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Simplified (and corrected for partially laid out rings) bridged ring …
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…placed, rather than changing the draw direction we just ensure the winding of the bridged atoms and the other share atoms is consistent.
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@johnmay
johnmay committed Jun 26, 2016
1 parent 8addbe5 commit 2d98f18
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Showing 2 changed files with 53 additions and 87 deletions.
6 changes: 1 addition & 5 deletions tool/sdg/src/main/java/org/openscience/cdk/layout/AtomPlacer.java
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Original file line number Diff line number Diff line change
Expand Up @@ -474,10 +474,6 @@ public void populatePolygonCorners(final List<IAtom> atoms,

for (IAtom atom : atoms) {
theta += thetaStep;
if (thetaBeg >= 2.0 * Math.PI) {
System.err.println("???");
theta -= 2.0 * Math.PI;
}
double x = Math.cos(theta) * radius;
double y = Math.sin(theta) * radius;
double newX = x + center.x;
Expand Down Expand Up @@ -718,7 +714,7 @@ static public String listNumbers(IAtomContainer mol, IAtomContainer ac) throws C
* atoms in an AtomContainer
*@exception java.lang.Exception Description of the Exception
*/
static public String listNumbers(IAtomContainer mol, List<IAtom> ac) throws java.lang.Exception {
static public String listNumbers(IAtomContainer mol, List<IAtom> ac) {
String s = "Numbers: ";
for (int f = 0; f < ac.size(); f++) {
s += (mol.getAtomNumber((IAtom) ac.get(f)) + 1) + " ";
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134 changes: 52 additions & 82 deletions tool/sdg/src/main/java/org/openscience/cdk/layout/RingPlacer.java
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Original file line number Diff line number Diff line change
Expand Up @@ -39,6 +39,7 @@
import javax.vecmath.Point2d;
import javax.vecmath.Tuple2d;
import javax.vecmath.Vector2d;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
Expand Down Expand Up @@ -223,6 +224,14 @@ public IAtomContainer placeRingSubstituents(IRingSet rs, double bondLength) {
return treatedAtoms;
}

private static double det(double xa, double ya, double xb, double yb, double xc, double yc) {
return (xa - xc) * (yb - yc) - (ya - yc) * (xb - xc);
}

private static double det(Point2d a, Point2d b, Point2d c) {
return det(a.x, a.y, b.x, b.y, c.x, c.y);
}

/**
* Generated coordinates for a given ring, which is connected to another ring a bridged ring,
* i.e. it shares more than two atoms with another ring.
Expand All @@ -238,12 +247,25 @@ private void placeBridgedRing(IRing ring, IAtomContainer sharedAtoms, Point2d sh
IAtom[] bridgeAtoms = getBridgeAtoms(sharedAtoms);
IAtom bondAtom1 = bridgeAtoms[0];
IAtom bondAtom2 = bridgeAtoms[1];
List<IAtom> otherAtoms = new ArrayList<>();
for (IAtom atom : sharedAtoms.atoms())
if (atom != bondAtom1 && atom != bondAtom2)
otherAtoms.add(atom);

final boolean snap = ring.getProperty(SNAP_HINT) != null && ring.getProperty(SNAP_HINT, Boolean.class);

boolean swap = snap ? det(bondAtom1.getPoint2d(), GeometryUtil.get2DCenter(otherAtoms), bondAtom2.getPoint2d()) < 0
: det(bondAtom1.getPoint2d(), GeometryUtil.get2DCenter(otherAtoms), bondAtom2.getPoint2d()) > 0;

if (swap) {
IAtom tmp = bondAtom1;
bondAtom1 = bondAtom2;
bondAtom2 = tmp;
}

Vector2d bondAtom1Vector = new Vector2d(bondAtom1.getPoint2d());
Vector2d bondAtom2Vector = new Vector2d(bondAtom2.getPoint2d());

final boolean snap = ring.getProperty(SNAP_HINT) != null && ring.getProperty(SNAP_HINT, Boolean.class);

Point2d midPoint = getMidPoint(bondAtom1Vector, bondAtom2Vector);
Point2d ringCenter = null;
double radius = getNativeRingRadius(ring, bondLength);
Expand All @@ -255,9 +277,7 @@ private void placeBridgedRing(IRing ring, IAtomContainer sharedAtoms, Point2d sh
new Vector2d(midPoint.x - sharedAtomsCenter.x, midPoint.y - sharedAtomsCenter.y));

offset = 0;
for (IAtom atom : sharedAtoms.atoms()) {
if (atom == bondAtom1 || atom == bondAtom2)
continue;
for (IAtom atom : otherAtoms) {
double dist = atom.getPoint2d().distance(midPoint);
if (dist > offset)
offset = dist;
Expand All @@ -270,92 +290,44 @@ private void placeBridgedRing(IRing ring, IAtomContainer sharedAtoms, Point2d sh
ringCenterVector.scale(radius-offset);
ringCenter.add(ringCenterVector);

bondAtom1Vector.sub(ringCenter);
bondAtom2Vector.sub(ringCenter);

