/**
* Get the expected set of molecules.
*
* @return The IAtomContainerSet
*/
private IAtomContainerSet getExpectedProducts() {
IAtomContainerSet setOfProducts = builder.newInstance(IAtomContainerSet.class);
IAtomContainer molecule = builder.newInstance(IAtomContainer.class);
molecule.addAtom(builder.newInstance(IAtom.class, "C"));
molecule.getAtom(0).setFormalCharge(1);
molecule.addAtom(builder.newInstance(IAtom.class, "C"));
molecule.addBond(0, 1, IBond.Order.SINGLE);
molecule.addAtom(builder.newInstance(IAtom.class, "C"));
molecule.addBond(1, 2, IBond.Order.SINGLE);
molecule.addAtom(builder.newInstance(IAtom.class, "C"));
molecule.addBond(2, 3, IBond.Order.SINGLE);
molecule.addAtom(builder.newInstance(IAtom.class, "C"));
molecule.addBond(3, 4, IBond.Order.SINGLE);
molecule.addAtom(builder.newInstance(IAtom.class, "C"));
molecule.addBond(4, 5, IBond.Order.SINGLE);
try {
addExplicitHydrogens(molecule);
} catch (Exception e) {
e.printStackTrace();
}
molecule.getAtom(0).setFormalCharge(0);
molecule.addSingleElectron(new SingleElectron(molecule.getAtom(0)));
try {
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(molecule);
makeSureAtomTypesAreRecognized(molecule);
} catch (CDKException e) {
e.printStackTrace();
}
setOfProducts.addAtomContainer(molecule);
return setOfProducts;
}
/**
* Adds all atoms and electronContainers of a given atomcontainer to this container.
*
* @param atomContainer The atomcontainer to be added
*/
public void add(IAtomContainer atomContainer) {
for (int f = 0; f < atomContainer.getAtomCount(); f++) {
if (!contains(atomContainer.getAtom(f))) {
addAtom(atomContainer.getAtom(f));
}
}
for (int f = 0; f < atomContainer.getBondCount(); f++) {
if (!contains(atomContainer.getBond(f))) {
addBond(atomContainer.getBond(f));
}
}
for (int f = 0; f < atomContainer.getLonePairCount(); f++) {
if (!contains(atomContainer.getLonePair(f))) {
addLonePair(atomContainer.getLonePair(f));
}
}
for (int f = 0; f < atomContainer.getSingleElectronCount(); f++) {
if (!contains(atomContainer.getSingleElectron(f))) {
addSingleElectron(atomContainer.getSingleElectron(f));
}
}
for (IStereoElement se : atomContainer.stereoElements()) stereoElements.add(se);
notifyChanged();
}
/**
* If no isomorphism is found the result is empty vector
*
* @param container
* @return
*/
public List<List<IAtom>> getAllIsomorphismMappings(IAtomContainer container) {
if (query == null) return null;
target = container;
FlagStoreIsomorphismNode = true;
isomorphismNodes.clear();
List<List<IAtom>> result = new ArrayList<List<IAtom>>();
if (query.getAtomCount() == 1) {
SMARTSAtom qa = (SMARTSAtom) query.getAtom(0);
for (int i = 0; i < target.getAtomCount(); i++) {
if (qa.matches(target.getAtom(i))) {
List<IAtom> v = new ArrayList<IAtom>();
v.add(target.getAtom(i));
result.add(v);
}
}
return result;
}
TopLayer.setAtomTopLayers(target, TopLayer.TLProp);
executeSequence(false);
if (isomorphismFound) {
// Getting the data from the all stored Nodes
for (int k = 0; k < isomorphismNodes.size(); k++) {
Node node = isomorphismNodes.get(k);
List<IAtom> v = new ArrayList<IAtom>();
