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stop reading in all Ids when in lazy mode

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This commit is contained in:
Greg Landrum
2016-01-09 10:55:23 +01:00
parent 700c59ff37
commit 606ae353ca
3 changed files with 212 additions and 136 deletions
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133
Code/DataStructs/testFPB.cpp
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@@ -17,6 +17,66 @@
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;
@@ -25,62 +85,21 @@ void test1FPBReaderBasics() {
{
std::string filename = pathName + "zim.head100.fpb";
FPBReader fps(filename);
fps.init();
TEST_ASSERT(fps.length() == 100);
TEST_ASSERT(fps.nBits() == 2048);
_basicsTest(fps);
}
BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
}
{ // 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");
}
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;
}
@@ -365,7 +384,7 @@ void test8FPBReaderContains() {
pathName += "/Code/DataStructs/testData/";
{
std::string filename = pathName + "zim.head100.fpb";
FPBReader fps(filename, true);
FPBReader fps(filename);
fps.init();
TEST_ASSERT(fps.length() == 100);
{
@@ -411,6 +430,8 @@ int main() {
RDLog::InitLogs();
test1FPBReaderBasics();
test9LazyFPBReaderBasics();
test2FPBReaderTanimoto();
test3FPBReaderTanimotoNeighbors();
test8FPBReaderContains();