/**
* 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());
}
}
/**
* Place ring with user provided angles.
*
* @param ring the ring to place.
* @param ringCenter center coordinates of the ring.
* @param bondLength given bond length.
* @param startAngles a map with start angles when drawing the ring.
*/
public void placeRing(
IRing ring, Point2d ringCenter, double bondLength, Map<Integer, Double> startAngles) {
double radius = this.getNativeRingRadius(ring, bondLength);
double addAngle = 2 * Math.PI / ring.getRingSize();
IAtom startAtom = ring.getFirstAtom();
Point2d p = new Point2d(ringCenter.x + radius, ringCenter.y);
startAtom.setPoint2d(p);
double startAngle = Math.PI * 0.5;
/* Different ring sizes get different start angles to have
* visually correct placement */
int ringSize = ring.getRingSize();
if (startAngles.get(ringSize) != null) startAngle = startAngles.get(ringSize);
List<IBond> bonds = ring.getConnectedBondsList(startAtom);
/*
* Store all atoms to draw in consecutive order relative to the
* chosen bond.
*/
Vector<IAtom> atomsToDraw = new Vector<IAtom>();
IAtom currentAtom = startAtom;
IBond currentBond = (IBond) bonds.get(0);
for (int i = 0; i < ring.getBondCount(); i++) {
currentBond = ring.getNextBond(currentBond, currentAtom);
currentAtom = currentBond.getConnectedAtom(currentAtom);
atomsToDraw.addElement(currentAtom);
}
atomPlacer.populatePolygonCorners(atomsToDraw, ringCenter, startAngle, addAngle, radius);
}
/**
* 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;
}
/**
* Generated coordinates for a given ring, which is connected to a spiro ring. The rings share
* exactly one atom.
*
* @param ring The ring to be placed
* @param sharedAtoms The atoms of this ring, also members of another ring, which are already
* placed
* @param sharedAtomsCenter The geometric center of these atoms
* @param ringCenterVector A vector pointing the the center of the new ring
* @param bondLength The standard bondlength
*/
public void placeSpiroRing(
IRing ring,
IAtomContainer sharedAtoms,
Point2d sharedAtomsCenter,
Vector2d ringCenterVector,
double bondLength) {
logger.debug("placeSpiroRing");
double radius = getNativeRingRadius(ring, bondLength);
Point2d ringCenter = new Point2d(sharedAtomsCenter);
ringCenterVector.normalize();
ringCenterVector.scale(radius);
ringCenter.add(ringCenterVector);
double addAngle = 2 * Math.PI / ring.getRingSize();
IAtom startAtom = sharedAtoms.getAtom(0);
// double centerX = ringCenter.x;
// double centerY = ringCenter.y;
// int direction = 1;
IAtom currentAtom = startAtom;
double startAngle =
GeometryTools.getAngle(
startAtom.getPoint2d().x - ringCenter.x, startAtom.getPoint2d().y - ringCenter.y);
/*
* Get one bond connected to the spiro bridge atom.
* It doesn't matter in which direction we draw.
*/
java.util.List bonds = ring.getConnectedBondsList(startAtom);
IBond currentBond = (IBond) bonds.get(0);
Vector atomsToDraw = new Vector();
/*
* Store all atoms to draw in consequtive order relative to the
* chosen bond.
*/
for (int i = 0; i < ring.getBondCount(); i++) {
currentBond = ring.getNextBond(currentBond, currentAtom);
currentAtom = currentBond.getConnectedAtom(currentAtom);
atomsToDraw.addElement(currentAtom);
}
logger.debug("currentAtom " + currentAtom);
logger.debug("startAtom " + startAtom);
atomPlacer.populatePolygonCorners(atomsToDraw, ringCenter, startAngle, addAngle, radius);
}
/**
* Generated coordinates for a given ring, which is fused to another ring. The rings share exactly
* one bond.
