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rdkit/Code/DataStructs/testFPB.cpp
Greg Landrum 3130578930 additional tests
2016-01-12 12:09:56 +01:00

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//
// Copyright (C) 2016 Greg Landrum
//
// @@ All Rights Reserved @@
// This file is part of the RDKit.
// The contents are covered by the terms of the BSD license
// which is included in the file license.txt, found at the root
// of the RDKit source tree.
//
#include <RDGeneral/Invariant.h>
#include <RDGeneral/RDLog.h>
#include <RDGeneral/Exceptions.h>
#include <RDGeneral/utils.h>
#include <DataStructs/ExplicitBitVect.h>
#include <DataStructs/FPBReader.h>
using namespace RDKit;
void _basicsTest(FPBReader &fps) {
fps.init();
TEST_ASSERT(fps.length() == 100);
TEST_ASSERT(fps.nBits() == 2048);
{ // pop counts
std::pair<unsigned int, unsigned int> offsets;
offsets = fps.getFPIdsInCountRange(17, 17);
TEST_ASSERT(offsets.first == 0);
TEST_ASSERT(offsets.second == 1);
offsets = fps.getFPIdsInCountRange(60, 65);
TEST_ASSERT(offsets.first == 96);
TEST_ASSERT(offsets.second == 100);
offsets = fps.getFPIdsInCountRange(160, 165);
TEST_ASSERT(offsets.first == 100);
TEST_ASSERT(offsets.second == 100);
}
{ // get* version
std::string nm = fps.getId(0);
// std::cerr << " nm: >" << nm << "<" << std::endl;
TEST_ASSERT(nm == "ZINC00902219");
boost::shared_ptr<ExplicitBitVect> fp = fps.getFP(0);
TEST_ASSERT(fp);
TEST_ASSERT(fp->getNumBits() == 2048);
TEST_ASSERT(fp->getNumOnBits() == 17);
unsigned int obs[17] = {1, 80, 183, 222, 227, 231, 482, 650, 807,
811, 831, 888, 1335, 1411, 1664, 1820, 1917};
for (unsigned int i = 0; i < fp->getNumOnBits(); ++i) {
TEST_ASSERT(fp->getBit(obs[i]));
}
}
{ // operator[] version
std::pair<boost::shared_ptr<ExplicitBitVect>, std::string> tpl = fps[0];
boost::shared_ptr<ExplicitBitVect> fp = tpl.first;
TEST_ASSERT(fp);
TEST_ASSERT(fp->getNumBits() == 2048);
TEST_ASSERT(fp->getNumOnBits() == 17);
unsigned int obs[17] = {1, 80, 183, 222, 227, 231, 482, 650, 807,
811, 831, 888, 1335, 1411, 1664, 1820, 1917};
for (unsigned int i = 0; i < fp->getNumOnBits(); ++i) {
TEST_ASSERT(fp->getBit(obs[i]));
}
TEST_ASSERT(tpl.second == "ZINC00902219");
}
{ // test another fp
boost::shared_ptr<ExplicitBitVect> fp = fps.getFP(3);
TEST_ASSERT(fp);
TEST_ASSERT(fp->getNumBits() == 2048);
TEST_ASSERT(fp->getNumOnBits() == 20);
unsigned int obs[20] = {1, 8, 80, 95, 222, 227, 457,
482, 650, 680, 715, 807, 831, 845,
888, 1226, 1556, 1711, 1917, 1982};
for (unsigned int i = 0; i < fp->getNumOnBits(); ++i) {
TEST_ASSERT(fp->getBit(obs[i]));
}
std::string nm = fps.getId(3);
TEST_ASSERT(nm == "ZINC04803506");
}
}
void test1FPBReaderBasics() {
BOOST_LOG(rdInfoLog) << "-----------------------\n Testing FPBReader basics "
<< std::endl;
std::string pathName = getenv("RDBASE");
pathName += "/Code/DataStructs/testData/";
{
std::string filename = pathName + "zim.head100.fpb";
