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111 lines
3.1 KiB
C++
111 lines
3.1 KiB
C++
//
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// Copyright (C) 2021 Greg Landrum
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//
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// @@ All Rights Reserved @@
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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 "catch.hpp"
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#include <GraphMol/RDKitBase.h>
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#include <GraphMol/SmilesParse/SmilesParse.h>
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#include <GraphMol/Descriptors/ConnectivityDescriptors.h>
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using namespace RDKit;
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TEST_CASE("Kier kappa2", "[2D]") {
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SECTION("values from https://doi.org/10.1002/qsar.19860050103") {
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std::vector<std::pair<std::string, double>> data = {
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// Table 5 from the paper
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{"c1ccccc15.Cl5", 1.987},
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{"c1ccccc15.F5", 1.735},
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{"c1ccccc15.[N+]5(=O)O", 2.259},
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{"c1ccccc15.C5(=O)C", 2.444},
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#if 0
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// expected values from paper (differences are due to hybridization mismatches)
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{"c1ccccc15.N5(C)C", 2.646},
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{"c1ccccc15.C5(=O)N", 2.416},
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{"c1ccccc15.C5(=O)O", 2.416},
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{"c1ccccc15.S5(=O)(=O)C", 2.617},
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{"c1ccccc15.O5", 1.756},
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#else
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{"c1ccccc15.N5(C)C", 2.53},
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{"c1ccccc15.C5(=O)N", 2.31},
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{"c1ccccc15.C5(=O)O", 2.31},
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{"c1ccccc15.S5(=O)(=O)C", 2.42},
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{"c1ccccc15.O5", 1.65},
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#endif
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};
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for (const auto &pr : data) {
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std::unique_ptr<ROMol> m(SmilesToMol(pr.first));
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REQUIRE(m);
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auto k2 = Descriptors::calcKappa2(*m);
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CHECK(k2 == Approx(pr.second).epsilon(0.01));
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}
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}
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}
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TEST_CASE("Kier Phi", "[2D]") {
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SECTION("regression-test values from the paper") {
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std::vector<std::pair<std::string, double>> data = {
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// Table 1 from the paper
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{"CCCCCC", 5.00},
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{"CCCCCCC", 6.00},
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{"CCCCCCCC", 7.00},
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{"CCC(C)CC", 3.20},
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{"CC(C)C(C)C", 2.22},
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{"CC(C)(C)CC", 1.63},
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{"C1CCCC1", 0.92},
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{"C1CCCCC1", 1.54},
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{"C1CCCCCC1", 2.25},
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{"CCCCC=C", 4.53},
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{"C=CCCC=C", 4.07},
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{"C#CCCCC", 4.21},
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{"c1ccccc1", 0.91},
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// additional from Table 2
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{"C=CCC=CC", 4.09},
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{"CC=CC=CC", 4.09},
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{"C1=CCCCC1", 1.31},
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{"C1=CC=CCC1", 1.1},
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{"C1=CCC=CC1", 1.1},
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// additional from Table 3
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{"CCCCCCCCCC", 9.00},
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{"CC(C)CCCCC", 5.14},
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{"CCC(C)CCCC", 5.14},
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{"CC(C)CCCC", 4.17},
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{"CCC(C)CCC", 4.17},
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{"CCC(CC)CCC", 5.14},
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{"CCC(CC)CC", 4.17},
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{"CC(C)(C)CCC", 2.34},
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{"CC(C)C(C)CC", 3.06},
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{"CCC(C)(C)CC", 2.34},
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{"CC(C)(C)C(C)C", 1.85},
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// additional from table 4
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{"CCOCC", 3.93},
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{"CCC(=O)CC", 2.73},
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{"CCc1ccc(CC)cc1", 2.49},
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{"CCC(O)CC", 3.14},
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{"CCCC(Cl)(Cl)CCC", 4.69},
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{"CCC(F)C(F)CC", 3.75},
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#if 0
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// expected values from paper (differences are due to hybridization mismatches)
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{"CCOC(=O)CC", 3.61},
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{"CCC(=O)Nc1ccc(CC)cc1", 3.65},
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#else
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{"CCOC(=O)CC", 3.38},
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{"CCC(=O)Nc1ccc(CC)cc1", 3.50},
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#endif
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};
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for (const auto &pr : data) {
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std::unique_ptr<ROMol> m(SmilesToMol(pr.first));
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REQUIRE(m);
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auto val = Descriptors::calcPhi(*m);
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CHECK(val == Approx(pr.second).epsilon(0.01));
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}
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}
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}
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