for (int i = 0; i < node.atoms.length; i++) v.add(node.atoms[i]);
result.add(v);
}
}
return result;
}
/**
* This function returns null if no isomorphism is found
*
* @param container
* @return
*/
public List<IAtom> getIsomorphismMapping(IAtomContainer container) {
if (query == null) return null;
target = container;
FlagStoreIsomorphismNode = true;
isomorphismNodes.clear();
if (query.getAtomCount() == 1) {
SMARTSAtom qa = (SMARTSAtom) query.getAtom(0);
for (int i = 0; i < target.getAtomCount(); i++) {
if (qa.matches(target.getAtom(i))) {
List<IAtom> v = new ArrayList<IAtom>();
v.add(target.getAtom(i));
return (v);
}
}
return null;
}
TopLayer.setAtomTopLayers(target, TopLayer.TLProp);
executeSequence(true);
if (isomorphismFound) {
// Getting the data from the Node
Node node = isomorphismNodes.get(0);
List<IAtom> v = new ArrayList<IAtom>();
for (int i = 0; i < node.atoms.length; i++) v.add(node.atoms[i]);
return (v);
} else return (null);
}
/**
* (2S)-butan-2-ol
*
* @cdk.inchi InChI=1/C4H10O/c1-3-4(2)5/h4-5H,3H2,1-2H3/t4-/s2
*/
@Test
public void _2S_butan_2_ol() throws Exception {
IAtomContainer ac = new AtomContainer();
ac.addAtom(new Atom("C"));
ac.addAtom(new Atom("C"));
ac.addAtom(new Atom("C"));
ac.addAtom(new Atom("C"));
ac.addAtom(new Atom("O"));
ac.addAtom(new Atom("H"));
ac.addBond(0, 1, SINGLE);
ac.addBond(1, 2, SINGLE);
ac.addBond(2, 3, SINGLE);
ac.addBond(2, 4, SINGLE);
ac.addBond(2, 5, SINGLE);
ac.addStereoElement(
new TetrahedralChirality(
ac.getAtom(2),
new IAtom[] {
ac.getAtom(1), // C-C
ac.getAtom(3), // C
ac.getAtom(4), // O
ac.getAtom(5), // H
},
ANTI_CLOCKWISE));
Graph g = convert(ac);
assertThat(g.toSmiles(), is("CC[C@](C)(O)[H]"));
}
@Test
public void testGetChiralAtom() {
TetrahedralChirality chirality =
new TetrahedralChirality(molecule.getAtom(1), ligands, Stereo.CLOCKWISE);
Assert.assertNotNull(chirality);
Assert.assertEquals(molecule.getAtom(1), chirality.getChiralAtom());
}
/**
* @param list
* @param source
* @param target
*/
protected synchronized void identifySingleAtomsMatchedParts(
List<CDKRMap> list, IAtomContainer source, IAtomContainer target) {
// List<IAtom> array1 = new ArrayList<>();
// List<IAtom> array2 = new ArrayList<>();
/* We have serial numbers of the bonds/Atoms to delete
* Now we will collect the actual bond/Atoms rather than
* serial number for deletion. RonP flag check whether reactant is
* mapped on product or Vise Versa
*/
TreeMap<Integer, Integer> atomNumbersFromContainer = new TreeMap<>();
for (CDKRMap rmap : list) {
// System.err.print("Map " + o.getClass());
IAtom sAtom = source.getAtom(rmap.getId1());
IAtom tAtom = target.getAtom(rmap.getId2());
// array1.add(sAtom);
// array2.add(tAtom);
int indexI = source.getAtomNumber(sAtom);
int indexJ = target.getAtomNumber(tAtom);
atomNumbersFromContainer.put(indexI, indexJ);
/*Added the Mapping Numbers to the FinalMapping*
*/
getMappings().add(atomNumbersFromContainer);
}
}
/**
* Constructs an AtomContainer with a copy of the atoms and electronContainers of another
* AtomContainer (A shallow copy, i.e., with the same objects as in the original AtomContainer).