*
* @param ring The ring to be placed
* @param sharedAtoms The atoms of this ring, also members of another ring, which are already
* placed
* @param sharedAtomsCenter The geometric center of these atoms
* @param ringCenterVector A vector pointing the the center of the new ring
* @param bondLength The standard bondlength
*/
public void placeFusedRing(
IRing ring,
IAtomContainer sharedAtoms,
Point2d sharedAtomsCenter,
Vector2d ringCenterVector,
double bondLength) {
logger.debug("RingPlacer.placeFusedRing() start");
Point2d ringCenter = new Point2d(sharedAtomsCenter);
double radius = getNativeRingRadius(ring, bondLength);
double newRingPerpendicular = Math.sqrt(Math.pow(radius, 2) - Math.pow(bondLength / 2, 2));
ringCenterVector.normalize();
logger.debug("placeFusedRing->: ringCenterVector.length()" + ringCenterVector.length());
ringCenterVector.scale(newRingPerpendicular);
ringCenter.add(ringCenterVector);
IAtom bondAtom1 = sharedAtoms.getAtom(0);
IAtom bondAtom2 = sharedAtoms.getAtom(1);
Vector2d bondAtom1Vector = new Vector2d(bondAtom1.getPoint2d());
Vector2d bondAtom2Vector = new Vector2d(bondAtom2.getPoint2d());
Vector2d originRingCenterVector = new Vector2d(ringCenter);
bondAtom1Vector.sub(originRingCenterVector);
bondAtom2Vector.sub(originRingCenterVector);
double occupiedAngle = bondAtom1Vector.angle(bondAtom2Vector);
double remainingAngle = (2 * Math.PI) - occupiedAngle;
double addAngle = remainingAngle / (ring.getRingSize() - 1);
logger.debug("placeFusedRing->occupiedAngle: " + Math.toDegrees(occupiedAngle));
logger.debug("placeFusedRing->remainingAngle: " + Math.toDegrees(remainingAngle));
logger.debug("placeFusedRing->addAngle: " + Math.toDegrees(addAngle));
IAtom startAtom;
double centerX = ringCenter.x;
double centerY = ringCenter.y;
double xDiff = bondAtom1.getPoint2d().x - bondAtom2.getPoint2d().x;
double yDiff = bondAtom1.getPoint2d().y - bondAtom2.getPoint2d().y;
double startAngle;
;
int direction = 1;
// if bond is vertical
if (xDiff == 0) {
logger.debug("placeFusedRing->Bond is vertical");
// starts with the lower Atom
if (bondAtom1.getPoint2d().y > bondAtom2.getPoint2d().y) {
startAtom = bondAtom1;
} else {
startAtom = bondAtom2;
}
// changes the drawing direction
if (centerX < bondAtom1.getPoint2d().x) {
direction = 1;
} else {
direction = -1;
}
}
// if bond is not vertical
else {
// starts with the left Atom
if (bondAtom1.getPoint2d().x > bondAtom2.getPoint2d().x) {
startAtom = bondAtom1;
} else {
startAtom = bondAtom2;
}
// changes the drawing direction
if (centerY - bondAtom1.getPoint2d().y
> (centerX - bondAtom1.getPoint2d().x) * yDiff / xDiff) {
direction = 1;
} else {
direction = -1;
}
}
startAngle =
GeometryTools.getAngle(
startAtom.getPoint2d().x - ringCenter.x, startAtom.getPoint2d().y - ringCenter.y);
IAtom currentAtom = startAtom;
// determine first bond in Ring
// int k = 0;
// for (k = 0; k < ring.getElectronContainerCount(); k++) {
// if (ring.getElectronContainer(k) instanceof IBond) break;
// }
IBond currentBond = sharedAtoms.getBond(0);
Vector atomsToDraw = new Vector();
for (int i = 0; i < ring.getBondCount() - 2; i++) {
currentBond = ring.getNextBond(currentBond, currentAtom);
currentAtom = currentBond.getConnectedAtom(currentAtom);
atomsToDraw.addElement(currentAtom);
}
addAngle = addAngle * direction;
try {
logger.debug("placeFusedRing->startAngle: " + Math.toDegrees(startAngle));
logger.debug("placeFusedRing->addAngle: " + Math.toDegrees(addAngle));
logger.debug("placeFusedRing->startAtom is: " + (molecule.getAtomNumber(startAtom) + 1));
logger.debug("AtomsToDraw: " + atomPlacer.listNumbers(molecule, atomsToDraw));
} catch (Exception exc) {
logger.debug("Caught an exception while logging in RingPlacer");
}
atomPlacer.populatePolygonCorners(atomsToDraw, ringCenter, startAngle, addAngle, radius);
}
