TEST_F(MoleculeSerializationTest, roundTrip)
{
MoleculeSerializer serializer(&this->ethane);
size_t size = serializer.size();
uint8 *data = new uint8[size];
bool success = serializer.serialize(data, size);
EXPECT_TRUE(success);
Molecule after;
MoleculeDeserializer deserializer(&after);
success = deserializer.deserialize(data, size);
EXPECT_TRUE(success);
delete[] data;
EXPECT_EQ(this->ethane.atomicNumbers(), after.atomicNumbers());
std::vector<Avogadro::Vector2> expected2d = this->ethane.atomPositions2d();
std::vector<Avogadro::Vector2> actual2d = after.atomPositions2d();
EXPECT_EQ(expected2d.size(), actual2d.size());
for (size_t i = 0; i < expected2d.size(); i++)
EXPECT_TRUE(this->equal(expected2d[i], actual2d[i]));
std::vector<Avogadro::Vector3> expected3d = this->ethane.atomPositions3d();
std::vector<Avogadro::Vector3> actual3d = after.atomPositions3d();
EXPECT_EQ(expected3d.size(), actual3d.size());
for (size_t i = 0; i < expected3d.size(); i++)
EXPECT_TRUE(this->equal(expected3d[i], actual3d[i]));
const std::vector<std::pair<size_t, size_t> > expectedBondPairs
= this->ethane.bondPairs();
const std::vector<std::pair<size_t, size_t> > actualBondPairs
= after.bondPairs();
EXPECT_EQ(expectedBondPairs.size(), actualBondPairs.size());
for (size_t i = 0; i < expectedBondPairs.size(); i++) {
EXPECT_EQ(expectedBondPairs[i].first, actualBondPairs[i].first);
EXPECT_EQ(expectedBondPairs[i].second, actualBondPairs[i].second);
}
const std::vector<unsigned char> expectedBondOrder
= this->ethane.bondOrders();
const std::vector<unsigned char> actualBondOrder = after.bondOrders();
for (size_t i = 0; i < expectedBondOrder.size(); i++)
EXPECT_EQ(expectedBondOrder[i], actualBondOrder[i]);
}
void HydrogenTools::removeAllHydrogens(Molecule &molecule)
{
const Array<unsigned char> atomicNums(molecule.atomicNumbers());
size_t atomIndex = molecule.atomCount() - 1;
for (Array<unsigned char>::const_reverse_iterator
it = atomicNums.rbegin(), itEnd = atomicNums.rend(); it != itEnd;
++it, --atomIndex) {
if (*it == 1)
molecule.removeAtom(atomIndex);
}
}
