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550 lines
18 KiB
C++
550 lines
18 KiB
C++
//
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// Copyright (C) 2016-2025 Greg Landrum and other RDKit contributors
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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 <catch2/catch_all.hpp>
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#include <RDGeneral/utils.h>
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#include <DataStructs/ExplicitBitVect.h>
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#include <DataStructs/FPBReader.h>
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using namespace RDKit;
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void _basicsTest(FPBReader &fps) {
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fps.init();
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REQUIRE(fps.length() == 100);
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REQUIRE(fps.nBits() == 2048);
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{ // pop counts
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std::pair<unsigned int, unsigned int> offsets;
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offsets = fps.getFPIdsInCountRange(17, 17);
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REQUIRE(offsets.first == 0);
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REQUIRE(offsets.second == 1);
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offsets = fps.getFPIdsInCountRange(60, 65);
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REQUIRE(offsets.first == 96);
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REQUIRE(offsets.second == 100);
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offsets = fps.getFPIdsInCountRange(160, 165);
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REQUIRE(offsets.first == 100);
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REQUIRE(offsets.second == 100);
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}
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{ // get* version
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std::string nm = fps.getId(0);
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REQUIRE(nm == "ZINC00902219");
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boost::shared_ptr<ExplicitBitVect> fp = fps.getFP(0);
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REQUIRE(fp);
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REQUIRE(fp->getNumBits() == 2048);
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REQUIRE(fp->getNumOnBits() == 17);
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unsigned int obs[17] = {1, 80, 183, 222, 227, 231, 482, 650, 807,
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811, 831, 888, 1335, 1411, 1664, 1820, 1917};
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for (unsigned int i = 0; i < fp->getNumOnBits(); ++i) {
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REQUIRE(fp->getBit(obs[i]));
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}
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}
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{ // operator[] version
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std::pair<boost::shared_ptr<ExplicitBitVect>, std::string> tpl = fps[0];
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boost::shared_ptr<ExplicitBitVect> fp = tpl.first;
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REQUIRE(fp);
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REQUIRE(fp->getNumBits() == 2048);
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REQUIRE(fp->getNumOnBits() == 17);
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unsigned int obs[17] = {1, 80, 183, 222, 227, 231, 482, 650, 807,
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811, 831, 888, 1335, 1411, 1664, 1820, 1917};
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for (unsigned int i = 0; i < fp->getNumOnBits(); ++i) {
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REQUIRE(fp->getBit(obs[i]));
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}
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REQUIRE(tpl.second == "ZINC00902219");
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}
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{ // test another fp
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boost::shared_ptr<ExplicitBitVect> fp = fps.getFP(3);
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REQUIRE(fp);
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REQUIRE(fp->getNumBits() == 2048);
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REQUIRE(fp->getNumOnBits() == 20);
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unsigned int obs[20] = {1, 8, 80, 95, 222, 227, 457,
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482, 650, 680, 715, 807, 831, 845,
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888, 1226, 1556, 1711, 1917, 1982};
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for (unsigned int i = 0; i < fp->getNumOnBits(); ++i) {
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REQUIRE(fp->getBit(obs[i]));
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}
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std::string nm = fps.getId(3);
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REQUIRE(nm == "ZINC04803506");
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}
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}
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TEST_CASE("FPBReader Basics") {
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std::string pathName = getenv("RDBASE");
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pathName += "/Code/DataStructs/testData/";
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{
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std::string filename = pathName + "zim.head100.fpb";
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FPBReader fps(filename);
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_basicsTest(fps);
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fps.cleanup(); // make sure this doesn't cause problems
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}