FPBReader fps(filename);
_basicsTest(fps);
}
BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
}
void test9LazyFPBReaderBasics() {
BOOST_LOG(rdInfoLog)
<< "-----------------------\n Testing Lazy FPBReader basics "
<< std::endl;
std::string pathName = getenv("RDBASE");
pathName += "/Code/DataStructs/testData/";
{
std::string filename = pathName + "zim.head100.fpb";
FPBReader fps(filename, true);
_basicsTest(fps);
}
BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
}
void test2FPBReaderTanimoto() {
BOOST_LOG(rdInfoLog)
<< "-----------------------\n Testing FPBReader tanimoto " << std::endl;
std::string pathName = getenv("RDBASE");
pathName += "/Code/DataStructs/testData/";
{
std::string filename = pathName + "zim.head100.fpb";
FPBReader fps(filename);
fps.init();
TEST_ASSERT(fps.length() == 100);
{
boost::shared_array<boost::uint8_t> bytes = fps.getBytes(0);
TEST_ASSERT(bytes);
TEST_ASSERT(feq(fps.getTanimoto(0, bytes), 1.0));
TEST_ASSERT(feq(fps.getTanimoto(1, bytes), 0.3703));
}
{
boost::shared_array<boost::uint8_t> bytes = fps.getBytes(1);
TEST_ASSERT(bytes);
TEST_ASSERT(feq(fps.getTanimoto(1, bytes), 1.0));
TEST_ASSERT(feq(fps.getTanimoto(0, bytes), 0.3703));
TEST_ASSERT(feq(fps.getTanimoto(2, bytes), 1.0));
TEST_ASSERT(feq(fps.getTanimoto(5, bytes), 0.2903));
}
}
BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
}
void test3FPBReaderTanimotoNeighbors() {
BOOST_LOG(rdInfoLog)
<< "-----------------------\n Testing FPBReader tanimoto neighbors"
<< std::endl;
std::string pathName = getenv("RDBASE");
pathName += "/Code/DataStructs/testData/";
{
std::string filename = pathName + "zim.head100.fpb";
FPBReader fps(filename);
fps.init();
TEST_ASSERT(fps.length() == 100);
{
boost::shared_array<boost::uint8_t> bytes = fps.getBytes(0);
TEST_ASSERT(bytes);
std::vector<std::pair<double, unsigned int> > nbrs =
fps.getTanimotoNeighbors(bytes);
TEST_ASSERT(nbrs.size() == 1);
TEST_ASSERT(feq(nbrs[0].first, 1.));
TEST_ASSERT(nbrs[0].second == 0);
}
{ // with a threshold
boost::shared_array<boost::uint8_t> bytes = fps.getBytes(0);
TEST_ASSERT(bytes);
std::vector<std::pair<double, unsigned int> > nbrs =
fps.getTanimotoNeighbors(bytes, 0.30);
TEST_ASSERT(nbrs.size() == 5);
TEST_ASSERT(feq(nbrs[0].first, 1.));
TEST_ASSERT(nbrs[0].second == 0);
TEST_ASSERT(feq(nbrs[1].first, 0.3703));
TEST_ASSERT(nbrs[1].second == 1);
}
{ // with a threshold
boost::shared_array<boost::uint8_t> bytes = fps.getBytes(95);
TEST_ASSERT(bytes);
std::vector<std::pair<double, unsigned int> > nbrs =
fps.getTanimotoNeighbors(bytes, 0.30);
TEST_ASSERT(nbrs.size() == 2);
TEST_ASSERT(feq(nbrs[0].first, 1.));
TEST_ASSERT(nbrs[0].second == 95);
TEST_ASSERT(feq(nbrs[1].first, 0.4125));
TEST_ASSERT(nbrs[1].second == 89);
}
}
BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
}
void test4LazyFPBReaderBasics() {
BOOST_LOG(rdInfoLog)
<< "-----------------------\n Testing Lazy FPBReader basics "
