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96353c3a8b
* [WIP] Add BCUT 2D descriptors * Use the standard RDKit license * Add Check for EIGEN3 * Add vector param, fix some formatting, remove debug print * Add make_burden function, optimize symmetric eigenvalues * Add some tests, finalize API * Make the python API return tuples * Updates docs * Remove unused variable * Fixed up C++ tests * Remove std::pair wrapper, don't build BCUT when missing EIGEN * Add bigger test case for BCUTs * Accidentally removed the wrong code
89 lines
3.9 KiB
C++
89 lines
3.9 KiB
C++
//
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// Copyright (C) 2020 Brian P. Kelley
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// @@ All Rights Reserved @@
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//
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// This file is part of the RDKit.
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// The contents are covered by the terms of the BSD license
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// which is included in the file license.txt, found at the root
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// of the RDKit source tree.
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//
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#include <RDGeneral/test.h>
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#include <RDGeneral/Invariant.h>
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#include <GraphMol/RDKitBase.h>
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#include <GraphMol/SmilesParse/SmilesParse.h>
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#include <GraphMol/FileParsers/MolSupplier.h>
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#include <RDGeneral/RDLog.h>
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#include <vector>
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#include <GraphMol/Descriptors/BCUT.h>
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using namespace RDKit;
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// from knuth.
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bool feq(float a, float b, float epsilon=1e-6)
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{
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return fabs(a - b) <= ( (fabs(a) < fabs(b) ? fabs(b) : fabs(a)) * epsilon);
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}
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void test1(){
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BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
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BOOST_LOG(rdErrorLog) << " Basic BCUT tests." << std::endl;
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std::vector<std::string> vec = {"c1ccccc1S", "c1cscc1", "CC(=S)C", "CSC", "CS(=O)C",
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"CP(C)C", "CP=O", "CP(C)(C)=O",
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"C[PH](C)=O"};
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std::vector<std::vector<double>> expected = {
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{32.11691025659743, 10.3711255714102, 1.7258015589384423, -1.813025067747632, 2.0032623406582895, -1.5648237280483932, 7.798895708674262, 1.480463460412681},
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{32.133385673916855, 10.690498814349603, 1.5812862454321042, -1.3924158848795094, 1.9109090827066813, -1.1624011856503906, 7.073072952311218, 2.0294988143496093},
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{32.09203038492705, 10.585642854940236, 1.5531725323483636, -1.6095571920399787, 1.6095355058255407, -1.6264025009240035, 7.798379459554676, 1.8522004089765778},
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{32.16623472793675, 11.912765272063261, 1.3229624149945334, -1.5095023144073105, 1.699644712375421, -1.2539447123754206, 7.974132068991219, 2.370867931008784},
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{32.19696040763111, 11.912196087574864, 1.571634336328628, -1.5986639964786287, 1.4708186703193278, -1.7011978973115978, 7.829987043024966, 0.6900118228151252},
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{31.130920829765557, 11.856079170234391, 1.652795743173261, -1.8120831465729346, 2.1415709560249625, -1.4818709560249614, 7.546153955380794, 2.12884604461921},
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{31.059700934072303, 11.958086319851176, 1.271920282698931, -1.2044337292760101, 1.6734005705339297, -0.9875941256320955, 7.220415332975225, 0.601201124030627},
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{31.163638790374048, 11.855143433013291, 1.8876168729214116, -1.862911092419536, 2.279553713445213, -1.6070814330824321, 7.610231826377116, 0.5859042224902173},
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{31.111807418763107, 11.906469225329653, 1.5848247701762241, -1.5909887821270712, 2.0038391834918317, -1.3277290609201042, 7.422700514979134, 0.5941465179281992}
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};
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for (size_t i=0; i<vec.size(); ++i) {
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std::unique_ptr<ROMol> m(SmilesToMol(vec[i]));
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auto bcut = Descriptors::BCUT2D(*m);
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TEST_ASSERT(bcut.size() == expected[i].size());
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for(size_t j=0; j<bcut.size(); ++j) {
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TEST_ASSERT(feq(bcut[j],expected[i][j]));
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}
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}
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BOOST_LOG(rdErrorLog) << " done" << std::endl;
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}
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void test2() {
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BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
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BOOST_LOG(rdErrorLog) << " Larger BCUT tests." << std::endl;
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std::string pathName = getenv("RDBASE");
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std::string sdfName =
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pathName + "/Code/GraphMol/Descriptors/test_data/bace_200_bcut.sdf";
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RDKit::SDMolSupplier reader(sdfName, true, false);
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while(!reader.atEnd()) {
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std::unique_ptr<RDKit::ROMol> m(reader.next());
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TEST_ASSERT(m.get());
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std::vector<double> bcuts = Descriptors::BCUT2D(*m);
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TEST_ASSERT(bcuts.size() == 8);
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TEST_ASSERT(feq(bcuts[0], m->getProp<double>("bcut1")));
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TEST_ASSERT(feq(bcuts[1], m->getProp<double>("bcut2")));
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TEST_ASSERT(feq(bcuts[2], m->getProp<double>("bcut3")));
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TEST_ASSERT(feq(bcuts[3], m->getProp<double>("bcut4")));
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TEST_ASSERT(feq(bcuts[4], m->getProp<double>("bcut5")));
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TEST_ASSERT(feq(bcuts[5], m->getProp<double>("bcut6")));
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TEST_ASSERT(feq(bcuts[6], m->getProp<double>("bcut7")));
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TEST_ASSERT(feq(bcuts[7], m->getProp<double>("bcut8")));
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}
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}
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int main() {
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RDLog::InitLogs();
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test1();
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test2();
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}
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