*
* @param container An AtomContainer to copy the atoms and electronContainers from
*/
public AtomContainer(IAtomContainer container) {
this.atomCount = container.getAtomCount();
this.bondCount = container.getBondCount();
this.lonePairCount = container.getLonePairCount();
this.singleElectronCount = container.getSingleElectronCount();
this.atoms = new IAtom[this.atomCount];
this.bonds = new IBond[this.bondCount];
this.lonePairs = new ILonePair[this.lonePairCount];
this.singleElectrons = new ISingleElectron[this.singleElectronCount];
stereoElements = new HashSet<IStereoElement>(atomCount / 2);
for (IStereoElement element : container.stereoElements()) {
addStereoElement(element);
}
for (int f = 0; f < container.getAtomCount(); f++) {
atoms[f] = container.getAtom(f);
container.getAtom(f).addListener(this);
}
for (int f = 0; f < this.bondCount; f++) {
bonds[f] = container.getBond(f);
container.getBond(f).addListener(this);
}
for (int f = 0; f < this.lonePairCount; f++) {
lonePairs[f] = container.getLonePair(f);
container.getLonePair(f).addListener(this);
}
for (int f = 0; f < this.singleElectronCount; f++) {
singleElectrons[f] = container.getSingleElectron(f);
container.getSingleElectron(f).addListener(this);
}
}
/**
* Creates a ligand attached to a single chiral atom, where the involved atoms are identified by
* there index in the {@link IAtomContainer}. For ligand atom, {@link #HYDROGEN} can be passed as
* index, which will indicate the presence of an implicit hydrogen, not explicitly present in the
* chemical graph of the given <code>container</code>.
*
* @param container {@link IAtomContainer} for which the returned {@link ILigand}s are defined
* @param visitedAtoms a list of atoms already visited in the analysis
* @param chiralAtom an integer pointing to the {@link IAtom} index of the chiral atom
* @param ligandAtom an integer pointing to the {@link IAtom} index of the {@link ILigand}
* @return the created {@link ILigand}
*/
public static ILigand defineLigand(
IAtomContainer container, VisitedAtoms visitedAtoms, int chiralAtom, int ligandAtom) {
if (ligandAtom == HYDROGEN) {
return new ImplicitHydrogenLigand(container, visitedAtoms, container.getAtom(chiralAtom));
} else {
return new Ligand(
container, visitedAtoms, container.getAtom(chiralAtom), container.getAtom(ligandAtom));
}
}
@Test
public void s_penta_2_3_diene_expl_h() throws Exception {
IAtomContainer m = new AtomContainer(5, 4, 0, 0);
m.addAtom(new Atom("C"));
m.addAtom(new Atom("C"));
m.addAtom(new Atom("C"));
m.addAtom(new Atom("C"));
m.addAtom(new Atom("C"));
m.addAtom(new Atom("H"));
m.addAtom(new Atom("H"));
m.addBond(0, 1, IBond.Order.SINGLE);
m.addBond(1, 2, IBond.Order.DOUBLE);
m.addBond(2, 3, IBond.Order.DOUBLE);
m.addBond(3, 4, IBond.Order.SINGLE);
m.addBond(1, 5, IBond.Order.SINGLE);
m.addBond(3, 6, IBond.Order.SINGLE);
int[][] atoms =
new int[][] {
{0, 5, 6, 4},
{5, 0, 6, 4},
{5, 0, 4, 6},
{0, 5, 4, 6},
{4, 6, 5, 0},
{4, 6, 0, 5},
{6, 4, 0, 5},
{6, 4, 5, 0},
};
Stereo[] stereos =
new Stereo[] {
Stereo.CLOCKWISE,
Stereo.ANTI_CLOCKWISE,
Stereo.CLOCKWISE,
Stereo.ANTI_CLOCKWISE,
Stereo.CLOCKWISE,
Stereo.ANTI_CLOCKWISE,
Stereo.CLOCKWISE,
Stereo.ANTI_CLOCKWISE
};
for (int i = 0; i < atoms.length; i++) {
IStereoElement element =
new ExtendedTetrahedral(
m.getAtom(2),
new IAtom[] {
m.getAtom(atoms[i][0]),
m.getAtom(atoms[i][1]),
m.getAtom(atoms[i][2]),
m.getAtom(atoms[i][3])
},
stereos[i]);
m.setStereoElements(Collections.singletonList(element));
assertThat(convert(m).toSmiles(), is("CC(=[C@]=C(C)[H])[H]"));
}
}
@Test
public void testGetStereo() {
TetrahedralChirality chirality =
new TetrahedralChirality(molecule.getAtom(1), ligands, Stereo.CLOCKWISE);
Assert.assertNotNull(chirality);
Assert.assertEquals(molecule.getAtom(1), chirality.getChiralAtom());
for (int i = 0; i < ligands.length; i++) {
Assert.assertEquals(ligands[i], chirality.getLigands()[i]);
}
Assert.assertEquals(TetrahedralChirality.Stereo.CLOCKWISE, chirality.getStereo());
}
@Test
public void writeAtomClass() throws Exception {
IAtomContainer ac = new AtomContainer();
ac.addAtom(new Atom("C"));
ac.addAtom(new Atom("C"));
ac.addAtom(new Atom("O"));
ac.addBond(0, 1, SINGLE);
ac.addBond(1, 2, SINGLE);
ac.getAtom(0).setProperty(CDKConstants.ATOM_ATOM_MAPPING, 3);
ac.getAtom(1).setProperty(CDKConstants.ATOM_ATOM_MAPPING, 1);
ac.getAtom(2).setProperty(CDKConstants.ATOM_ATOM_MAPPING, 2);
assertThat(convert(ac).toSmiles(), is("[CH3:3][CH2:1][OH:2]"));
}
/**
* A unit test suite for JUnit.