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() - sharedAtoms.getAtomCount() + 1);
final int numUnplaced = ring.getRingSize() - sharedAtoms.getAtomCount();

logger.debug("placeBridgedRing->occupiedAngle: " + Math.toDegrees(occupiedAngle));
logger.debug("placeBridgedRing->remainingAngle: " + Math.toDegrees(remainingAngle));
double dot = bondAtom2Vector.x * bondAtom1Vector.x + bondAtom2Vector.y * bondAtom1Vector.y;
double det = bondAtom2Vector.x * bondAtom1Vector.y - bondAtom2Vector.y * bondAtom1Vector.x;

logger.debug("placeBridgedRing->addAngle: " + Math.toDegrees(addAngle));
// theta remain/step
double tRemain = Math.atan2(det, dot);
if (tRemain < 0) tRemain = Math.PI + (Math.PI + tRemain);
double tStep = tRemain / (numUnplaced + 1);

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;
logger.debug("placeBridgedRing->tRemain: " + Math.toDegrees(tRemain));
logger.debug("placeBridgedRing->tStep: " + Math.toDegrees(tStep));

double startAngle;
int direction = -1;

int direction = 1;
// if bond is vertical
if (xDiff == 0) {
logger.debug("placeBridgedRing->Bond is vertical");
//starts with the lower Atom
if (bondAtom1.getPoint2d().y > bondAtom2.getPoint2d().y) {
startAtom = bondAtom1;
} else {
startAtom = bondAtom2;
}
startAngle = GeometryUtil.getAngle(bondAtom1.getPoint2d().x - ringCenter.x, bondAtom1.getPoint2d().y - ringCenter.y);

//changes the drawing direction
if (centerX < sharedAtomsCenter.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 - sharedAtomsCenter.y > (centerX - sharedAtomsCenter.x) * yDiff / xDiff) {
direction = 1;
} else {
direction = -1;
}
}
startAngle = GeometryUtil.getAngle(startAtom.getPoint2d().x - ringCenter.x, startAtom.getPoint2d().y
- ringCenter.y);

IAtom currentAtom = startAtom;
IAtom currentAtom = bondAtom1;
IBond currentBond = sharedAtoms.getConnectedBondsList(currentAtom).get(0);

Vector atomsToDraw = new Vector();
List<IAtom> atoms = new ArrayList<>();
for (int i = 0; i < ring.getBondCount(); i++) {
currentBond = ring.getNextBond(currentBond, currentAtom);
currentAtom = currentBond.getConnectedAtom(currentAtom);
if (!sharedAtoms.contains(currentAtom)) {
atomsToDraw.addElement(currentAtom);
atoms.add(currentAtom);
}
}
try {
logger.debug("placeBridgedRing->atomsToPlace: " + AtomPlacer.listNumbers(molecule, atomsToDraw));
logger.debug("placeBridgedRing->startAtom is: " + (molecule.getAtomNumber(startAtom) + 1));
logger.debug("placeBridgedRing->startAngle: " + Math.toDegrees(startAngle));
logger.debug("placeBridgedRing->addAngle: " + Math.toDegrees(addAngle));
} catch (Exception exc) {
logger.debug("Caught an exception while logging in RingPlacer");
}

addAngle = addAngle * direction;
atomPlacer.populatePolygonCorners(atomsToDraw, ringCenter, startAngle, addAngle, radius);
logger.debug("placeBridgedRing->atomsToPlace: " + AtomPlacer.listNumbers(molecule, atoms));
logger.debug("placeBridgedRing->startAngle: " + Math.toDegrees(startAngle));
logger.debug("placeBridgedRing->tStep: " + Math.toDegrees(tStep));

atomPlacer.populatePolygonCorners(atoms, ringCenter, startAngle, -tStep, radius);
}

/**
Expand Down Expand Up @@ -524,14 +496,12 @@ public void placeFusedRing(IRing ring,
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");
}

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));

atomPlacer.populatePolygonCorners(atomsToDraw, ringCenter, startAngle, addAngle, radius);
}

Expand Down

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