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}
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TEST_CASE("Lazy FPBReader Basics") {
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std::string pathName = getenv("RDBASE");
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pathName += "/Code/DataStructs/testData/";
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{
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std::string filename = pathName + "zim.head100.fpb";
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FPBReader fps(filename, true);
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_basicsTest(fps);
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fps.cleanup(); // make sure this doesn't cause problems
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}
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}
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TEST_CASE("FPBReader Tanimoto") {
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std::string pathName = getenv("RDBASE");
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pathName += "/Code/DataStructs/testData/";
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{
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std::string filename = pathName + "zim.head100.fpb";
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FPBReader fps(filename);
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fps.init();
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REQUIRE(fps.length() == 100);
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{
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boost::shared_array<std::uint8_t> bytes = fps.getBytes(0);
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REQUIRE(bytes);
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REQUIRE(feq(fps.getTanimoto(0, bytes), 1.0));
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REQUIRE(feq(fps.getTanimoto(1, bytes), 0.3703));
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}
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{
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boost::shared_array<std::uint8_t> bytes = fps.getBytes(1);
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REQUIRE(bytes);
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REQUIRE(feq(fps.getTanimoto(1, bytes), 1.0));
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REQUIRE(feq(fps.getTanimoto(0, bytes), 0.3703));
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REQUIRE(feq(fps.getTanimoto(2, bytes), 1.0));
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REQUIRE(feq(fps.getTanimoto(5, bytes), 0.2903));
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}
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}
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}
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TEST_CASE("FPBReader Tanimoto Neighbors") {
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std::string pathName = getenv("RDBASE");
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pathName += "/Code/DataStructs/testData/";
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{
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std::string filename = pathName + "zim.head100.fpb";
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FPBReader fps(filename);
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fps.init();
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REQUIRE(fps.length() == 100);
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{
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boost::shared_array<std::uint8_t> bytes = fps.getBytes(0);
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REQUIRE(bytes);
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std::vector<std::pair<double, unsigned int>> nbrs =
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fps.getTanimotoNeighbors(bytes);
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REQUIRE(nbrs.size() == 1);
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REQUIRE(feq(nbrs[0].first, 1.));
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REQUIRE(nbrs[0].second == 0);
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}
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{ // with a threshold
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boost::shared_array<std::uint8_t> bytes = fps.getBytes(0);
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REQUIRE(bytes);
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std::vector<std::pair<double, unsigned int>> nbrs =
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fps.getTanimotoNeighbors(bytes, 0.30);
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REQUIRE(nbrs.size() == 5);
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REQUIRE(feq(nbrs[0].first, 1.));
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REQUIRE(nbrs[0].second == 0);
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REQUIRE(feq(nbrs[1].first, 0.3703));
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REQUIRE(nbrs[1].second == 1);
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}
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{ // with a threshold, no screen
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boost::shared_array<std::uint8_t> bytes = fps.getBytes(0);
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REQUIRE(bytes);
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std::vector<std::pair<double, unsigned int>> nbrs =
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fps.getTanimotoNeighbors(bytes, 0.30, false);
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REQUIRE(nbrs.size() == 5);
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REQUIRE(feq(nbrs[0].first, 1.));
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REQUIRE(nbrs[0].second == 0);
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REQUIRE(feq(nbrs[1].first, 0.3703));
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REQUIRE(nbrs[1].second == 1);
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}
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{ // with a threshold
