mirror of
https://github.com/rdkit/rdkit.git
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370 lines
13 KiB
C++
370 lines
13 KiB
C++
//
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// Copyright (C) 2015 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 <RDGeneral/Invariant.h>
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#include <RDGeneral/RDLog.h>
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#include <RDGeneral/Exceptions.h>
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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 test1FPBReaderBasics() {
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BOOST_LOG(rdInfoLog) << "-----------------------\n Testing FPBReader basics "
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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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TEST_ASSERT(fps.length() == 100);
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TEST_ASSERT(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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TEST_ASSERT(offsets.first == 0);
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TEST_ASSERT(offsets.second == 1);
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offsets = fps.getFPIdsInCountRange(60, 65);
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TEST_ASSERT(offsets.first == 96);
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TEST_ASSERT(offsets.second == 100);
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offsets = fps.getFPIdsInCountRange(160, 165);
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TEST_ASSERT(offsets.first == 100);
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TEST_ASSERT(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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TEST_ASSERT(nm == "ZINC00902219");
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boost::shared_ptr<ExplicitBitVect> fp = fps.getFP(0);
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TEST_ASSERT(fp);
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TEST_ASSERT(fp->getNumBits() == 2048);
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TEST_ASSERT(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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TEST_ASSERT(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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TEST_ASSERT(fp);
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TEST_ASSERT(fp->getNumBits() == 2048);
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TEST_ASSERT(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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TEST_ASSERT(fp->getBit(obs[i]));
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}
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TEST_ASSERT(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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TEST_ASSERT(fp);
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TEST_ASSERT(fp->getNumBits() == 2048);
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TEST_ASSERT(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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TEST_ASSERT(fp->getBit(obs[i]));
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}
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std::string nm = fps.getId(3);
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TEST_ASSERT(nm == "ZINC04803506");
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}
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}
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BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
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}
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void test2FPBReaderTanimoto() {
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BOOST_LOG(rdInfoLog)
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<< "-----------------------\n Testing FPBReader tanimoto " << 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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TEST_ASSERT(fps.length() == 100);
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{
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boost::shared_array<boost::uint8_t> bytes = fps.getBytes(0);
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TEST_ASSERT(bytes);
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TEST_ASSERT(feq(fps.getTanimoto(0, bytes), 1.0));
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TEST_ASSERT(feq(fps.getTanimoto(1, bytes), 0.3703));
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}
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{
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boost::shared_array<boost::uint8_t> bytes = fps.getBytes(1);
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TEST_ASSERT(bytes);
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TEST_ASSERT(feq(fps.getTanimoto(1, bytes), 1.0));
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TEST_ASSERT(feq(fps.getTanimoto(0, bytes), 0.3703));
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TEST_ASSERT(feq(fps.getTanimoto(2, bytes), 1.0));
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TEST_ASSERT(feq(fps.getTanimoto(5, bytes), 0.2903));
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}
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}
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BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
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}
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void test3FPBReaderTanimotoNeighbors() {
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BOOST_LOG(rdInfoLog)
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<< "-----------------------\n Testing FPBReader tanimoto neighbors"
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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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TEST_ASSERT(fps.length() == 100);
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{
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boost::shared_array<boost::uint8_t> bytes = fps.getBytes(0);
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TEST_ASSERT(bytes);
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std::vector<std::pair<double, unsigned int> > nbrs =
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fps.getTanimotoNeighbors(bytes);
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TEST_ASSERT(nbrs.size() == 1);
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TEST_ASSERT(feq(nbrs[0].first, 1.));
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TEST_ASSERT(nbrs[0].second == 0);
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}
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{ // with a threshold
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boost::shared_array<boost::uint8_t> bytes = fps.getBytes(0);
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TEST_ASSERT(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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TEST_ASSERT(nbrs.size() == 5);
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TEST_ASSERT(feq(nbrs[0].first, 1.));
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TEST_ASSERT(nbrs[0].second == 0);
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TEST_ASSERT(feq(nbrs[1].first, 0.3703));
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TEST_ASSERT(nbrs[1].second == 1);
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}
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{ // with a threshold
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boost::shared_array<boost::uint8_t> bytes = fps.getBytes(95);
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TEST_ASSERT(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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TEST_ASSERT(nbrs.size() == 2);
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TEST_ASSERT(feq(nbrs[0].first, 1.));
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TEST_ASSERT(nbrs[0].second == 95);
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TEST_ASSERT(feq(nbrs[1].first, 0.4125));
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TEST_ASSERT(nbrs[1].second == 89);
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}
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}
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BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
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}
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void test4LazyFPBReaderBasics() {
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BOOST_LOG(rdInfoLog)
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<< "-----------------------\n Testing Lazy FPBReader basics "
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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, true);
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fps.init();
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TEST_ASSERT(fps.length() == 100);
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TEST_ASSERT(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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TEST_ASSERT(offsets.first == 0);
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TEST_ASSERT(offsets.second == 1);
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offsets = fps.getFPIdsInCountRange(60, 65);
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TEST_ASSERT(offsets.first == 96);
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TEST_ASSERT(offsets.second == 100);
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offsets = fps.getFPIdsInCountRange(160, 165);
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TEST_ASSERT(offsets.first == 100);
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TEST_ASSERT(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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TEST_ASSERT(nm == "ZINC00902219");
