// construtor
public boundReceptorPair(Receptor3 irecA, Receptor3 irecB)
{
recA = irecA;
recB = irecB;
// binding receptors
recA.bound = true;
recB.bound = true;
// Report binding to cell output values
/*recA.cell.outputValues.reportBinding(recA.receptorId, recA.recPosition - recA.cell.transform.position);
* recB.cell.outputValues.reportBinding(recB.receptorId, recB.recPosition - recB.cell.transform.position); */
// if both cells visible, display a line between them.
if (bothRecsVisible())
{
lineObject = GameObject.Instantiate(Resources.Load("LineBetweenReceptors", typeof(LineRenderer))) as LineRenderer;
// Draw the line itself
lineObject.SetPosition(0, recA.recPosition);
lineObject.SetPosition(1, recB.recPosition);
lineObject.SetWidth(0.01f, 0.01f);
//Debug.Log ("//// BOUND visual receptors: cell: " + recA.cell.gameObject.name + " rec id: " + recA.receptorId + " position: " + recA.recPosition + " , cell: " + recB.cell.gameObject.name + " rec id: " + recB.receptorId + " position: " + recB.recPosition);
}
/* haloA = (Behaviour)recA.GetComponent("Halo");
* haloB = (Behaviour)recB.GetComponent("Halo");
* haloA.enabled = true;
* haloB.enabled = true;
*
* particleA = recA.GetComponent<ParticleSystem>();
* particleB = recB.GetComponent<ParticleSystem>();*/
}
// Update is called once per frame
void FixedUpdate()
{
allCellsReady();
// CANCELING THE TIME EFFECT - EXP SHOULD RUN AS FAST AS IT CAN
//elapsedTime = Time.time - latestBioTickTime;
// Rounding biotick time to prevent problems with running in wrong times ?
if (Mathf.Abs(elapsedTime - timeStepsInSeconds) < 1E-06)
{
elapsedTime = timeStepsInSeconds;
}
// Are we ready for the next timestep (in bioticks)
if ((biotick > -1) && (biotick < steps)) //&& (elapsedTime >= timeStepsInSeconds)
{
Profiler.BeginSample("update interaction radius");
// Moving the cell output biotick initalization to here, for now... (because a new biotick is first run here, and we may need to add values to the output arrays, so we have to initalize them here).
/*cell1.outputValues.updateBiotick(biotick);
* cell2.outputValues.updateBiotick(biotick);*/
// update receptors within interaction radius for both interacting cells:
cellInteraction.updateReceptorsInInteractionRadius();
Profiler.EndSample();
Profiler.BeginSample("binding");
/*Debug.Log("num of cell in int area A " + cellInteraction.cellA_receptorsInInteractionRadius_listLength);
* Debug.Log("aera B " + cellInteraction.cellB_receptorsInInteractionRadius_listLength);*/
for (int j = 0; j < cellInteraction.cellA_receptorsInInteractionRadius_listLength; j++)
{
recA = cellInteraction.cellA_receptorsInInteractionRadius[j];
if (!recA.bound) // receptor can bind only if not currently bound
{
for (int k = 0; k < cellInteraction.cellB_receptorsInInteractionRadius_listLength; k++)
{
recB = cellInteraction.cellB_receptorsInInteractionRadius[k];
if (!recB.bound) // receptor can bind only if not currently bound
{
if (rand.NextDouble() <= bindingProbability) // What's the probability for binding?
// only perform check if we passed the probabily check, which is cheaper computationally.
{
if (closeEnough(recA.recPosition, recB.recPosition))
{
// receptors bound!
boundReceptors.Add(new boundReceptorPair(recA, recB));
// After binding two receptors, we of course have to break, so that rec A wouldn't bind any other receptors (we've already passed the "is it bound" check, so it's a risk)
break;
}
}
}
}
}
}
Profiler.EndSample();
Profiler.BeginSample("removing bound receptors");
// running all receptor pairs - should they release signal, should they unbind? Doing this first so to not bind and then instantly unbind a receptor pair.
for (int i = 0; i < boundReceptors.Count; i++)
{
// if returned true, remove from bound receptors list.
if (boundReceptors[i].runReceptorsForBiotick(this, rand))
{
// Using i-- after removing an element from the list, all the other elements go back by 1. Decrementing i will cause us to check the same index again (because it increments again in the for), which is actually the next memeber on the list.
boundReceptors.RemoveAt(i--);
}
}
Profiler.EndSample();
// reports before end of biotick
//cell1.outputValues.reportReceptorAmount(cell1.receptors.Count);
//cell2.outputValues.reportReceptorAmount(cell2.receptors.Count);
biotick++;
receptorNumbersText.text = "Delta receptors (visible): " + cell1.receptors.Count + " (" + cell1.receptorMeshVertices.Count() / 4 + ")" + "\nNotch receptors (visible): " + cell2.receptors.Count + " (" + cell2.receptorMeshVertices.Count() / 4 + ")";
totalSignalText.text = "Number of bound receptors: " + boundReceptors.Count + "\nTotal signal released: " + totalSignal;
timeText.text = "" + Mathf.Floor(biotick * timeStepsInSeconds);
//latestBioTickTime = Mathf.Floor(Time.time * 10)/10 ;
latestBioTickTime = Time.time;
//Debug.Log ("t: " + Time.time + " biotick: " + biotick); // + " Sim time: " + biotick/10.0
}
else if (biotick == steps)
{
// REPORTS
// After sim finished, save everything
//float diffusionLengthScale = Utils.calcDiffusionLengthScale(diffusion_in_micrometers_squared_per_second, endocytosisRate); // endocytosis rate of both cells is equal!