*
* @return The test suite
*/
@Test
public void testCDKConstants_REACTIVE_CENTER() throws Exception {
IReactionProcess type = new RadicalSiteHrBetaReaction();
IAtomContainerSet setOfReactants = getExampleReactants();
IAtomContainer molecule = setOfReactants.getAtomContainer(0);
/* manually put the reactive center */
molecule.getAtom(3).setFlag(CDKConstants.REACTIVE_CENTER, true);
molecule.getAtom(0).setFlag(CDKConstants.REACTIVE_CENTER, true);
molecule.getAtom(6).setFlag(CDKConstants.REACTIVE_CENTER, true);
molecule.getBond(5).setFlag(CDKConstants.REACTIVE_CENTER, true);
List<IParameterReact> paramList = new ArrayList<IParameterReact>();
IParameterReact param = new SetReactionCenter();
param.setParameter(Boolean.TRUE);
paramList.add(param);
type.setParameterList(paramList);
/* initiate */
IReactionSet setOfReactions = type.initiate(setOfReactants, null);
IAtomContainer reactant = setOfReactions.getReaction(0).getReactants().getAtomContainer(0);
Assert.assertTrue(molecule.getAtom(6).getFlag(CDKConstants.REACTIVE_CENTER));
Assert.assertTrue(reactant.getAtom(6).getFlag(CDKConstants.REACTIVE_CENTER));
Assert.assertTrue(molecule.getAtom(0).getFlag(CDKConstants.REACTIVE_CENTER));
Assert.assertTrue(reactant.getAtom(0).getFlag(CDKConstants.REACTIVE_CENTER));
Assert.assertTrue(molecule.getAtom(3).getFlag(CDKConstants.REACTIVE_CENTER));
Assert.assertTrue(reactant.getAtom(3).getFlag(CDKConstants.REACTIVE_CENTER));
Assert.assertTrue(molecule.getBond(5).getFlag(CDKConstants.REACTIVE_CENTER));
Assert.assertTrue(reactant.getBond(5).getFlag(CDKConstants.REACTIVE_CENTER));
}
private void processBondsBlock(int lineCount, IAtomContainer container) throws IOException {
for (int i = 0; i < lineCount; i++) {
String line = input.readLine();
int atom1 = Integer.parseInt(line.substring(10, 13).trim()) - 1;
int atom2 = Integer.parseInt(line.substring(16, 19).trim()) - 1;
if (container.getBond(container.getAtom(atom1), container.getAtom(atom2)) == null) {
IBond bond =
container.getBuilder().newBond(container.getAtom(atom1), container.getAtom(atom2));
int order = Integer.parseInt(line.substring(23).trim());
bond.setOrder(BondManipulator.createBondOrder((double) order));
container.addBond(bond);
} // else: bond already present; CTX store the bonds twice
}
}
/**
* Place hydrogens connected to the provided atom <i>atom</i> using the specified
* <i>bondLength</i>.
*
* @param container atom container
* @param bondLength bond length to user
* @throws IllegalArgumentException thrown if the <i>atom</i> or <i>container</i> was null or the
* atom has connected atoms which have not been placed.