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boost::shared_array<std::uint8_t> bytes = fps.getBytes(95);
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REQUIRE(bytes);
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std::vector<std::pair<double, unsigned int>> nbrs =
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fps.getTanimotoNeighbors(bytes, 0.30);
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REQUIRE(nbrs.size() == 2);
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REQUIRE(feq(nbrs[0].first, 1.));
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REQUIRE(nbrs[0].second == 95);
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REQUIRE(feq(nbrs[1].first, 0.4125));
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REQUIRE(nbrs[1].second == 89);
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}
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}
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}
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TEST_CASE("Lazy FPBReader Basics 2") {
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std::string pathName = getenv("RDBASE");
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pathName += "/Code/DataStructs/testData/";
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{
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std::string filename = pathName + "zim.head100.fpb";
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FPBReader fps(filename, true);
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fps.init();
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REQUIRE(fps.length() == 100);
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REQUIRE(fps.nBits() == 2048);
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{ // pop counts
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std::pair<unsigned int, unsigned int> offsets;
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offsets = fps.getFPIdsInCountRange(17, 17);
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REQUIRE(offsets.first == 0);
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REQUIRE(offsets.second == 1);
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offsets = fps.getFPIdsInCountRange(60, 65);
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REQUIRE(offsets.first == 96);
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REQUIRE(offsets.second == 100);
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offsets = fps.getFPIdsInCountRange(160, 165);
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REQUIRE(offsets.first == 100);
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REQUIRE(offsets.second == 100);
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}
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{ // get* version
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std::string nm = fps.getId(0);
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REQUIRE(nm == "ZINC00902219");
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boost::shared_ptr<ExplicitBitVect> fp = fps.getFP(0);
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REQUIRE(fp);
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REQUIRE(fp->getNumBits() == 2048);
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REQUIRE(fp->getNumOnBits() == 17);
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unsigned int obs[17] = {1, 80, 183, 222, 227, 231, 482, 650, 807,
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811, 831, 888, 1335, 1411, 1664, 1820, 1917};
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for (unsigned int i = 0; i < fp->getNumOnBits(); ++i) {
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REQUIRE(fp->getBit(obs[i]));
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}
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}
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{ // operator[] version
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std::pair<boost::shared_ptr<ExplicitBitVect>, std::string> tpl = fps[0];
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boost::shared_ptr<ExplicitBitVect> fp = tpl.first;
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REQUIRE(fp);
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REQUIRE(fp->getNumBits() == 2048);
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REQUIRE(fp->getNumOnBits() == 17);
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unsigned int obs[17] = {1, 80, 183, 222, 227, 231, 482, 650, 807,
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811, 831, 888, 1335, 1411, 1664, 1820, 1917};
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for (unsigned int i = 0; i < fp->getNumOnBits(); ++i) {
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REQUIRE(fp->getBit(obs[i]));
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}
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REQUIRE(tpl.second == "ZINC00902219");
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}
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{ // test another fp
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boost::shared_ptr<ExplicitBitVect> fp = fps.getFP(3);
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REQUIRE(fp);
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REQUIRE(fp->getNumBits() == 2048);
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REQUIRE(fp->getNumOnBits() == 20);
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unsigned int obs[20] = {1, 8, 80, 95, 222, 227, 457,
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482, 650, 680, 715, 807, 831, 845,
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888, 1226, 1556, 1711, 1917, 1982};
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for (unsigned int i = 0; i < fp->getNumOnBits(); ++i) {
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REQUIRE(fp->getBit(obs[i]));
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}
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std::string nm = fps.getId(3);
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REQUIRE(nm == "ZINC04803506");
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}
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}
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}
