/**
* Test for SF bug #1309731.
*
* @cdk.bug 1309731
*/
@Test
public void testModelBuilder3D_keepChemObjectIDs() throws Exception {
ModelBuilder3D mb3d = ModelBuilder3D.getInstance();
IMolecule methanol = new org.openscience.cdk.Molecule();
IChemObjectBuilder builder = methanol.getBuilder();
IAtom carbon1 = builder.newInstance(IAtom.class, "C");
carbon1.setID("carbon1");
methanol.addAtom(carbon1);
for (int i = 0; i < 3; i++) {
IAtom hydrogen = builder.newInstance(IAtom.class, "H");
methanol.addAtom(hydrogen);
methanol.addBond(builder.newInstance(IBond.class, carbon1, hydrogen, IBond.Order.SINGLE));
}
IAtom oxygen1 = builder.newInstance(IAtom.class, "O");
oxygen1.setID("oxygen1");
methanol.addAtom(oxygen1);
methanol.addBond(builder.newInstance(IBond.class, carbon1, oxygen1, IBond.Order.SINGLE));
IAtom hydrogen = builder.newInstance(IAtom.class, "H");
methanol.addAtom(hydrogen);
methanol.addBond(builder.newInstance(IBond.class, hydrogen, oxygen1, IBond.Order.SINGLE));
Assert.assertEquals(6, methanol.getAtomCount());
Assert.assertEquals(5, methanol.getBondCount());
mb3d.generate3DCoordinates(methanol, false);
checkAverageBondLength(methanol);
Assert.assertEquals("carbon1", carbon1.getID());
Assert.assertEquals("oxygen1", oxygen1.getID());
}
/*
* @cdk.bug 1241421
*/
@Test
public void testModelBuilder3D_bug_1241421() throws Exception {
ModelBuilder3D mb3d = ModelBuilder3D.getInstance();
String filename = "data/mdl/bug1241421.mol";
InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
MDLV2000Reader reader = new MDLV2000Reader(ins);
ChemFile chemFile = (ChemFile) reader.read((ChemObject) new ChemFile());
List containersList = ChemFileManipulator.getAllAtomContainers(chemFile);
IMolecule ac = new NNMolecule((IAtomContainer) containersList.get(0));
ac = mb3d.generate3DCoordinates(ac, false);
checkAverageBondLength(ac);
}
@Test
public void testModelBuilder3D_CccccC() throws Exception {
ModelBuilder3D mb3d = ModelBuilder3D.getInstance();
String smile = "CccccC";
SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
IMolecule mol = sp.parseSmiles(smile);
addExplicitHydrogens(mol);
mol = mb3d.generate3DCoordinates(mol, false);
for (int i = 0; i < mol.getAtomCount(); i++) {
Assert.assertNotNull(mol.getAtom(i).getPoint3d());
}
checkAverageBondLength(mol);
// logger.debug("Layout molecule with SMILE: "+smile);
}
@Test
public void testModelBuilder3D_reserpine() throws Exception {
ModelBuilder3D mb3d = ModelBuilder3D.getInstance();
String filename = "data/mdl/reserpine.mol";
InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
MDLV2000Reader reader = new MDLV2000Reader(ins);
ChemFile chemFile = (ChemFile) reader.read((ChemObject) new ChemFile());
List containersList = ChemFileManipulator.getAllAtomContainers(chemFile);
IMolecule ac = new NNMolecule((IAtomContainer) containersList.get(0));
ac = mb3d.generate3DCoordinates(ac, false);
for (int i = 0; i < ac.getAtomCount(); i++) {
Assert.assertNotNull(ac.getAtom(i).getPoint3d());
}
checkAverageBondLength(ac);
}
@Test
public void testModelBuilder3D_C1CCCCCCC1CC() throws Exception {
Assume.assumeTrue(runSlowTests());
ModelBuilder3D mb3d = ModelBuilder3D.getInstance();
String smile = "C1CCCCCCC1CC";
SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
IMolecule mol = sp.parseSmiles(smile);
addExplicitHydrogens(mol);
mol = mb3d.generate3DCoordinates(mol, false);
for (int i = 0; i < mol.getAtomCount(); i++) {
Assert.assertNotNull(mol.getAtom(i).getPoint3d());
}
checkAverageBondLength(mol);
}
/** @cdk.bug 1315823 */
@Test
public void testModelBuilder3D_232() throws Exception {
Assume.assumeTrue(runSlowTests());
ModelBuilder3D mb3d = ModelBuilder3D.getInstance();
String filename = "data/mdl/allmol232.mol";
InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
MDLV2000Reader reader = new MDLV2000Reader(ins);
ChemFile chemFile = (ChemFile) reader.read((ChemObject) new ChemFile());
List containersList = ChemFileManipulator.getAllAtomContainers(chemFile);