*/
@TestMethod("testNoConnections,testNullContainer,unplacedNonHydrogen")
public void placeHydrogens2D(IAtomContainer container, IAtom atom, double bondLength) {
if (container == null)
throw new IllegalArgumentException("cannot place hydrogens, no container provided");
if (atom.getPoint2d() == null)
throw new IllegalArgumentException("cannot place hydrogens on atom without coordinates");
logger.debug(
"placing hydrogens connected to atom ", atom.getSymbol(),
": ", atom.getPoint2d());
logger.debug("bond length", bondLength);
AtomPlacer atomPlacer = new AtomPlacer();
atomPlacer.setMolecule(container);
List<IAtom> connected = container.getConnectedAtomsList(atom);
IAtomContainer placed = container.getBuilder().newInstance(IAtomContainer.class);
IAtomContainer unplaced = container.getBuilder().newInstance(IAtomContainer.class);
// divide connected atoms into those which are have and haven't been placed
for (final IAtom conAtom : connected) {
if (conAtom.getPoint2d() == null) {
if (conAtom.getSymbol().equals("H")) {
unplaced.addAtom(conAtom);
} else {
throw new IllegalArgumentException(
"cannot place hydrogens, atom has connected" + " non-hydrogens without coordinates");
}
} else {
placed.addAtom(conAtom);
}
}
logger.debug("Atom placement before procedure:");
logger.debug("Centre atom ", atom.getSymbol(), ": ", atom.getPoint2d());
for (int i = 0; i < unplaced.getAtomCount(); i++) {
logger.debug("H-" + i, ": ", unplaced.getAtom(i).getPoint2d());
}
Point2d centerPlacedAtoms = GeometryTools.get2DCenter(placed);
atomPlacer.distributePartners(atom, placed, centerPlacedAtoms, unplaced, bondLength);
logger.debug("Atom placement after procedure:");
logger.debug("Centre atom ", atom.getSymbol(), ": ", atom.getPoint2d());
for (int i = 0; i < unplaced.getAtomCount(); i++) {
logger.debug("H-" + i, ": ", unplaced.getAtom(i).getPoint2d());
}
}
/**
* Procedure required by the CDOInterface. This function is only supposed to be called by the JCFL
* library
*/
public void endObject(String objectType) {
logger.debug("END: " + objectType);
if (objectType.equals("Molecule")) {
eventReader.fireFrameRead();
clearData();
} else if (objectType.equals("Atom")) {
currentMolecule.addAtom(currentAtom);
} else if (objectType.equals("Bond")) {
logger.debug("Bond(" + bond_id + "): " + bond_a1 + ", " + bond_a2 + ", " + bond_order);
if (bond_a1 > currentMolecule.getAtomCount() || bond_a2 > currentMolecule.getAtomCount()) {
logger.error(
"Cannot add bond between at least one non-existant atom: "
+ bond_a1
+ " and "
+ bond_a2);
} else {
IAtom a1 = currentMolecule.getAtom(bond_a1);
IAtom a2 = currentMolecule.getAtom(bond_a2);
IBond b = builder.newBond(a1, a2, bond_order);
if (bond_id != null) b.setID(bond_id);
if (bond_stereo != -99) {
b.setStereo(bond_stereo);
}
currentMolecule.addBond(b);
}
}
}
void executeSequence(boolean stopAtFirstMapping) {
isomorphismFound = false;
stack.clear();
// Initial nodes
QuerySequenceElement el = sequence.get(0);
for (int k = 0; k < target.getAtomCount(); k++) {
IAtom at = target.getAtom(k);
if (el.center.matches(at)) {
Node node = new Node();
node.sequenceElNum = 0;
node.nullifyAtoms(query.getAtomCount());
node.atoms[el.centerNum] = at;
stack.push(node);
}
}
// Expanding the tree of all possible mappings
if (stopAtFirstMapping) {
while (!stack.isEmpty()) {
expandNode(stack.pop());
if (isomorphismFound) break;
}
} else {
while (!stack.isEmpty()) expandNode(stack.pop());
}
}
/**
* Obtain the coordinates of atoms in a cycle.
