TEST_F(MoleculeTest, removeAtom) { Molecule molecule; Atom atom0 = molecule.addAtom(6); Atom atom1 = molecule.addAtom(1); Atom atom2 = molecule.addAtom(1); Atom atom3 = molecule.addAtom(1); Atom atom4 = molecule.addAtom(1); molecule.addBond(atom0, atom1, 1); molecule.addBond(atom0, atom2, 1); molecule.addBond(atom0, atom3, 1); molecule.addBond(atom0, atom4, 1); EXPECT_EQ(5, molecule.atomCount()); EXPECT_EQ(4, molecule.bondCount()); molecule.removeAtom(atom0); EXPECT_EQ(4, molecule.atomCount()); EXPECT_EQ(0, molecule.bondCount()); molecule.clearAtoms(); EXPECT_EQ(0, molecule.atomCount()); }
TEST_F(MoleculeTest, removeBond) { Molecule molecule; Atom a = molecule.addAtom(1); Atom b = molecule.addAtom(1); Bond bondAB = molecule.addBond(a, b); Atom c = molecule.addAtom(1); molecule.addBond(b, c, 2); EXPECT_EQ(3, molecule.atomCount()); EXPECT_EQ(2, molecule.bondCount()); EXPECT_TRUE(molecule.bond(a, b).isValid()); EXPECT_TRUE(molecule.bond(b, c).isValid()); molecule.removeBond(bondAB); EXPECT_EQ(3, molecule.atomCount()); EXPECT_EQ(1, molecule.bondCount()); EXPECT_FALSE(molecule.bond(a, b).isValid()); EXPECT_TRUE(molecule.bond(b, c).isValid()); molecule.clearBonds(); EXPECT_EQ(0, molecule.bondCount()); }
void BallAndStick::process(const Molecule &molecule, Rendering::GroupNode &node) { // Add a sphere node to contain all of the spheres. GeometryNode *geometry = new GeometryNode; node.addChild(geometry); SphereGeometry *spheres = new SphereGeometry; spheres->identifier().molecule = &molecule; spheres->identifier().type = Rendering::AtomType; geometry->addDrawable(spheres); for (Index i = 0; i < molecule.atomCount(); ++i) { Core::Atom atom = molecule.atom(i); unsigned char atomicNumber = atom.atomicNumber(); const unsigned char *c = Elements::color(atomicNumber); Vector3ub color(c[0], c[1], c[2]); spheres->addSphere(atom.position3d().cast<float>(), color, static_cast<float>(Elements::radiusVDW(atomicNumber)) * 0.3f); } float bondRadius = 0.1f; CylinderGeometry *cylinders = new CylinderGeometry; cylinders->identifier().molecule = &molecule; cylinders->identifier().type = Rendering::BondType; geometry->addDrawable(cylinders); for (Index i = 0; i < molecule.bondCount(); ++i) { Core::Bond bond = molecule.bond(i); Vector3f pos1 = bond.atom1().position3d().cast<float>(); Vector3f pos2 = bond.atom2().position3d().cast<float>(); Vector3ub color1(Elements::color(bond.atom1().atomicNumber())); Vector3ub color2(Elements::color(bond.atom2().atomicNumber())); Vector3f bondVector = pos2 - pos1; float bondLength = bondVector.norm(); bondVector /= bondLength; switch (bond.order()) { case 3: { Vector3f delta = bondVector.unitOrthogonal() * (2.0f * bondRadius); cylinders->addCylinder(pos1 + delta, bondVector, bondLength, bondRadius, color1, color2, i); cylinders->addCylinder(pos1 - delta, bondVector, bondLength, bondRadius, color1, color2, i); } default: case 1: cylinders->addCylinder(pos1, bondVector, bondLength, bondRadius, color1, color2, i); break; case 2: { Vector3f delta = bondVector.unitOrthogonal() * bondRadius; cylinders->addCylinder(pos1 + delta, bondVector, bondLength, bondRadius, color1, color2, i); cylinders->addCylinder(pos1 - delta, bondVector, bondLength, bondRadius, color1, color2, i); } } } }
TEST_F(MoleculeTest, perceiveBondsSimple) { Molecule molecule; Atom o1 = molecule.addAtom(8); Atom h2 = molecule.addAtom(1); Atom h3 = molecule.addAtom(1); o1.setPosition3d(Vector3(0, 0, 0)); h2.setPosition3d(Vector3(0.6, -0.5, 0)); h3.setPosition3d(Vector3(-0.6, -0.5, 0)); EXPECT_EQ(molecule.bondCount(), 0); molecule.perceiveBondsSimple(); EXPECT_EQ(molecule.bondCount(), 2); EXPECT_TRUE(molecule.bond(o1, h2).isValid()); EXPECT_TRUE(molecule.bond(o1, h3).isValid()); EXPECT_FALSE(molecule.bond(h2, h3).isValid()); }