<< std::endl;
std::string pathName = getenv("RDBASE");
pathName += "/Code/DataStructs/testData/";
{
std::string filename = pathName + "zim.head100.fpb";
FPBReader fps(filename, true);
fps.init();
TEST_ASSERT(fps.length() == 100);
TEST_ASSERT(fps.nBits() == 2048);
{ // pop counts
std::pair<unsigned int, unsigned int> offsets;
offsets = fps.getFPIdsInCountRange(17, 17);
TEST_ASSERT(offsets.first == 0);
TEST_ASSERT(offsets.second == 1);
offsets = fps.getFPIdsInCountRange(60, 65);
TEST_ASSERT(offsets.first == 96);
TEST_ASSERT(offsets.second == 100);
offsets = fps.getFPIdsInCountRange(160, 165);
TEST_ASSERT(offsets.first == 100);
TEST_ASSERT(offsets.second == 100);
}
{ // get* version
std::string nm = fps.getId(0);
TEST_ASSERT(nm == "ZINC00902219");
boost::shared_ptr<ExplicitBitVect> fp = fps.getFP(0);
TEST_ASSERT(fp);
TEST_ASSERT(fp->getNumBits() == 2048);
TEST_ASSERT(fp->getNumOnBits() == 17);
unsigned int obs[17] = {1, 80, 183, 222, 227, 231, 482, 650, 807,
811, 831, 888, 1335, 1411, 1664, 1820, 1917};
for (unsigned int i = 0; i < fp->getNumOnBits(); ++i) {
TEST_ASSERT(fp->getBit(obs[i]));
}
}
{ // operator[] version
std::pair<boost::shared_ptr<ExplicitBitVect>, std::string> tpl = fps[0];
boost::shared_ptr<ExplicitBitVect> fp = tpl.first;
TEST_ASSERT(fp);
TEST_ASSERT(fp->getNumBits() == 2048);
TEST_ASSERT(fp->getNumOnBits() == 17);
unsigned int obs[17] = {1, 80, 183, 222, 227, 231, 482, 650, 807,
811, 831, 888, 1335, 1411, 1664, 1820, 1917};
for (unsigned int i = 0; i < fp->getNumOnBits(); ++i) {
TEST_ASSERT(fp->getBit(obs[i]));
}
TEST_ASSERT(tpl.second == "ZINC00902219");
}
{ // test another fp
boost::shared_ptr<ExplicitBitVect> fp = fps.getFP(3);
TEST_ASSERT(fp);
TEST_ASSERT(fp->getNumBits() == 2048);
TEST_ASSERT(fp->getNumOnBits() == 20);
unsigned int obs[20] = {1, 8, 80, 95, 222, 227, 457,
482, 650, 680, 715, 807, 831, 845,
888, 1226, 1556, 1711, 1917, 1982};
for (unsigned int i = 0; i < fp->getNumOnBits(); ++i) {
TEST_ASSERT(fp->getBit(obs[i]));
}
std::string nm = fps.getId(3);
TEST_ASSERT(nm == "ZINC04803506");
}
}
BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
}
void test5LazyFPBReaderTanimoto() {
BOOST_LOG(rdInfoLog)
<< "-----------------------\n Testing Lazy FPBReader tanimoto "
<< std::endl;
std::string pathName = getenv("RDBASE");
pathName += "/Code/DataStructs/testData/";
{
std::string filename = pathName + "zim.head100.fpb";
FPBReader fps(filename, true);
fps.init();
TEST_ASSERT(fps.length() == 100);
{
boost::shared_array<boost::uint8_t> bytes = fps.getBytes(0);
TEST_ASSERT(bytes);
TEST_ASSERT(feq(fps.getTanimoto(0, bytes), 1.0));
TEST_ASSERT(feq(fps.getTanimoto(1, bytes), 0.3703));
}
{
boost::shared_ptr<ExplicitBitVect> ebv = fps.getFP(0);
TEST_ASSERT(ebv);
TEST_ASSERT(feq(fps.getTanimoto(0, *ebv.get()), 1.0));
TEST_ASSERT(feq(fps.getTanimoto(1, *ebv.get()), 0.3703));
}
{
boost::shared_array<boost::uint8_t> bytes = fps.getBytes(1);
TEST_ASSERT(bytes);