*
* @param cycle vertices that form a cycles
* @param container structure representation
* @return coordinates of the cycle
*/
private static Point2d[] coordinatesOfCycle(int[] cycle, IAtomContainer container) {
Point2d[] points = new Point2d[cycle.length];
for (int i = 0; i < cycle.length; i++) {
points[i] = container.getAtom(cycle[i]).getPoint2d();
}
return points;
}
/**
* The method returns partial charges assigned to an heavy atom through MMFF94 method. It is
* needed to call the addExplicitHydrogensToSatisfyValency method from the class
* tools.HydrogenAdder.
*
* @param atom The IAtom for which the DescriptorValue is requested
* @param org AtomContainer
* @return partial charge of parameter atom
*/
@Override
public DescriptorValue calculate(IAtom atom, IAtomContainer org) {
if (atom.getProperty(CHARGE_CACHE) == null) {
IAtomContainer copy;
try {
copy = org.clone();
} catch (CloneNotSupportedException e) {
return new DescriptorValue(
getSpecification(),
getParameterNames(),
getParameters(),
new DoubleResult(Double.NaN),
NAMES);
}
for (IAtom a : org.atoms()) {
if (a.getImplicitHydrogenCount() == null || a.getImplicitHydrogenCount() != 0) {
logger.error("Hydrogens must be explict for MMFF charge calculation");
return new DescriptorValue(
getSpecification(),
getParameterNames(),
getParameters(),
new DoubleResult(Double.NaN),
NAMES);
}
}
if (!mmff.assignAtomTypes(copy))
logger.warn("One or more atoms could not be assigned an MMFF atom type");
mmff.partialCharges(copy);
mmff.clearProps(copy);
// cache charges
for (int i = 0; i < org.getAtomCount(); i++) {
org.getAtom(i).setProperty(CHARGE_CACHE, copy.getAtom(i).getCharge());
}
}
return new DescriptorValue(
getSpecification(),
getParameterNames(),
getParameters(),
new DoubleResult(atom.getProperty(CHARGE_CACHE, Double.class)),
NAMES);
}
/**
* Given a projected cycle, assign the exocyclic substituents to being above of below the
* projection. For Haworth projections, the substituents must be directly up or down (within some
* threshold).
*
* @param cycle vertices that form a cycle
* @param above vertices that will be above the cycle (filled by method)
* @param below vertices that will be below the cycle (filled by method)
* @param projection the type of projection
* @param horizontalXy offset from the horizontal axis
* @return assignment okay (true), not okay (false)
*/
private boolean assignSubstituents(
int[] cycle, int[] above, int[] below, WoundProjection projection, Point2d horizontalXy) {
boolean haworth = projection.projection == Projection.Haworth;
int found = 0;
for (int i = 1; i <= cycle.length; i++) {
int j = i % cycle.length;
int prev = cycle[i - 1];
int curr = cycle[j];
int next = cycle[(i + 1) % cycle.length];
// get the substituents not in the ring (i.e. excl. prev and next)
int[] ws = filter(graph[curr], prev, next);
if (ws.length > 2 || ws.length < 1) continue;
Point2d centerXy = container.getAtom(curr).getPoint2d();
// determine the direction of each substituent
for (final int w : ws) {
Point2d otherXy = container.getAtom(w).getPoint2d();
Direction direction = direction(centerXy, otherXy, horizontalXy, haworth);
switch (direction) {
case Up:
if (above[j] != curr) return false;
above[j] = w;
break;
case Down:
if (below[j] != curr) return false;
below[j] = w;
break;
case Other:
return false;
}
}
if (above[j] != curr || below[j] != curr) found++;
}
// must have at least 2 that look projected for Haworth
return found > 1 || projection.projection != Projection.Haworth;
}
@Test
public void testBuilder() {
TetrahedralChirality chirality =
new TetrahedralChirality(molecule.getAtom(1), ligands, Stereo.CLOCKWISE);
