch> matches2Mol3{match2Mol3};
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std::vector<std::vector<RGroupMatch>> allMatches2 = {
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matches2Mol1, matches2Mol2, matches2Mol3};
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auto test1 = matchScore(permutation, allMatches1, labels);
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auto test2 = matchScore(permutation, allMatches2, labels);
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// expect test1 to have better score than test2 since all halogens are on R1
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TEST_ASSERT(test1 > test2);
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auto testFp1 = fingerprintVarianceScore(permutation, allMatches1, labels);
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auto testFp2 = fingerprintVarianceScore(permutation, allMatches2, labels);
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TEST_ASSERT(testFp1 > testFp2);
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}
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void testGeminalRGroups() {
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BOOST_LOG(rdInfoLog)
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<< "********************************************************\n";
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BOOST_LOG(rdInfoLog) << "Test scoring function for Geminal R-Groups- see GitHub #3924" << std::endl;
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std::vector<int> attachments {5, 6};
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R_DECOMP decomp1Mol1 = {
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makeRData(-6, "*[H]"),
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makeRData(-5, "*[H]"),
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makeRData(-4, "*[H]"),
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makeRData(-3, "*[H]"),
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makeRData(-2, "*[H]"),
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makeRData(5, attachments, "*C([H])([H])C(*)([H])[H]"),
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makeRData(6, attachments, "*C([H])([H])C(*)([H])[H]")
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};
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R_DECOMP decomp1Mol2 = {
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makeRData(-6, "*[H]"),
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makeRData(-5, "*[H]"),
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makeRData(-4, "*[H]"),
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makeRData(-3, "*[H]"),
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makeRData(-2, "*[H]"),
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makeRData(5, "*C([H])([H])[H]"),
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makeRData(6, "*C([H])([H])[H]")
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};
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R_DECOMP decomp1Mol3 = {
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makeRData(-6, "*[H]"),
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makeRData(-5, "*[H]"),
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makeRData(-4, "*[H]"),
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makeRData(-3, "*[H]"),
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makeRData(-2, "*[H]"),
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makeRData(5, "*Cl"),
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makeRData(6, "*Br")
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};
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RGroupMatch match1Mol1(0, 0, decomp1Mol1, nullptr);
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RGroupMatch match1Mol2(0, 0, decomp1Mol2, nullptr);
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RGroupMatch match1Mol3(0, 0, decomp1Mol3, nullptr);
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std::set<int> labels{-6, -5, -4, -3, -2, 5, 6};
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std::vector<RGroupMatch> matches1Mol1{match1Mol1};
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std::vector<RGroupMatch> matches1Mol2{match1Mol2};
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std::vector<RGroupMatch> matches1Mol3{match1Mol3};
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std::vector<std::vector<RGroupMatch>> allMatches1 = {
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matches1Mol1, matches1Mol2, matches1Mol3};
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std::vector<size_t> permutation{0, 0, 0};
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R_DECOMP decomp2Mol1 = {
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makeRData(-6, " *C([H])([H])C(*)([H])[H]"),
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makeRData(-5, "*[H]"),
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makeRData(-4, "*[H]"),
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makeRData(-3, "*[H]"),
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makeRData(-2, "*[H]"),
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makeRData(5, "*[H]"),
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makeRData(6, "*[H]")
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};
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R_DECOMP decomp2Mol2 = {
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makeRData(-6, "*C([H])([H])[H].*C([H])([H])[H]"),
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makeRData(-5, "*[H]"),
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makeRData(-4, "*[H]"),
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makeRData(-3, "*[H]"),
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makeRData(-2, "*[H]"),
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makeRData(5, "*[H]"),
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makeRData(6, "*[H]")
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};
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R_DECOMP decomp2Mol3 = {
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makeRData(-6, "*Cl.*Br"),
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makeRData(-5, "*[H]"),
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makeRData(-4, "*[H]"),
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makeRData(-3, "*[H]"),
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makeRData(-2, "*[H]"),
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makeRData(5, "*[H]"),
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makeRData(6, "*[H]")
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};
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RGroupMatch match2Mol1(0, 2, decomp2Mol1, nullptr);
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RGroupMatch match2Mol2(0, 2, decomp2Mol2, nullptr);
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RGroupMatch match2Mol3(0, 2, decomp2Mol3, nullptr);
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std::vector<RGroupMatch> matches2Mol1{match2Mol1};
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std::vector<RGroupMatch> matches2Mol2{match2Mol2};
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std::vector<RGroupMatch> matches2Mol3{match2Mol3};
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std::vector<std::vector<RGroupMatch>> allMatches2 = {
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matches2Mol1, matches2Mol2, matches2Mol3};
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std::vector<size_t> permutation2{0, 0, 0};
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auto test1 = matchScore(permutation, allMatches1, labels);
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auto test2 = matchScore(permutation, allMatches2, labels);
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TEST_ASSERT(test1 > test2);
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auto testFp1 = fingerprintVarianceScore(permutation, allMatches1, labels);
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auto testFp2 = fingerprintVarianceScore(permutation, allMatches2, labels);
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TEST_ASSERT(testFp1 > testFp2);
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}
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void testGithub3746() {
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BOOST_LOG(rdInfoLog)
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<< "********************************************************\n";
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BOOST_LOG(rdInfoLog) << "Test GA falls over to exhaustive on simple system"
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<< std::endl;
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const std::vector<ROMOL_SPTR> cores{"c1([*:1])c([*:2])c([*:3])ccc1"_smiles,
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"c1([*:1])c([*:2])c([*:3])cnc1"_smiles};
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const std::vector<const char *> smilesData{"c1(CO)cc(CN)ccc1",
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"c1(CO)cc(CN)cnc1"};
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RGroupDecompositionParameters params;
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params.onlyMatchAtRGroups = true;
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params.removeHydrogensPostMatch = true;
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params.matchingStrategy = GA;
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params.removeHydrogensPostMatch = true;
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RGroupDecomposition decomposition(cores, params);
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size_t i = 0;
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for (const auto &smi : smilesData) {
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ROMOL_SPTR mol(static_cast<ROMol *>(SmilesToMol(smi)));
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TEST_ASSERT(decomposition.add(*mol) == static_cast<int>(i++));
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}
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auto data = decomposition.data;
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RGroupGa ga(*data);
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auto numberPermutations = ga.numberPermutations();
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TEST_ASSERT(numberPermutations == 4);
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// criteria for exhaustive search instead of GA
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TEST_ASSERT(numberPermutations < ga.getPopsize() * 100);
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}
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int main() {
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RDLog::InitLogs();
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boost::logging::disable_logs("rdApp.debug");
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BOOST_LOG(rdInfoLog)
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<< "********************************************************\n";
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BOOST_LOG(rdInfoLog) << "Testing R-Group Decomposition Internals\n";
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testRingMatching3Score();
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testGeminalRGroups();
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testGithub3746();
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testCoresLabelledProperly();
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BOOST_LOG(rdInfoLog)
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<< "********************************************************\n";
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return 0;
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}
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