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TEST_CASE("Lazy FPBReader Tanimoto") {
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std::string pathName = getenv("RDBASE");
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pathName += "/Code/DataStructs/testData/";
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{
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std::string filename = pathName + "zim.head100.fpb";
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FPBReader fps(filename, true);
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fps.init();
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REQUIRE(fps.length() == 100);
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{
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boost::shared_array<std::uint8_t> bytes = fps.getBytes(0);
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REQUIRE(bytes);
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REQUIRE(feq(fps.getTanimoto(0, bytes), 1.0));
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REQUIRE(feq(fps.getTanimoto(1, bytes), 0.3703));
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}
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{
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boost::shared_ptr<ExplicitBitVect> ebv = fps.getFP(0);
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REQUIRE(ebv);
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REQUIRE(feq(fps.getTanimoto(0, *ebv.get()), 1.0));
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REQUIRE(feq(fps.getTanimoto(1, *ebv.get()), 0.3703));
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}
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{
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boost::shared_array<std::uint8_t> bytes = fps.getBytes(1);
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REQUIRE(bytes);
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REQUIRE(feq(fps.getTanimoto(1, bytes), 1.0));
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REQUIRE(feq(fps.getTanimoto(0, bytes), 0.3703));
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REQUIRE(feq(fps.getTanimoto(2, bytes), 1.0));
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REQUIRE(feq(fps.getTanimoto(5, bytes), 0.2903));
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}
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}
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}
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TEST_CASE("Lazy FPBReader Tanimoto Neighbors") {
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std::string pathName = getenv("RDBASE");
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pathName += "/Code/DataStructs/testData/";
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{
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std::string filename = pathName + "zim.head100.fpb";
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FPBReader fps(filename, true);
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fps.init();
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REQUIRE(fps.length() == 100);
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{
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boost::shared_array<std::uint8_t> bytes = fps.getBytes(0);
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REQUIRE(bytes);
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std::vector<std::pair<double, unsigned int>> nbrs =
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fps.getTanimotoNeighbors(bytes);
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REQUIRE(nbrs.size() == 1);
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REQUIRE(feq(nbrs[0].first, 1.));
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REQUIRE(nbrs[0].second == 0);
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}
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{ // with a threshold
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boost::shared_array<std::uint8_t> bytes = fps.getBytes(0);
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REQUIRE(bytes);
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std::vector<std::pair<double, unsigned int>> nbrs =
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fps.getTanimotoNeighbors(bytes, 0.30);
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REQUIRE(nbrs.size() == 5);
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REQUIRE(feq(nbrs[0].first, 1.));
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REQUIRE(nbrs[0].second == 0);
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REQUIRE(feq(nbrs[1].first, 0.3703));
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REQUIRE(nbrs[1].second == 1);
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}
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{ // with a threshold
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boost::shared_array<std::uint8_t> bytes = fps.getBytes(95);
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REQUIRE(bytes);
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std::vector<std::pair<double, unsigned int>> nbrs =
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fps.getTanimotoNeighbors(bytes, 0.30);
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REQUIRE(nbrs.size() == 2);
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REQUIRE(feq(nbrs[0].first, 1.));
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REQUIRE(nbrs[0].second == 95);
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REQUIRE(feq(nbrs[1].first, 0.4125));
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REQUIRE(nbrs[1].second == 89);
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}
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{ // ebv with a threshold
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boost::shared_ptr<ExplicitBitVect> ebv = fps.getFP(95);
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REQUIRE(ebv);
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std::vector<std::pair<double, unsigned int>> nbrs =
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fps.getTanimotoNeighbors(*ebv.get(), 0.30);
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REQUIRE(nbrs.size() == 2);