Assert.assertNull(chirality.getBuilder());
chirality.setBuilder(DefaultChemObjectBuilder.getInstance());
Assert.assertEquals(DefaultChemObjectBuilder.getInstance(), chirality.getBuilder());
}
@BeforeClass
public static void setup() throws Exception {
molecule = new AtomContainer();
molecule.addAtom(new Atom("Cl"));
molecule.addAtom(new Atom("C"));
molecule.addAtom(new Atom("Br"));
molecule.addAtom(new Atom("I"));
molecule.addAtom(new Atom("H"));
molecule.addBond(0, 1, Order.SINGLE);
molecule.addBond(1, 2, Order.SINGLE);
molecule.addBond(1, 3, Order.SINGLE);
molecule.addBond(1, 4, Order.SINGLE);
ligands =
new IAtom[] {
molecule.getAtom(4), molecule.getAtom(3), molecule.getAtom(2), molecule.getAtom(0)
};
}
@Test
public void testToString() {
TetrahedralChirality chirality =
new TetrahedralChirality(molecule.getAtom(1), ligands, Stereo.CLOCKWISE);
String stringRepr = chirality.toString();
Assert.assertNotSame(0, stringRepr.length());
Assert.assertFalse(stringRepr.contains("\n"));
}
/**
* Fixes Aromaticity of the molecule i.e. need to find rings and aromaticity again since added H's
*
* @param mol
*/
@TestMethod("testFixAromaticity")
public static void configure(IAtomContainer mol) {
// need to find rings and aromaticity again since added H's
IRingSet ringSet = null;
try {
AllRingsFinder arf = new AllRingsFinder();
ringSet = arf.findAllRings(mol);
} catch (Exception e) {
e.printStackTrace();
}
try {
// figure out which atoms are in aromatic rings:
CDKHydrogenAdder cdk = CDKHydrogenAdder.getInstance(DefaultChemObjectBuilder.getInstance());
cdk.addImplicitHydrogens(mol);
ExtAtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol);
CDKHueckelAromaticityDetector.detectAromaticity(mol);
// figure out which rings are aromatic:
RingSetManipulator.markAromaticRings(ringSet);
// figure out which simple (non cycles) rings are aromatic:
// only atoms in 6 membered rings are aromatic
// determine largest ring that each atom is a part of
for (int i = 0; i < mol.getAtomCount(); i++) {
mol.getAtom(i).setFlag(CDKConstants.ISAROMATIC, false);
jloop:
for (int j = 0; j < ringSet.getAtomContainerCount(); j++) {
// logger.debug(i+"\t"+j);
IRing ring = (IRing) ringSet.getAtomContainer(j);
if (!ring.getFlag(CDKConstants.ISAROMATIC)) {
continue jloop;
}
boolean haveatom = ring.contains(mol.getAtom(i));
// logger.debug("haveatom="+haveatom);
if (haveatom && ring.getAtomCount() == 6) {
mol.getAtom(i).setFlag(CDKConstants.ISAROMATIC, true);
}
}
}
} catch (Exception e) {
e.printStackTrace();
}
}
/**
* Helper method, used to help construct a configuration.
*
* @param atom
* @param container
* @return the array position of atom in container
*/
private int getAtomPosition(IAtom atom, IAtomContainer container) {
for (int i = 0; i < container.getAtomCount(); i++) {
if (atom.equals(container.getAtom(i))) {
return i;
}
}
return -1;
}
public int findFirstAtomIndexForSymbol(IAtomContainer container, String symbol) {
for (int i = 0; i < container.getAtomCount(); i++) {
if (container.getAtom(i).getSymbol().equals(symbol)) {
return i;
}
}
return -1;
}
/**
* A unit test for JUnit with C=CCCl # C=CC[Cl+*]
*
* @cdk.inchi InChI=1/C3H7Cl/c1-2-3-4/h2-3H2,1H3
*/
@Test
public void testCompareIonized() throws Exception {
IAtomContainer molA = builder.newInstance(IAtomContainer.class);
molA.addAtom(builder.newInstance(IAtom.class, "C"));
molA.addAtom(builder.newInstance(IAtom.class, "C"));
molA.addBond(0, 1, IBond.Order.SINGLE);
molA.addAtom(builder.newInstance(IAtom.class, "C"));
molA.addBond(1, 2, IBond.Order.SINGLE);
molA.addAtom(builder.newInstance(IAtom.class, "Cl"));
