/**
* 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());
}
}
/**
* Positions the aliphatic substituents of a ring system
*
* @param rs The RingSystem for which the substituents are to be laid out
* @return A list of atoms that where laid out
*/
public IAtomContainer placeRingSubstituents(IRingSet rs, double bondLength) {
logger.debug("RingPlacer.placeRingSubstituents() start");
IRing ring = null;
IAtom atom = null;
IRingSet rings = null;
IAtomContainer unplacedPartners = rs.getBuilder().newInstance(IAtomContainer.class);
IAtomContainer sharedAtoms = rs.getBuilder().newInstance(IAtomContainer.class);
IAtomContainer primaryAtoms = rs.getBuilder().newInstance(IAtomContainer.class);
IAtomContainer treatedAtoms = rs.getBuilder().newInstance(IAtomContainer.class);
Point2d centerOfRingGravity = null;
for (int j = 0; j < rs.getAtomContainerCount(); j++) {
ring = (IRing) rs.getAtomContainer(j); /* Get the j-th Ring in RingSet rs */
for (int k = 0; k < ring.getAtomCount(); k++) {
unplacedPartners.removeAllElements();
sharedAtoms.removeAllElements();
primaryAtoms.removeAllElements();
atom = ring.getAtom(k);
rings = rs.getRings(atom);
centerOfRingGravity = GeometryTools.get2DCenter(rings);
atomPlacer.partitionPartners(atom, unplacedPartners, sharedAtoms);
atomPlacer.markNotPlaced(unplacedPartners);
try {
for (int f = 0; f < unplacedPartners.getAtomCount(); f++) {
logger.debug(
"placeRingSubstituents->unplacedPartners: "
+ (molecule.getAtomNumber(unplacedPartners.getAtom(f)) + 1));
}
} catch (Exception exc) {
}
treatedAtoms.add(unplacedPartners);
if (unplacedPartners.getAtomCount() > 0) {
atomPlacer.distributePartners(
atom, sharedAtoms, centerOfRingGravity, unplacedPartners, bondLength);
}
}
}
logger.debug("RingPlacer.placeRingSubstituents() end");
return treatedAtoms;
}