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REQUIRE(feq(nbrs[0].first, 1.));
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REQUIRE(nbrs[0].second == 95);
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REQUIRE(feq(nbrs[1].first, 0.4125));
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REQUIRE(nbrs[1].second == 89);
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}
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}
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}
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// need forward declarations of some of the detail functions (doesn't make sense
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// to include these in a public interface and there aren't enough of them to
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// make it worth adding a detail header)
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namespace RDKit {
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namespace detail {
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boost::dynamic_bitset<> *bytesToBitset(const std::uint8_t *fpData,
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std::uint32_t nBits);
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std::uint8_t *bitsetToBytes(const boost::dynamic_bitset<> &bitset);
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} // namespace detail
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} // namespace RDKit
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TEST_CASE("Bitset Details") {
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BOOST_LOG(rdInfoLog)
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<< "-----------------------\n Testing some internal bitset details"
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<< std::endl;
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std::string pathName = getenv("RDBASE");
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pathName += "/Code/DataStructs/testData/";
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{ // test round-tripping bytes -> dynamic_bitest -> bytes
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std::string filename = pathName + "zim.head100.fpb";
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FPBReader fps(filename, true);
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fps.init();
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REQUIRE(fps.length() == 100);
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{
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boost::shared_array<std::uint8_t> bytes = fps.getBytes(0);
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REQUIRE(bytes);
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// -------------------
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// start with bytes -> a bitset
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boost::dynamic_bitset<> *dbs =
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RDKit::detail::bytesToBitset(bytes.get(), fps.nBits());
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REQUIRE(dbs);
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REQUIRE(dbs->size() == fps.nBits());
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REQUIRE(dbs->count() == 17);
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unsigned int obs[17] = {1, 80, 183, 222, 227, 231, 482, 650, 807,
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811, 831, 888, 1335, 1411, 1664, 1820, 1917};
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for (unsigned int i = 0; i < dbs->count(); ++i) {
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REQUIRE((*dbs)[obs[i]]);
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}
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// -------------------
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// and now go the other way
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std::uint8_t *newBytes = RDKit::detail::bitsetToBytes(*dbs);
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REQUIRE(newBytes);
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for (unsigned int i = 0; i < fps.nBits() / 8; ++i) {
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REQUIRE(newBytes[i] == bytes[i]);
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}
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delete dbs;
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delete[] newBytes;
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}
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}
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}
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TEST_CASE("FPBReader Contains") {
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BOOST_LOG(rdInfoLog)
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<< "-----------------------\n Testing FPBReader contains search"
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<< std::endl;
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std::string pathName = getenv("RDBASE");
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pathName += "/Code/DataStructs/testData/";
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{
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std::string filename = pathName + "zim.head100.fpb";
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FPBReader fps(filename);
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fps.init();
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REQUIRE(fps.length() == 100);
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{
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boost::shared_array<std::uint8_t> bytes = fps.getBytes(0);
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REQUIRE(bytes);
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std::vector<unsigned int> nbrs = fps.getContainingNeighbors(bytes);
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REQUIRE(nbrs.size() == 1);
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REQUIRE(nbrs[0] == 0);
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}
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{
