TEST(RWMoleculeTest, setAtomPosition3d)
{
Molecule m;
RWMolecule mol(m);
mol.addAtom(1);
mol.addAtom(2);
mol.addAtom(3);
mol.addAtom(4);
mol.addAtom(5);
mol.undoStack().clear();
EXPECT_TRUE(mol.atomPositions3d().empty());
mol.setAtomPosition3d(0, Vector3(Real(1), Real(2), Real(3)));
EXPECT_EQ(mol.atomicNumbers().size(), mol.atomPositions3d().size());
EXPECT_EQ(Real(1), mol.atomPosition3d(0).x());
EXPECT_EQ(Real(2), mol.atomPosition3d(0).y());
EXPECT_EQ(Real(3), mol.atomPosition3d(0).z());
for (Index i = 1; i < 5; ++i)
EXPECT_EQ(Vector3::Zero(), mol.atomPosition3d(i));
mol.undoStack().undo();
for (Index i = 0; i < 5; ++i)
EXPECT_EQ(Vector3::Zero(), mol.atomPosition3d(i));
mol.undoStack().redo();
EXPECT_EQ(Real(1), mol.atomPosition3d(0).x());
EXPECT_EQ(Real(2), mol.atomPosition3d(0).y());
EXPECT_EQ(Real(3), mol.atomPosition3d(0).z());
for (Index i = 1; i < 5; ++i)
EXPECT_EQ(Vector3::Zero(), mol.atomPosition3d(i));
mol.undoStack().undo();
mol.undoStack().clear();
// Test command merging for interactive editing:
mol.setInteractive(true);
mol.setAtomPosition3d(0, Vector3(Real(1), Real(2), Real(3)));
mol.setAtomPosition3d(3, Vector3(Real(4), Real(5), Real(6)));
mol.setAtomPosition3d(0, Vector3(Real(7), Real(8), Real(9)));
mol.setAtomPosition3d(1, Vector3(Real(6), Real(4), Real(2)));
mol.setInteractive(false);
Array<Vector3> pos(mol.atomPositions3d());
EXPECT_EQ(Vector3(Real(7), Real(8), Real(9)), pos[0]);
EXPECT_EQ(Vector3(Real(6), Real(4), Real(2)), pos[1]);
EXPECT_EQ(Vector3::Zero(), pos[2]);
EXPECT_EQ(Vector3(Real(4), Real(5), Real(6)), pos[3]);
EXPECT_EQ(Vector3::Zero(), pos[4]);
EXPECT_EQ(1, mol.undoStack().count());
mol.undoStack().undo();
for (Index i = 1; i < 5; ++i)
EXPECT_EQ(Vector3::Zero(), mol.atomPosition3d(i));
mol.undoStack().redo();
EXPECT_TRUE(std::equal(pos.begin(), pos.end(),
mol.atomPositions3d().begin()));
}
TEST(RWMoleculeTest, AtomType)
{
Molecule m;
RWMolecule mol(m);
typedef RWMolecule::AtomType Atom;
Atom a0 = mol.addAtom(1);
Atom a1 = mol.addAtom(2);
EXPECT_TRUE(a0.isValid());
EXPECT_FALSE(Atom().isValid());
EXPECT_FALSE(Atom(&mol, 2).isValid());
EXPECT_EQ(&mol, a0.molecule());
EXPECT_EQ(0, a0.index());
EXPECT_EQ(1, a0.atomicNumber());
EXPECT_EQ(1, mol.atomicNumber(0));
EXPECT_EQ(2, a1.atomicNumber());
EXPECT_EQ(2, mol.atomicNumber(1));
a0.setPosition3d(Vector3(Real(3), Real(4), Real(5)));
a1.setPosition3d(Vector3(Real(6), Real(7), Real(8)));
EXPECT_EQ(Vector3(Real(3), Real(4), Real(5)), a0.position3d());
EXPECT_EQ(Vector3(Real(3), Real(4), Real(5)), mol.atomPosition3d(0));
EXPECT_EQ(Vector3(Real(6), Real(7), Real(8)), a1.position3d());
EXPECT_EQ(Vector3(Real(6), Real(7), Real(8)), mol.atomPosition3d(1));
Atom other(&mol, 0);
EXPECT_EQ(a0, other);
EXPECT_NE(a1, other);
}
TEST(RWMoleculeTest, clearAtoms)
{
Molecule m;
RWMolecule mol(m);
typedef RWMolecule::AtomType Atom;
Atom a0 = mol.addAtom(1); // H
Atom a1 = mol.addAtom(2); // He
Atom a2 = mol.addAtom(3); // Li
Atom a3 = mol.addAtom(4); // Be
Atom a4 = mol.addAtom(5); // B
const Vector3 pos(Real(1), Real(2), Real(3));
mol.setAtomPosition3d(0, pos);
ASSERT_EQ(5, mol.atomCount());
ASSERT_EQ(std::string("HHeLiBeB"), formula(mol));
// Add some bonds to ensure that they are properly added/removed when a bonded
// atom is removed.
ASSERT_TRUE(mol.addBond(a0, a1, 0).isValid());
ASSERT_TRUE(mol.addBond(a1, a2, 1).isValid());
ASSERT_TRUE(mol.addBond(a2, a3, 2).isValid());
ASSERT_TRUE(mol.addBond(a3, a4, 3).isValid());
ASSERT_TRUE(mol.addBond(a0, a2, 4).isValid());
ASSERT_TRUE(mol.addBond(a1, a3, 5).isValid());
ASSERT_TRUE(mol.addBond(a2, a4, 6).isValid());
ASSERT_TRUE(mol.addBond(a0, a3, 7).isValid());
ASSERT_TRUE(mol.addBond(a1, a4, 8).isValid());
ASSERT_TRUE(mol.addBond(a0, a4, 9).isValid());
ASSERT_EQ(10, mol.bondCount());
mol.clearAtoms();
EXPECT_EQ(0, mol.atomCount());
EXPECT_EQ(0, mol.bondCount());
mol.undoStack().undo();
ASSERT_EQ(5, mol.atomCount());
ASSERT_EQ(10, mol.bondCount());
ASSERT_EQ(std::string("HHeLiBeB"), formula(mol));
for (Index i = 0; i < mol.atomCount(); ++i) {
EXPECT_EQ(static_cast<unsigned char>(i + 1), mol.atomicNumber(i));
EXPECT_EQ(i, mol.atomUniqueId(i));
}
#define VALIDATE_BOND(ind, atom1, atom2, order, uid) \
EXPECT_EQ(std::make_pair(Index(atom1), Index(atom2)), mol.bondPair(ind)); \
EXPECT_EQ(static_cast<unsigned char>(order), mol.bondOrder(ind)); \
EXPECT_EQ(uid, mol.bondUniqueId(ind))
VALIDATE_BOND(0, 0, 1, 0, 0);
VALIDATE_BOND(1, 1, 2, 1, 1);
VALIDATE_BOND(2, 2, 3, 2, 2);
VALIDATE_BOND(3, 3, 4, 3, 3);
VALIDATE_BOND(4, 0, 2, 4, 4);
VALIDATE_BOND(5, 1, 3, 5, 5);
VALIDATE_BOND(6, 2, 4, 6, 6);
VALIDATE_BOND(7, 0, 3, 7, 7);
VALIDATE_BOND(8, 1, 4, 8, 8);
VALIDATE_BOND(9, 0, 4, 9, 9);
#undef VALIDATE_BOND
}
