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));
}
// Retrieve desired value
bool BondVariable::retrieveAccessor(int i, ReturnValue& rv, bool hasArrayIndex, int arrayIndex)
{
Messenger::enter("BondVariable::retrieveAccessor");
// Cast 'i' into Accessors enum value
if ((i < 0) || (i >= nAccessors))
{
printf("Internal Error: Accessor id %i is out of range for Bond type.\n", i);
Messenger::exit("BondVariable::retrieveAccessor");
return false;
}
Accessors acc = (Accessors) i;
// Check for correct lack/presence of array index given
if ((accessorData[i].arraySize == 0) && hasArrayIndex)
{
Messenger::print("Error: Unnecessary array index provided for member '%s'.", qPrintable(accessorData[i].name));
Messenger::exit("BondVariable::retrieveAccessor");
return false;
}
else if ((accessorData[i].arraySize > 0) && (hasArrayIndex))
{
if ((arrayIndex < 1) || (arrayIndex > accessorData[i].arraySize))
{
Messenger::print("Error: Array index out of bounds for member '%s' (%i, range is 1-%i).", qPrintable(accessorData[i].name), arrayIndex, accessorData[i].arraySize);
Messenger::exit("BondVariable::retrieveAccessor");
return false;
}
}
// Get current data from ReturnValue
bool result = true;
Bond* ptr = (Bond*) rv.asPointer(VTypes::BondData, result);
if ((!result) || (ptr == NULL))
{
Messenger::print("Invalid (NULL) %s reference encountered.", VTypes::dataType(VTypes::BondData));
result = false;
}
if (result) switch (acc)
{
case (BondVariable::I):
rv.set(VTypes::AtomData, ptr->atomI());
break;
case (BondVariable::J):
rv.set(VTypes::AtomData, ptr->atomJ());
break;
case (BondVariable::Order):
rv.set(ptr->order());
break;
case (BondVariable::Type):
rv.set(Bond::bondType(ptr->type()));
break;
default:
printf("Internal Error: Access to member '%s' has not been defined in BondVariable.\n", qPrintable(accessorData[i].name));
result = false;
break;
}
Messenger::exit("BondVariable::retrieveAccessor");
return result;
}
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));
}