IMolecule ac = new NNMolecule((IAtomContainer) containersList.get(0));
addExplicitHydrogens(ac);
ac = mb3d.generate3DCoordinates(ac, false);
Assert.assertNotNull(ac.getAtom(0).getPoint3d());
checkAverageBondLength(ac);
}
// A unit test for JUnit with methylenfluoride\
@Test
public void testModelBuilder3D_CF() throws Exception {
ModelBuilder3D mb3d = ModelBuilder3D.getInstance();
Point3d c_coord = new Point3d(1.392, 0.0, 0.0);
Point3d f_coord = new Point3d(0.0, 0.0, 0.0);
Point3d h1_coord = new Point3d(1.7439615035767404, 1.0558845107302222, 0.0);
Point3d h2_coord = new Point3d(1.7439615035767404, -0.5279422553651107, 0.914422809754875);
Point3d h3_coord = new Point3d(1.7439615035767402, -0.5279422553651113, -0.9144228097548747);
SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
IMolecule mol = sp.parseSmiles("CF");
addExplicitHydrogens(mol);
// mb3d.setTemplateHandler();
mol = mb3d.generate3DCoordinates(mol, false);
assertEquals(c_coord, mol.getAtom(0).getPoint3d(), 0.0001);
assertEquals(f_coord, mol.getAtom(1).getPoint3d(), 0.0001);
assertEquals(h1_coord, mol.getAtom(2).getPoint3d(), 0.0001);
assertEquals(h2_coord, mol.getAtom(3).getPoint3d(), 0.0001);
assertEquals(h3_coord, mol.getAtom(4).getPoint3d(), 0.0001);
checkAverageBondLength(mol);
}
/*
* this is a test contributed by mario baseda / see bug #1610997
* @cdk.bug 1610997
*/
@Test
public void testModel3D_bug_1610997() throws Exception {
Assume.assumeTrue(runSlowTests());
boolean notCalculatedResults = false;
List inputList = new ArrayList();
////////////////////////////////////////////////////////////////////////////////////////////
// generate the input molecules. This are molecules without x, y, z coordinats
String[] smiles =
new String[] {
"CC",
"OCC",
"O(C)CCC",
"c1ccccc1",
"C(=C)=C",
"OCC=CCc1ccccc1(C=C)",
"O(CC=C)CCN",
"CCCCCCCCCCCCCCC",
"OCC=CCO",
"NCCCCN"
};
SmilesParser sp = new SmilesParser(NoNotificationChemObjectBuilder.getInstance());
IAtomContainer[] atomContainer = new IAtomContainer[smiles.length];
for (int i = 0; i < smiles.length; i++) {
atomContainer[i] = sp.parseSmiles(smiles[i]);
inputList.add(atomContainer[i]);
}
System.out.println(inputList.size());
///////////////////////////////////////////////////////////////////////////////////////////
// Generate 2D coordinats for the input molecules with the Structure Diagram Generator
StructureDiagramGenerator str;
List resultList = new ArrayList();
for (Iterator iter = inputList.iterator(); iter.hasNext(); ) {
IAtomContainer molecules = (IAtomContainer) iter.next();
str = new StructureDiagramGenerator();
str.setMolecule((IMolecule) molecules);
str.generateCoordinates();
resultList.add(str.getMolecule());
}
inputList = resultList;
/////////////////////////////////////////////////////////////////////////////////////////////
// Delete x and y coordinats
for (Iterator iter = inputList.iterator(); iter.hasNext(); ) {
IAtomContainer molecules = (IAtomContainer) iter.next();
for (Iterator atom = molecules.atoms().iterator(); atom.hasNext(); ) {
Atom last = (Atom) atom.next();
last.setPoint2d(null);
}
}
////////////////////////////////////////////////////////////////////////////////////////////////////
// Test for the method Model3DBuildersWithMM2ForceField
ModelBuilder3D mb3d = ModelBuilder3D.getInstance();
for (Iterator iter = inputList.iterator(); iter.hasNext(); ) {
IAtomContainer molecules = (IAtomContainer) iter.next();
IMolecule mol = molecules.getBuilder().newInstance(IMolecule.class, molecules);
mol = mb3d.generate3DCoordinates(mol, false);
System.out.println("Calculation done");
}
for (Iterator iter = inputList.iterator(); iter.hasNext(); ) {
IAtomContainer molecule = (IAtomContainer) iter.next();
checkAverageBondLength(molecule);
for (Iterator atom = molecule.atoms().iterator(); atom.hasNext(); ) {
Atom last = (Atom) atom.next();
if (last.getPoint3d() == null) notCalculatedResults = true;
}
}
Assert.assertFalse(notCalculatedResults);
}
