Feature/low affinity values #186

meganrm · 2025-03-25T21:02:26Z

Problem

Estimated review size: md

The app needs to compensate for how different the values in module 2 are from module 1.
closes #177
closes #178

Solution

Updated a few more hard coded items.

The low affinity module also need MANY more spheres to be rendered, so I did some more testing on the collision checks and was able to simply things to make it more performant and also has less overlaps.

Type of change

Please delete options that are not relevant.

New feature (non-breaking change which adds functionality)

Steps to Verify:

bun dev
poke around

Screenshots (optional):

bound ligands have a more consistent position relative to the parent:

…into feature/low-affinity-values

meganrm · 2025-03-25T21:03:24Z

src/App.tsx

+        if (
+            section === Section.Experiment &&
+            timeFactor !== LiveSimulationData.DEFAULT_TIME_FACTOR
+        ) {
            setTimeFactor(LiveSimulationData.DEFAULT_TIME_FACTOR);
-        } else if (section === Section.Introduction) {
+        } else if (
+            section === Section.Introduction &&
+            timeFactor !== LiveSimulationData.INITIAL_TIME_FACTOR
+        ) {


these changes aren't directly connected, but I did realize i was doing more updates to state than I needed to, which became more of an issue when i'm pushing the rendering

You could alternatively pull the const { section } = content[currentModule][page] out of the useEffect and have the useEffect only trigger on changes to it?

meganrm · 2025-03-25T21:04:20Z

src/components/concentration-display/ConcentrationSlider.tsx

            min={min}
            max={max}
-            step={2}
+            step={stepSize.current}


the second module has a much bigger range, so we're showing bigger jumps between markers

meganrm · 2025-03-25T21:06:42Z

src/simulation/BindingSimulator2D.ts

-            this.currentNumberOfUnbindingEvents = 0;
+    }
+
+    private resolveChildPositions() {


this is the big change: before I was using the "isTrigger" flag to keep the detect-collisions library from doing the overlap check if the spheres were bound, and then doing my own collision detection of the complex. But now, I'm just manually moving the child back in place after the system has resolved. This means the bound ligands can sometimes overlap each other but it's not super serious, and better than how it looked before

ShrimpCryptid

Left some questions/suggestions!

ShrimpCryptid · 2025-03-25T22:19:25Z

src/App.tsx

            const agentId = LiveSimulationData.AVAILABLE_AGENTS[agentName].id;
            clientSimulator.changeConcentration(agentId, value);
-            simulariumController.gotoTime(time + 1);
+            simulariumController.gotoTime(1); // the number isn't used, but it triggers the update


In an ideal world, what would the API for this look like? Something like update() or advance() for simulations?

I think the way I was doing it before may be more ideal (ie "give me the next time step"). the issue was because of the async nature of the connection between the app and the viewer, sometimes what the app thought was the next frame, the viewer thought was the current frame, so it wouldn't update.

It might be nice to be able to pass something like "++1" to gotoTime meaning "whatever you think is the next frame, give it to me".

ShrimpCryptid · 2025-03-25T22:25:18Z

src/App.tsx

+        if (
+            section === Section.Experiment &&
+            timeFactor !== LiveSimulationData.DEFAULT_TIME_FACTOR
+        ) {
            setTimeFactor(LiveSimulationData.DEFAULT_TIME_FACTOR);
-        } else if (section === Section.Introduction) {
+        } else if (
+            section === Section.Introduction &&
+            timeFactor !== LiveSimulationData.INITIAL_TIME_FACTOR
+        ) {


You could alternatively pull the const { section } = content[currentModule][page] out of the useEffect and have the useEffect only trigger on changes to it?

ShrimpCryptid · 2025-03-26T01:43:44Z

src/components/AdminUi.tsx

                        max={100}
                        step={1}
                        initialValue={timeFactor}
+                        overrideValue={timeFactor}


What does overrideValue here do? Just keeping it synced with timeFactor until a user interacts with it?

yeah, it's basically "value". it's because Slider itself is a wrapper on the Antd component that already stores it's own value on update

ShrimpCryptid · 2025-03-26T01:47:58Z

src/components/concentration-display/ConcentrationSlider.tsx

    // eslint-disable-next-line react-hooks/exhaustive-deps
    const disabledNumbers = [0];
-
+    const stepSize = useRef(0);


Could this just be, const stepSize = (max - min) / 5 instead of a ref? It looks like the useMemo updates whenever max and min do anyways.

+1 to this; alternately, could become its own useMemo, or be returned from the useMemo for marks below in a 2-tuple or object

src/App.tsx

frasercl · 2025-04-02T20:06:22Z

src/components/quiz-questions/KdQuestion.tsx

+    const getSuccessMessage = (selectedAnswer: number) => {
+        if (selectedAnswer < 5) {
+            return (


optional: function could live outside component body

src/components/concentration-display/ConcentrationSlider.tsx

frasercl · 2025-04-02T20:58:20Z

src/components/concentration-display/ConcentrationSlider.tsx

    // eslint-disable-next-line react-hooks/exhaustive-deps
    const disabledNumbers = [0];
-
+    const stepSize = useRef(0);


+1 to this; alternately, could become its own useMemo, or be returned from the useMemo for marks below in a 2-tuple or object

Co-authored-by: Cameron Fraser <[email protected]>

meganrm added 12 commits March 10, 2025 12:40

move equ check

4b46385

change values for low affinity

7798a02

adjust numbers

0649009

change scale for each module

662c7e9

make response module specific

c29a3af

adjust axis

259648b

use input number for module change

2701ae8

make slope check a little looser

edaaa71

simply collision checks

8cc356c

keep from doing muliple set state calls

5d4ba32

Merge branch 'main' of https://github.com/simularium/binding-sim-edu …

2acfa93

…into feature/low-affinity-values

remove log

1afdc20

meganrm requested a review from a team as a code owner March 25, 2025 21:02

meganrm requested review from ShrimpCryptid and frasercl and removed request for a team March 25, 2025 21:02

meganrm commented Mar 25, 2025

View reviewed changes

ShrimpCryptid approved these changes Mar 26, 2025

View reviewed changes

meganrm added 2 commits March 27, 2025 10:34

make clearer function name

a714d6c

simplify useEffect

88965e2

frasercl approved these changes Apr 2, 2025

View reviewed changes

meganrm and others added 3 commits April 3, 2025 12:47

Update src/components/concentration-display/ConcentrationSlider.tsx

d3e750c

Co-authored-by: Cameron Fraser <[email protected]>

Update src/App.tsx

bee4391

Co-authored-by: Cameron Fraser <[email protected]>

useMemo for stepsize

2d145db

meganrm merged commit 4630c06 into main Apr 3, 2025
3 checks passed

meganrm deleted the feature/low-affinity-values branch April 3, 2025 19:54

Feature/low affinity values #186

Feature/low affinity values #186

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meganrm commented Mar 25, 2025 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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meganrm commented Mar 25, 2025 •

edited

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