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boost::shared_array<std::uint8_t> bytes = fps.getBytes(1);
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REQUIRE(bytes);
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std::vector<unsigned int> nbrs = fps.getContainingNeighbors(bytes);
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REQUIRE(nbrs.size() == 4);
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REQUIRE(nbrs[0] == 1);
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REQUIRE(nbrs[1] == 2);
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REQUIRE(nbrs[2] == 3);
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REQUIRE(nbrs[3] == 4);
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}
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{
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boost::shared_array<std::uint8_t> bytes = fps.getBytes(16);
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REQUIRE(bytes);
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std::vector<unsigned int> nbrs = fps.getContainingNeighbors(bytes);
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REQUIRE(nbrs.size() == 2);
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REQUIRE(nbrs[0] == 16);
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REQUIRE(nbrs[1] == 17);
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}
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{
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boost::shared_array<std::uint8_t> bytes = fps.getBytes(87);
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REQUIRE(bytes);
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std::vector<unsigned int> nbrs = fps.getContainingNeighbors(bytes);
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REQUIRE(nbrs.size() == 4);
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REQUIRE(nbrs[0] == 85);
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REQUIRE(nbrs[1] == 86);
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REQUIRE(nbrs[2] == 87);
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REQUIRE(nbrs[3] == 88);
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|
}
|
|
{
|
|
boost::shared_ptr<ExplicitBitVect> ebv = fps.getFP(87);
|
|
REQUIRE(ebv);
|
|
std::vector<unsigned int> nbrs = fps.getContainingNeighbors(*ebv.get());
|
|
REQUIRE(nbrs.size() == 4);
|
|
REQUIRE(nbrs[0] == 85);
|
|
REQUIRE(nbrs[1] == 86);
|
|
REQUIRE(nbrs[2] == 87);
|
|
REQUIRE(nbrs[3] == 88);
|
|
}
|
|
}
|
|
}
|
|
|
|
TEST_CASE("FPBReader Tversky") {
|
|
std::string pathName = getenv("RDBASE");
|
|
pathName += "/Code/DataStructs/testData/";
|
|
{
|
|
std::string filename = pathName + "zim.head100.fpb";
|
|
FPBReader fps(filename);
|
|
fps.init();
|
|
REQUIRE(fps.length() == 100);
|
|
{
|
|
boost::shared_array<std::uint8_t> bytes = fps.getBytes(0);
|
|
REQUIRE(bytes);
|
|
REQUIRE(feq(fps.getTversky(0, bytes, 1., 1.), 1.0));
|
|
REQUIRE(feq(fps.getTversky(1, bytes, 1., 1.), 0.3703));
|
|
}
|
|
{
|
|
boost::shared_array<std::uint8_t> bytes = fps.getBytes(1);
|
|
REQUIRE(bytes);
|
|
REQUIRE(feq(fps.getTversky(1, bytes, 1., 1.), 1.0));
|
|
REQUIRE(feq(fps.getTversky(0, bytes, 1., 1.), 0.3703));
|
|
REQUIRE(feq(fps.getTversky(2, bytes, 1, 1.), 1.0));
|
|
REQUIRE(feq(fps.getTversky(5, bytes, 1., 1.), 0.2903));
|
|
}
|
|
}
|
|
}
|
|
|
|
TEST_CASE("FPBReader Tversky Neighbors") {
|
|
std::string pathName = getenv("RDBASE");
|
|
pathName += "/Code/DataStructs/testData/";
|
|
{
|
|
std::string filename = pathName + "zim.head100.fpb";
|
|
FPBReader fps(filename);
|
|
fps.init();
|
|
REQUIRE(fps.length() == 100);
|
|
{
|
|
boost::shared_array<std::uint8_t> bytes = fps.getBytes(0);
|
|
REQUIRE(bytes);
|
|
std::vector<std::pair<double, unsigned int>> nbrs =
|
|
fps.getTverskyNeighbors(bytes, 1., 1.);
|
|
REQUIRE(nbrs.size() == 1);
|
|
REQUIRE(feq(nbrs[0].first, 1.));
|
|
REQUIRE(nbrs[0].second == 0);
|
|
}
|
|
{ // with a threshold
|
|
boost::shared_array<std::uint8_t> bytes = fps.getBytes(0);
|
|
REQUIRE(bytes);
|
|
std::vector<std::pair<double, unsigned int>> nbrs =
|
|
fps.getTverskyNeighbors(bytes, 1., 1., 0.3);
|
|
REQUIRE(nbrs.size() == 5);
|
|
REQUIRE(feq(nbrs[0].first, 1.));
|
|
REQUIRE(nbrs[0].second == 0);
|
|
REQUIRE(feq(nbrs[1].first, 0.3703));
|
|
REQUIRE(nbrs[1].second == 1);
|
|
}
|
|
{ // with a threshold, asymmetric
|
|
boost::shared_array<std::uint8_t> bytes = fps.getBytes(0);
|
|
REQUIRE(bytes);
|
|
std::vector<std::pair<double, unsigned int>> nbrs =
|
|
fps.getTverskyNeighbors(bytes, 1., 0.5, 0.3);
|
|
REQUIRE(nbrs.size() == 5);
|
|
REQUIRE(feq(nbrs[0].first, 1.));
|
|
REQUIRE(nbrs[0].second == 0);
|
|
REQUIRE(feq(nbrs[1].first, 0.4255));
|
|
REQUIRE(nbrs[1].second == 1);
|
|
}
|
|
{ // with a threshold, no screen
|
|
boost::shared_array<std::uint8_t> bytes = fps.getBytes(0);
|
|
REQUIRE(bytes);
|
|
std::vector<std::pair<double, unsigned int>> nbrs =
|
|
fps.getTverskyNeighbors(bytes, 1., 1., 0.3, false);
|
|
REQUIRE(nbrs.size() == 5);
|
|
REQUIRE(feq(nbrs[0].first, 1.));
|
|
REQUIRE(nbrs[0].second == 0);
|
|
REQUIRE(feq(nbrs[1].first, 0.3703));
|
|
REQUIRE(nbrs[1].second == 1);
|
|
}
|
|
{ // with a threshold, asymmetric, no screen
|
|
boost::shared_array<std::uint8_t> bytes = fps.getBytes(0);
|
|
REQUIRE(bytes);
|
|
std::vector<std::pair<double, unsigned int>> nbrs =
|
|
fps.getTverskyNeighbors(bytes, 1., 0.5, 0.3, false);
|
|
REQUIRE(nbrs.size() == 5);
|
|
REQUIRE(feq(nbrs[0].first, 1.));
|
|
REQUIRE(nbrs[0].second == 0);
|
|
REQUIRE(feq(nbrs[1].first, 0.4255));
|
|
REQUIRE(nbrs[1].second == 1);
|
|
}
|
|
}
|
|
}
|
|
|
|
TEST_CASE("Github Issue 1118") {
|
|
BOOST_LOG(rdInfoLog) << "-----------------------\n Testing github issue "
|
|
"1118: deleting non-initialized FPBReader causes seg "
|
|
"fault"
|
|
<< std::endl;
|
|
std::string pathName = getenv("RDBASE");
|
|
pathName += "/Code/DataStructs/testData/";
|
|
{
|
|
std::string filename = pathName + "zim.head100.fpb";
|
|
auto *fps = new FPBReader(filename);
|
|
delete fps;
|
|
}
|
|
{
|
|
auto *fps = new FPBReader();
|
|
delete fps;
|
|
}
|
|
{
|
|
std::string filename = pathName + "zim.head100.fpb";
|
|
std::ifstream ifs(filename.c_str());
|
|
auto *fps = new FPBReader(&ifs, false);
|
|
delete fps;
|
|
}
|
|
BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
|
|
}
|