TEST_ASSERT(feq(fps.getTanimoto(1, bytes), 1.0));
TEST_ASSERT(feq(fps.getTanimoto(0, bytes), 0.3703));
TEST_ASSERT(feq(fps.getTanimoto(2, bytes), 1.0));
TEST_ASSERT(feq(fps.getTanimoto(5, bytes), 0.2903));
}
}
BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
}
void test6LazyFPBReaderTanimotoNeighbors() {
BOOST_LOG(rdInfoLog)
<< "-----------------------\n Testing Lazy FPBReader tanimoto neighbors"
<< std::endl;
std::string pathName = getenv("RDBASE");
pathName += "/Code/DataStructs/testData/";
{
std::string filename = pathName + "zim.head100.fpb";
FPBReader fps(filename, true);
fps.init();
TEST_ASSERT(fps.length() == 100);
{
boost::shared_array<boost::uint8_t> bytes = fps.getBytes(0);
TEST_ASSERT(bytes);
std::vector<std::pair<double, unsigned int> > nbrs =
fps.getTanimotoNeighbors(bytes);
TEST_ASSERT(nbrs.size() == 1);
TEST_ASSERT(feq(nbrs[0].first, 1.));
TEST_ASSERT(nbrs[0].second == 0);
}
{ // with a threshold
boost::shared_array<boost::uint8_t> bytes = fps.getBytes(0);
TEST_ASSERT(bytes);
std::vector<std::pair<double, unsigned int> > nbrs =
fps.getTanimotoNeighbors(bytes, 0.30);
TEST_ASSERT(nbrs.size() == 5);
TEST_ASSERT(feq(nbrs[0].first, 1.));
TEST_ASSERT(nbrs[0].second == 0);
TEST_ASSERT(feq(nbrs[1].first, 0.3703));
TEST_ASSERT(nbrs[1].second == 1);
}
{ // with a threshold
boost::shared_array<boost::uint8_t> bytes = fps.getBytes(95);
TEST_ASSERT(bytes);
std::vector<std::pair<double, unsigned int> > nbrs =
fps.getTanimotoNeighbors(bytes, 0.30);
TEST_ASSERT(nbrs.size() == 2);
TEST_ASSERT(feq(nbrs[0].first, 1.));
TEST_ASSERT(nbrs[0].second == 95);
TEST_ASSERT(feq(nbrs[1].first, 0.4125));
TEST_ASSERT(nbrs[1].second == 89);
}
{ // ebv with a threshold
boost::shared_ptr<ExplicitBitVect> ebv = fps.getFP(95);
TEST_ASSERT(ebv);
std::vector<std::pair<double, unsigned int> > nbrs =
fps.getTanimotoNeighbors(*ebv.get(), 0.30);
TEST_ASSERT(nbrs.size() == 2);
TEST_ASSERT(feq(nbrs[0].first, 1.));
TEST_ASSERT(nbrs[0].second == 95);
TEST_ASSERT(feq(nbrs[1].first, 0.4125));
TEST_ASSERT(nbrs[1].second == 89);
}
}
BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
}
// need forward declarations of some of the detail functions (doesn't make sense
// to include these in a public interface and there aren't enough of them to
// make it worth adding a detail header)
namespace RDKit {
namespace detail {
boost::dynamic_bitset<> *bytesToBitset(const boost::uint8_t *fpData,
boost::uint32_t nBits);
boost::uint8_t *bitsetToBytes(const boost::dynamic_bitset<> &bitset);
}
}
void test7BitsetDetails() {
BOOST_LOG(rdInfoLog)
<< "-----------------------\n Testing some internal bitset details"
<< std::endl;
std::string pathName = getenv("RDBASE");
pathName += "/Code/DataStructs/testData/";
{ // test round-tripping bytes -> dynamic_bitest -> bytes
std::string filename = pathName + "zim.head100.fpb";
FPBReader fps(filename, true);
fps.init();
TEST_ASSERT(fps.length() == 100);
{
