/**
* Layout all rings in the given RingSet that are connected to a given Ring
*
* @param rs The RingSet to be searched for rings connected to Ring
* @param ring The Ring for which all connected rings in RingSet are to be layed out.
*/
void placeConnectedRings(IRingSet rs, IRing ring, int handleType, double bondLength) {
IRingSet connectedRings = rs.getConnectedRings(ring);
IRing connectedRing;
IAtomContainer sharedAtoms;
int sac;
Point2d oldRingCenter, sharedAtomsCenter, tempPoint;
Vector2d tempVector, oldRingCenterVector, newRingCenterVector;
// logger.debug(rs.reportRingList(molecule));
for (IAtomContainer container : connectedRings.atomContainers()) {
connectedRing = (IRing) container;
if (!connectedRing.getFlag(CDKConstants.ISPLACED)) {
// logger.debug(ring.toString(molecule));
// logger.debug(connectedRing.toString(molecule));
sharedAtoms = AtomContainerManipulator.getIntersection(ring, connectedRing);
sac = sharedAtoms.getAtomCount();
logger.debug("placeConnectedRings-> connectedRing: " + (ring.toString()));
if ((sac == 2 && handleType == FUSED)
|| (sac == 1 && handleType == SPIRO)
|| (sac > 2 && handleType == BRIDGED)) {
sharedAtomsCenter = GeometryTools.get2DCenter(sharedAtoms);
oldRingCenter = GeometryTools.get2DCenter(ring);
tempVector = (new Vector2d(sharedAtomsCenter));
newRingCenterVector = new Vector2d(tempVector);
newRingCenterVector.sub(new Vector2d(oldRingCenter));
oldRingCenterVector = new Vector2d(newRingCenterVector);
logger.debug(
"placeConnectedRing -> tempVector: "
+ tempVector
+ ", tempVector.length: "
+ tempVector.length());
logger.debug("placeConnectedRing -> bondCenter: " + sharedAtomsCenter);
logger.debug(
"placeConnectedRing -> oldRingCenterVector.length(): "
+ oldRingCenterVector.length());
logger.debug(
"placeConnectedRing -> newRingCenterVector.length(): "
+ newRingCenterVector.length());
tempPoint = new Point2d(sharedAtomsCenter);
tempPoint.add(newRingCenterVector);
placeRing(connectedRing, sharedAtoms, sharedAtomsCenter, newRingCenterVector, bondLength);
connectedRing.setFlag(CDKConstants.ISPLACED, true);
placeConnectedRings(rs, connectedRing, handleType, bondLength);
}
}
}
}
/**
* 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();
}
}