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(HydrogenToolsTest, adjustHydrogens_C2H4O) { Molecule mol; Atom C1 = mol.addAtom(6); Atom C2 = mol.addAtom(6); Atom O1 = mol.addAtom(8); mol.addBond(C1, C2, 1); mol.addBond(C2, O1, 2); HydrogenTools::adjustHydrogens(mol); EXPECT_EQ(7, mol.atomCount()); EXPECT_EQ(6, mol.bondCount()); EXPECT_EQ(std::string("C2H4O"), mol.formula()); }
TEST(HydrogenToolsTest, adjustHydrogens_C3H8) { Molecule mol; Atom C1 = mol.addAtom(6); Atom C2 = mol.addAtom(6); Atom C3 = mol.addAtom(6); mol.addBond(C1, C2, 1); mol.addBond(C2, C3, 1); HydrogenTools::adjustHydrogens(mol); EXPECT_EQ(11, mol.atomCount()); EXPECT_EQ(10, mol.bondCount()); EXPECT_EQ(std::string("C3H8"), mol.formula()); }
TEST(CjsonTest, crystal) { CjsonFormat cjson; Molecule molecule; bool success = cjson.readFile(std::string(AVOGADRO_DATA) + "/data/rutile.cjson", molecule); EXPECT_TRUE(success); EXPECT_EQ(cjson.error(), ""); EXPECT_EQ(molecule.data("name").toString(), "TiO2 rutile"); EXPECT_EQ(molecule.atomCount(), static_cast<size_t>(6)); EXPECT_EQ(molecule.bondCount(), static_cast<size_t>(0)); const UnitCell *unitCell = molecule.unitCell(); ASSERT_NE(unitCell, (UnitCell*)NULL); EXPECT_TRUE(std::fabs((float)unitCell->a() - 2.95812f) < 1e-5f); EXPECT_TRUE(std::fabs((float)unitCell->b() - 4.59373f) < 1e-5f); EXPECT_TRUE(std::fabs((float)unitCell->c() - 4.59373f) < 1e-5f); EXPECT_TRUE(std::fabs((float)unitCell->alpha() - (.5f * PI_F)) < 1e-5f); EXPECT_TRUE(std::fabs((float)unitCell->beta() - (.5f * PI_F)) < 1e-5f); EXPECT_TRUE(std::fabs((float)unitCell->gamma() - (.5f * PI_F)) < 1e-5f); Atom atom = molecule.atom(5); EXPECT_EQ(atom.atomicNumber(), 8); EXPECT_TRUE(std::fabs((float)atom.position3d().x() - 1.479060f) < 1e-5f); EXPECT_TRUE(std::fabs((float)atom.position3d().y() - 3.699331f) < 1e-5f); EXPECT_TRUE(std::fabs((float)atom.position3d().z() - 0.894399f) < 1e-5f); std::string cjsonStr; cjson.writeString(cjsonStr, molecule); Molecule otherMolecule; cjson.readString(cjsonStr, otherMolecule); const UnitCell *otherUnitCell = otherMolecule.unitCell(); ASSERT_NE(otherUnitCell, (UnitCell*)NULL); EXPECT_FLOAT_EQ((float)otherUnitCell->a(), (float)unitCell->a()); EXPECT_FLOAT_EQ((float)otherUnitCell->b(), (float)unitCell->b()); EXPECT_FLOAT_EQ((float)otherUnitCell->c(), (float)unitCell->c()); EXPECT_FLOAT_EQ((float)otherUnitCell->alpha(), (float)unitCell->alpha()); EXPECT_FLOAT_EQ((float)otherUnitCell->beta(), (float)unitCell->beta()); EXPECT_FLOAT_EQ((float)otherUnitCell->gamma(), (float)unitCell->gamma()); Atom otherAtom = otherMolecule.atom(5); EXPECT_EQ(otherAtom.atomicNumber(), atom.atomicNumber()); EXPECT_FLOAT_EQ((float)otherAtom.position3d().x(), (float)atom.position3d().x()); EXPECT_FLOAT_EQ((float)otherAtom.position3d().y(), (float)atom.position3d().y()); EXPECT_FLOAT_EQ((float)otherAtom.position3d().z(), (float)atom.position3d().z()); }
TEST(RWMoleculeTest, MoleculeToRWMolecule) { Molecule mol; typedef Molecule::AtomType Atom; typedef Molecule::BondType Bond; Atom a0 = mol.addAtom(1); Atom a1 = mol.addAtom(6); Atom a2 = mol.addAtom(9); Bond b0 = mol.addBond(a0, a2); a1.setPosition3d(Vector3(0, 6, 9)); b0.setOrder(3); RWMolecule rwmol(mol, 0); EXPECT_EQ(rwmol.atomCount(), mol.atomCount()); EXPECT_EQ(rwmol.bondCount(), mol.bondCount()); EXPECT_EQ(rwmol.atom(2).atomicNumber(), mol.atom(2).atomicNumber()); EXPECT_EQ(rwmol.bond(0).order(), mol.bond(0).order()); }
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)); }