boost::shared_array<boost::uint8_t> bytes = fps.getBytes(0);
TEST_ASSERT(bytes);
// -------------------
// start with bytes -> a bitset
boost::dynamic_bitset<> *dbs =
RDKit::detail::bytesToBitset(bytes.get(), fps.nBits());
TEST_ASSERT(dbs);
TEST_ASSERT(dbs->size() == fps.nBits());
TEST_ASSERT(dbs->count() == 17);
unsigned int obs[17] = {1, 80, 183, 222, 227, 231, 482, 650, 807,
811, 831, 888, 1335, 1411, 1664, 1820, 1917};
for (unsigned int i = 0; i < dbs->count(); ++i) {
TEST_ASSERT((*dbs)[obs[i]]);
}
// -------------------
// and now go the other way
boost::uint8_t *newBytes = RDKit::detail::bitsetToBytes(*dbs);
TEST_ASSERT(newBytes);
for (unsigned int i = 0; i < fps.nBits() / 8; ++i) {
TEST_ASSERT(newBytes[i] == bytes[i]);
}
delete dbs;
delete[] newBytes;
}
}
BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
}
void test8FPBReaderContains() {
BOOST_LOG(rdInfoLog)
<< "-----------------------\n Testing FPBReader contains search"
<< std::endl;
std::string pathName = getenv("RDBASE");
pathName += "/Code/DataStructs/testData/";
{
std::string filename = pathName + "zim.head100.fpb";
FPBReader fps(filename);
fps.init();
TEST_ASSERT(fps.length() == 100);
{
boost::shared_array<boost::uint8_t> bytes = fps.getBytes(0);
TEST_ASSERT(bytes);
std::vector<unsigned int> nbrs = fps.getContainingNeighbors(bytes);
TEST_ASSERT(nbrs.size() == 1);
TEST_ASSERT(nbrs[0] == 0);
}
{
boost::shared_array<boost::uint8_t> bytes = fps.getBytes(1);
TEST_ASSERT(bytes);
std::vector<unsigned int> nbrs = fps.getContainingNeighbors(bytes);
TEST_ASSERT(nbrs.size() == 4);
TEST_ASSERT(nbrs[0] == 1);
TEST_ASSERT(nbrs[1] == 2);
TEST_ASSERT(nbrs[2] == 3);
TEST_ASSERT(nbrs[3] == 4);
}
{
boost::shared_array<boost::uint8_t> bytes = fps.getBytes(16);
TEST_ASSERT(bytes);
std::vector<unsigned int> nbrs = fps.getContainingNeighbors(bytes);
TEST_ASSERT(nbrs.size() == 2);
TEST_ASSERT(nbrs[0] == 16);
TEST_ASSERT(nbrs[1] == 17);
}
{
boost::shared_array<boost::uint8_t> bytes = fps.getBytes(87);
TEST_ASSERT(bytes);
std::vector<unsigned int> nbrs = fps.getContainingNeighbors(bytes);
TEST_ASSERT(nbrs.size() == 4);
TEST_ASSERT(nbrs[0] == 85);
TEST_ASSERT(nbrs[1] == 86);
TEST_ASSERT(nbrs[2] == 87);
TEST_ASSERT(nbrs[3] == 88);
}
{
boost::shared_ptr<ExplicitBitVect> ebv = fps.getFP(87);
TEST_ASSERT(ebv);
std::vector<unsigned int> nbrs = fps.getContainingNeighbors(*ebv.get());
TEST_ASSERT(nbrs.size() == 4);
TEST_ASSERT(nbrs[0] == 85);
TEST_ASSERT(nbrs[1] == 86);
TEST_ASSERT(nbrs[2] == 87);
TEST_ASSERT(nbrs[3] == 88);
}
}
BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
}
int main() {
RDLog::InitLogs();
test1FPBReaderBasics();
test9LazyFPBReaderBasics();
test2FPBReaderTanimoto();
test3FPBReaderTanimotoNeighbors();
test8FPBReaderContains();
test4LazyFPBReaderBasics();
test5LazyFPBReaderTanimoto();
test6LazyFPBReaderTanimotoNeighbors();
test7BitsetDetails();
return 0;
}
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