molA.addBond(2, 3, IBond.Order.SINGLE);
addExplicitHydrogens(molA);
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(molA);
lpcheck.saturate(molA);
double resultA =
((DoubleResult) descriptor.calculate(molA.getAtom(3), molA).getValue()).doubleValue();
IAtomContainer molB = builder.newInstance(IAtomContainer.class);
molB.addAtom(builder.newInstance(IAtom.class, "C"));
molB.addAtom(builder.newInstance(IAtom.class, "C"));
molB.addBond(0, 1, IBond.Order.SINGLE);
molB.addAtom(builder.newInstance(IAtom.class, "C"));
molB.addBond(1, 2, IBond.Order.SINGLE);
molB.addAtom(builder.newInstance(IAtom.class, "Cl"));
molB.getAtom(3).setFormalCharge(1);
molB.addSingleElectron(3);
molB.addLonePair(3);
molB.addLonePair(3);
molB.addBond(2, 3, IBond.Order.SINGLE);
addExplicitHydrogens(molB);
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(molB);
lpcheck.saturate(molB);
Assert.assertEquals(1, molB.getAtom(3).getFormalCharge(), 0.00001);
Assert.assertEquals(1, molB.getSingleElectronCount(), 0.00001);
Assert.assertEquals(2, molB.getLonePairCount(), 0.00001);
double resultB =
((DoubleResult) descriptor.calculate(molB.getAtom(3), molB).getValue()).doubleValue();
Assert.assertNotSame(resultA, resultB);
}
/**
* Returns the number of double bond equivalents in this molecule.
*
* @param formula The IMolecularFormula to calculate
* @return The number of DBEs
* @throws CDKException if DBE cannot be be evaluated
* @cdk.keyword DBE
* @cdk.keyword double bond equivalent
*/
public static double getDBE(IMolecularFormula formula) throws CDKException {
int valencies[] = new int[5];
IAtomContainer ac = getAtomContainer(formula);
AtomTypeFactory factory =
AtomTypeFactory.getInstance(
"org/openscience/cdk/config/data/structgen_atomtypes.xml", ac.getBuilder());
for (int f = 0; f < ac.getAtomCount(); f++) {
IAtomType[] types = factory.getAtomTypes(ac.getAtom(f).getSymbol());
if (types.length == 0)
throw new CDKException(
"Calculation of double bond equivalents not possible due to problems with element "
+ ac.getAtom(f).getSymbol());
// valencies[(int) (types[0].getBondOrderSum() + ac.getAtom(f).getFormalCharge())]++;
valencies[types[0].getBondOrderSum().intValue()]++;
}
return 1 + (valencies[4]) + (valencies[3] / 2) - (valencies[1] / 2);
}
@Test
public void testNotCharged() throws Exception {
IAtomContainer mol = builder.newInstance(IAtomContainer.class);
mol.addAtom(builder.newInstance(IAtom.class, "C"));
mol.getAtom(0).setFormalCharge(-1);
mol.addAtom(builder.newInstance(IAtom.class, "C"));
mol.addBond(0, 1, Order.DOUBLE);
mol.addAtom(builder.newInstance(IAtom.class, "F"));
mol.addBond(1, 2, Order.SINGLE);
addExplicitHydrogens(mol);
lpcheck.saturate(mol);
DoubleResult result = ((DoubleResult) descriptor.calculate(mol.getAtom(0), mol).getValue());
Assert.assertEquals(0.0, result.doubleValue(), 0.00001);
}
/**
* Helper method to generate 2d coordinates when JChempaint loads a molecule
* without 2D coordinates. Typically happens for SMILES strings.
*
* @param molecules
* @throws Exception
*/
private static void generate2dCoordinates(
final List<IAtomContainer> molecules) {
final StructureDiagramGenerator sdg = new StructureDiagramGenerator();
for (int atIdx = 0; atIdx < molecules.size(); atIdx++) {
final IAtomContainer mol = molecules.get(atIdx);
sdg.setMolecule(mol.getBuilder().newInstance(IAtomContainer.class,
mol));
try {
sdg.generateCoordinates();
} catch (final Exception e) {
e.printStackTrace();
}
final IAtomContainer ac = sdg.getMolecule();
for (int i = 0; i < ac.getAtomCount(); i++) {
mol.getAtom(i).setPoint2d(ac.getAtom(i).getPoint2d());
}
}
}