//// Save signal per biotick
//cell1.outputValues.saveSignal(interactionRadius, diffusionLengthScale);
//cell2.outputValues.saveSignal(interactionRadius, diffusionLengthScale);
//// Save the number of receptors per each biotick
//cell1.outputValues.saveReceptorAmounts(interactionRadius, diffusionLengthScale);
//cell2.outputValues.saveReceptorAmounts(interactionRadius, diffusionLengthScale);
//// Report AND save locations of all receptors in last biotick (steady state) for receptor profiles.
//foreach (Receptor3 rec in cell1.receptors) {
// cell1.outputValues.reportReceptorPositionInSS(rec.receptorId, rec.recPosition, rec.bound);
//}
// //cell1.outputValues.saveDistanceOfTypeFromInteractionPoint(interactionRadius, diffusionLengthScale);
// //cell1.outputValues.saveForCovarianceCalculationsAtLastBiotick(cell1.randomSeedForReceptorMovement, diffusionLengthScale);
//foreach (Receptor3 rec in cell2.receptors) {
// cell2.outputValues.reportReceptorPositionInSS(rec.receptorId, rec.recPosition, rec.bound);
//}
// //cell2.outputValues.saveDistanceOfTypeFromInteractionPoint(interactionRadius, diffusionLengthScale);
// //cell2.outputValues.saveForCovarianceCalculationsAtLastBiotick(cell2.randomSeedForReceptorMovement, diffusionLengthScale);
// // Diffusion calculations - distance of all receptor in EACH BIOTICK (SUPER WASTEFUL) // DONT FORGET TO BRING BACK ALL POSITION REPORTING! / ALSO BRING BACK INIT IN cellOutputValues / COMMENT THIS WHEN NO DIFF CALCULATIONS
// //cell1.outputValues.saveSquaredSDForDiffusionCalculations(cell1.randomSeedForReceptorMovement);
// //cell1.outputValues.saveAverageForDiffusionCalculations(cell1.randomSeedForReceptorMovement);
// //cell2.outputValues.saveSquaredSDForDiffusionCalculations(cell2.randomSeedForReceptorMovement);
// //cell2.outputValues.saveAverageForDiffusionCalculations(cell2.randomSeedForReceptorMovement);
// // FOR DLS calculations - Variance of distances from origin at last biotick
// /*cell1.outputValues.saveForDiffusionCalculationsAtLastBiotick(cell1.randomSeedForReceptorMovement, diffusionLengthScale);
//cell2.outputValues.saveForDiffusionCalculationsAtLastBiotick(cell2.randomSeedForReceptorMovement, diffusionLengthScale);*/
// int outerLoopLength = 0;
//if (autoDiffusion) {
// outerLoopLength = diffusionValues.Length;
//}
// else {
// outerLoopLength = exoEndoRates.endocytosisRates.Length;
//}
//// Advancing the indices
//if (valueCounterLS < outerLoopLength) {
// if (valueCounterIR < interactionRadii.Length) {
// resetExp(valueCounterLS, valueCounterIR);
// valueCounterIR++;
// } else {
// valueCounterIR = 0;
// valueCounterLS++;
// if (valueCounterLS < outerLoopLength) {
// resetExp(valueCounterLS, valueCounterIR);
// valueCounterIR++;
// }
// }
//}
//Debug.Log("outer loop length: " + outerLoopLength);
//// If we've gone through all the values
//if (valueCounterLS == outerLoopLength) {
// // Create diffusion length scale list:
// foreach(float diffusion in diffusionValues) {
// //foreach(float endoRate in exoEndoRates.endocytosisRates) {
// diffusionLengthScales.Add (Utils.calcDiffusionLengthScale(diffusion, endocytosisRate));
// //diffusionLengthScales.Add (Utils.getDiffusionLengthScale(speed_in_micrometers_per_second, endoRate, timeStepsInSeconds));
// }
// cell1.outputValues.saveDiffLengthScaleAndInteractionRadiiLists(interactionRadii, diffusionLengthScales.ToArray());
// // Move to the next biotick to stop operation
// biotick++;
//}
}
/* if (showInteractionRadius) {
* for (int i=0; i<8; i++) {
* // Setup vector
* radiusVector = Math3d.
* }
* }*/
}
