TEST(CjsonTest, saveFile)
{
CjsonFormat cjson;
Molecule savedMolecule, molecule;
bool success = cjson.readFile(std::string(AVOGADRO_DATA) +
"/data/ethane.cjson",
savedMolecule);
EXPECT_TRUE(success);
EXPECT_EQ(cjson.error(), "");
success = cjson.writeFile("ethanetmp.cjson", savedMolecule);
EXPECT_TRUE(success);
EXPECT_EQ(cjson.error(), "");
// Now read the file back in and check a few key values are still present.
success = cjson.readFile("ethanetmp.cjson", molecule);
EXPECT_TRUE(success);
EXPECT_EQ(cjson.error(), "");
EXPECT_EQ(molecule.data("name").toString(), "Ethane");
EXPECT_EQ(molecule.atomCount(), static_cast<size_t>(8));
EXPECT_EQ(molecule.bondCount(), static_cast<size_t>(7));
Atom atom = molecule.atom(7);
EXPECT_EQ(atom.atomicNumber(), static_cast<unsigned char>(1));
EXPECT_EQ(atom.position3d().x(), -1.184988);
EXPECT_EQ(atom.position3d().y(), 0.004424);
EXPECT_EQ(atom.position3d().z(), -0.987522);
Bond bond = molecule.bond(0);
EXPECT_EQ(bond.atom1().index(), static_cast<size_t>(0));
EXPECT_EQ(bond.atom2().index(), static_cast<size_t>(1));
EXPECT_EQ(bond.order(), static_cast<unsigned char>(1));
}
TEST_F(MoleculeTest, addBond)
{
Molecule molecule;
EXPECT_EQ(molecule.bondCount(), static_cast<Index>(0));
Atom a = molecule.addAtom(1);
Atom b = molecule.addAtom(1);
Bond bondAB = molecule.addBond(a, b);
EXPECT_TRUE(bondAB.isValid());
EXPECT_EQ(bondAB.molecule(), &molecule);
EXPECT_EQ(molecule.bondCount(), static_cast<Index>(1));
EXPECT_EQ(bondAB.index(), static_cast<Index>(0));
EXPECT_EQ(bondAB.atom1().index(), a.index());
EXPECT_EQ(bondAB.atom2().index(), b.index());
EXPECT_EQ(bondAB.order(), static_cast<unsigned char>(1));
Atom c = molecule.addAtom(1);
Bond bondBC = molecule.addBond(b, c, 2);
EXPECT_TRUE(bondBC.isValid());
EXPECT_EQ(molecule.bondCount(), static_cast<Index>(2));
EXPECT_EQ(bondBC.index(), static_cast<Index>(1));
EXPECT_EQ(bondBC.order(), static_cast<unsigned char>(2));
// try to lookup nonexistant bond
Bond bond = molecule.bond(a, c);
EXPECT_FALSE(bond.isValid());
// try to lookup bond between a and b
bond = molecule.bond(a, b);
EXPECT_TRUE(bond.isValid());
EXPECT_EQ(bond.molecule(), &molecule);
EXPECT_EQ(bond.atom1().index(), a.index());
EXPECT_EQ(bond.atom2().index(), b.index());
// try to lookup bond between b and c by index
bond = molecule.bond(1);
EXPECT_TRUE(bond.isValid());
EXPECT_EQ(bond.molecule(), &molecule);
EXPECT_EQ(bond.atom1().index(), b.index());
EXPECT_EQ(bond.atom2().index(), c.index());
}
TEST(CjsonTest, bonds)
{
CjsonFormat cjson;
Molecule molecule;
bool success = cjson.readFile(std::string(AVOGADRO_DATA) +
"/data/ethane.cjson", molecule);
EXPECT_TRUE(success);
EXPECT_EQ(cjson.error(), "");
EXPECT_EQ(molecule.data("name").toString(), "Ethane");
EXPECT_EQ(molecule.atomCount(), static_cast<size_t>(8));
EXPECT_EQ(molecule.bondCount(), static_cast<size_t>(7));
Bond bond = molecule.bond(0);
EXPECT_EQ(bond.atom1().index(), static_cast<size_t>(0));
EXPECT_EQ(bond.atom2().index(), static_cast<size_t>(1));
EXPECT_EQ(bond.order(), static_cast<unsigned char>(1));
bond = molecule.bond(6);
EXPECT_EQ(bond.atom1().index(), static_cast<size_t>(4));
EXPECT_EQ(bond.atom2().index(), static_cast<size_t>(7));
EXPECT_EQ(bond.order(), static_cast<unsigned char>(1));
}
TEST(FileFormatManagerTest, writeFileGuessCml)
{
Molecule readMol, writeMol;
FileFormatManager::instance().readFile(readMol,
std::string(AVOGADRO_DATA)
+ "/data/ethane.cml");
FileFormatManager::instance().writeFile(readMol, "ethanemanagertmp.cml");
// Now read the file back in and check a few key values are still present.
FileFormatManager::instance().readFile(writeMol, "ethanemanagertmp.cml");
EXPECT_EQ(writeMol.data("name").toString(), "Ethane");
EXPECT_EQ(writeMol.atomCount(), static_cast<size_t>(8));
EXPECT_EQ(writeMol.bondCount(), static_cast<size_t>(7));
Atom atom = writeMol.atom(7);
EXPECT_EQ(atom.atomicNumber(), static_cast<unsigned char>(1));
EXPECT_EQ(atom.position3d().x(), -1.18499);
EXPECT_EQ(atom.position3d().y(), 0.004424);
EXPECT_EQ(atom.position3d().z(), -0.987522);
Bond bond = writeMol.bond(0);
EXPECT_EQ(bond.atom1().index(), static_cast<size_t>(0));
EXPECT_EQ(bond.atom2().index(), static_cast<size_t>(1));
EXPECT_EQ(bond.order(), static_cast<unsigned char>(1));
}