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boost::shared_ptr<ExplicitBitVect> fp = fps.getFP(0);
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TEST_ASSERT(fp);
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TEST_ASSERT(fp->getNumBits() == 2048);
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TEST_ASSERT(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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TEST_ASSERT(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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TEST_ASSERT(fp);
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TEST_ASSERT(fp->getNumBits() == 2048);
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TEST_ASSERT(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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TEST_ASSERT(fp->getBit(obs[i]));
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}
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TEST_ASSERT(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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TEST_ASSERT(fp);
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TEST_ASSERT(fp->getNumBits() == 2048);
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TEST_ASSERT(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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TEST_ASSERT(fp->getBit(obs[i]));
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}
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std::string nm = fps.getId(3);
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TEST_ASSERT(nm == "ZINC04803506");
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}
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}
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BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
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}
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void test5LazyFPBReaderTanimoto() {
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BOOST_LOG(rdInfoLog)
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<< "-----------------------\n Testing Lazy FPBReader tanimoto "
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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, true);
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fps.init();
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TEST_ASSERT(fps.length() == 100);
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{
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boost::shared_array<boost::uint8_t> bytes = fps.getBytes(0);
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TEST_ASSERT(bytes);
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TEST_ASSERT(feq(fps.getTanimoto(0, bytes), 1.0));
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TEST_ASSERT(feq(fps.getTanimoto(1, bytes), 0.3703));
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}
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{
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boost::shared_array<boost::uint8_t> bytes = fps.getBytes(1);
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TEST_ASSERT(bytes);
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TEST_ASSERT(feq(fps.getTanimoto(1, bytes), 1.0));
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TEST_ASSERT(feq(fps.getTanimoto(0, bytes), 0.3703));
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TEST_ASSERT(feq(fps.getTanimoto(2, bytes), 1.0));
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TEST_ASSERT(feq(fps.getTanimoto(5, bytes), 0.2903));
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}
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}
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BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
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}
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void test6LazyFPBReaderTanimotoNeighbors() {
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BOOST_LOG(rdInfoLog)
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<< "-----------------------\n Testing Lazy FPBReader tanimoto neighbors"
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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, true);
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fps.init();
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TEST_ASSERT(fps.length() == 100);
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{
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boost::shared_array<boost::uint8_t> bytes = fps.getBytes(0);
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TEST_ASSERT(bytes);
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std::vector<std::pair<double, unsigned int> > nbrs =
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fps.getTanimotoNeighbors(bytes);
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TEST_ASSERT(nbrs.size() == 1);
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TEST_ASSERT(feq(nbrs[0].first, 1.));
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TEST_ASSERT(nbrs[0].second == 0);
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}
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{ // with a threshold
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boost::shared_array<boost::uint8_t> bytes = fps.getBytes(0);
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TEST_ASSERT(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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TEST_ASSERT(nbrs.size() == 5);
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TEST_ASSERT(feq(nbrs[0].first, 1.));
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TEST_ASSERT(nbrs[0].second == 0);
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TEST_ASSERT(feq(nbrs[1].first, 0.3703));
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TEST_ASSERT(nbrs[1].second == 1);
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}
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{ // with a threshold
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boost::shared_array<boost::uint8_t> bytes = fps.getBytes(95);
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TEST_ASSERT(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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TEST_ASSERT(nbrs.size() == 2);
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TEST_ASSERT(feq(nbrs[0].first, 1.));
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TEST_ASSERT(nbrs[0].second == 95);
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TEST_ASSERT(feq(nbrs[1].first, 0.4125));
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TEST_ASSERT(nbrs[1].second == 89);
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}
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}
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BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
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}
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namespace RDKit {
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namespace detail {
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boost::dynamic_bitset<> *bytesToBitset(const boost::uint8_t *fpData,
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boost::uint32_t nBits);
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boost::uint8_t *bitsetToBytes(const boost::dynamic_bitset<> &bitset);
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}
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}
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void test7BitsetDetails() {
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BOOST_LOG(rdInfoLog)
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<< "-----------------------\n Testing some bitset details" << 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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TEST_ASSERT(fps.length() == 100);
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{
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boost::shared_array<boost::uint8_t> bytes = fps.getBytes(0);
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TEST_ASSERT(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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TEST_ASSERT(dbs);
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TEST_ASSERT(dbs->size() == fps.nBits());
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TEST_ASSERT(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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TEST_ASSERT((*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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boost::uint8_t *newBytes = RDKit::detail::bitsetToBytes(*dbs);
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TEST_ASSERT(newBytes);
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for (unsigned int i = 0; i < fps.nBits() / 8; ++i) {
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TEST_ASSERT(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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BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
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}
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int main() {
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RDLog::InitLogs();
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test1FPBReaderBasics();
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test2FPBReaderTanimoto();
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test3FPBReaderTanimotoNeighbors();
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test4LazyFPBReaderBasics();
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test5LazyFPBReaderTanimoto();
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test6LazyFPBReaderTanimotoNeighbors();
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test7BitsetDetails();
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return 0;
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}
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