public void recalculatePositionDependentQuantities(BitSet bs) {
if (getHaveStraightness())
calculateStraightness();
recalculateLeadMidpointsAndWingVectors(-1);
BitSet bsModels = getModelBitSet(bs, false);
for (int i = bsModels.nextSetBit(0); i >= 0; i = bsModels.nextSetBit(i + 1))
shapeManager.refreshShapeTrajectories(i, viewer.getModelUndeletedAtomsBitSet(i));
}
public void connect(float[][] connections) {
// array of [index1 index2 order diameter energy]