Sandbox::https://github.com/molstar/molstar/pull/1726

agdturner · 2025-12-20T17:56:32Z

Description

Some generally useful geometry for aligning molecules

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Added description of changes to the [Unreleased] section of CHANGELOG.md
Updated headers of modified files
Added my name to package.json's contributors
(Optional but encouraged) Improved documentation in docs

Ribocode

Ribocode extension removed color as this is too project specific.

agdturner · 2025-12-20T18:01:49Z

The repository for Ribocode is: https://github.com/ribocode-slola/ribocode1/
The PWA is linked in the Readme.
I am already in the list of contributors in package.json.

Add/update package-lock.json

Ribocode

…ribocode

Ribocode

Code style changes to pass test

big.js types

big.js types workaround Added a fallback `declare module 'big.js';` because the CI build does not recognize the built-in types from `big.js@7.x`, even though it works locally. This disables type checking for `big.js` as a temporary workaround until the CI environment can properly resolve the package's built-in types.

arose · 2025-12-20T22:12:40Z

Did you see src\mol-math\linear-algebra\3d\minimize-rmsd.ts? I think it already offers mathematically 'optimal' alignment of point sets. Also note the recently added src\mol-math\linear-algebra\3d\tm-align.ts for potentially biologically more meaningful alignment.

agdturner · 2025-12-21T01:45:22Z

Ah, thanks @arose - no, I had not seen those - there are similarities and it would be good to compare the algorithms and performance on some data... Alignment can be difficult! I found that I could align some molecules better by eye than using the algorithm I implemented. I hard coded a 50 iteration limit for the Newton-Raphson iterative approximation which could be too small...

dsehnal

Thanks for this. Before we merge this though, should do some refactoring.

dsehnal · 2025-12-21T10:45:51Z

+ * NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+ * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+export class QCProt {


As @arose pointed out, there is already quaternion-based RMSD minimization code in https://github.com/molstar/molstar/blob/master/src/mol-math/linear-algebra/3d/minimize-rmsd.ts, although the implementation here does seem to better handle edge-cases.

I would prefer we improve the existing code instead of including a duplicate.

dsehnal · 2025-12-21T10:50:59Z

+ * @returns A promise that resolves to an object containing arrays of
+ * x, y, z coordinates and atom types.
+ */
+export async function getAlignmentData(plugin: PluginUIContext, trajectory: any) {


This is a very hacky way of getting the position elements -- generally I would at least get this from the Model which has types data.

Is the purpose of the loadMoleculeFileToViewer only to get the positions? The way this thing is coded seems quite specific to the application you want to use this in.

Ah, but you know better what you are doing with Mol* and I am trying to learn how to use it @dsehnal!

The molecule is centralised so that the coordinate origin is at the centre of the molecule (the position of each atom is translated by the average of all the atom positions). If alignment data are provided, then the atoms are also rotated. If the user requests alignment data to be returned, then the centralised atom locations are returned.

Let's step back a little. The functionality you want is:

Load two or more ribosomes

Compute their alignment and apply it to the structures

Output the translations and matrices to the user

Am I missing something?

No, I think that is the gist of it @dsehnal.

Ok, then you want to structure your library differently. I would suggest

Load all the structures using built-in methods (you don't need the trajectory.ts file you added)

Find the superpositions

I am having some trouble understanding what alignmentData.type means in relation to selectedAtomTypes in alignDataset, but basically the method should get a selection you want to align and output a transformation matrix

Apply TransformStructureConformation based on the transformations to update the visuals

To the user, you can either output the transformation matrix or the transformed positions

But this would be part of your particular instance of Mol*, not necessarily the extension.

I would again encourage you to have a look at #1723 which achives a lot of what you want (= adding an alternative superposition method)

dsehnal · 2025-12-21T10:59:21Z

+ * @param z Z coordinates to align with
+ * @return Aligned coordinates as {alignedX, alignedY, alignedZ}
+ */
+export function alignDataset(


@ddelalamo-takeda recently added support for tm-align #1723 which follows the existing patterns for superposing structures (notably the input of Structure.Loci instead of the selectedAtomTypes filtering you have inside the function). Can you follow this pattern here as well?

Due to the usage of big.js, I would still prefer this being a separate extension instead of part of the core library.

dsehnal · 2025-12-21T11:00:51Z

+ * @param coords Array of BigVec3 coordinates.
+ * @returns Centroid as Vec3
+ */
+export function computeBigCentroid(coords: Vec3[]): Vec3 {


Out of curiosity, how big structures to force the use of an arbitrary precision library?

Ribosome datasets can have hundreds of thousands of atoms.

I could be wrong, but the precision of the atom positions themselves isn't very accurate and 15 significant digits still seems quite good.

What is generally the error between using the 64bit floats vs the arbitrary precision computation? And if the different centroid is used in the RMSD calculation, what is the difference then?

dsehnal · 2025-12-21T11:17:45Z

Extra file that should not be here?

Sorry, not sure where that is from. I did not include it intentionally.

dsehnal · 2025-12-21T11:21:49Z

    "@types/node-fetch": "^2.6.13",
    "@types/swagger-ui-dist": "3.30.6",
    "argparse": "^2.0.1",
+    "big.js": "^7.0.1",


Generally, I prefer not to include 3rd party dependencies if it could be avoided.

BigJS is MIT and just a single file, which means we could actually just copy-paste it into mol-util/big.ts (and include proper typescript definition). I could help with that if you want.

I read that type definitions are included in big.js 7.0.1, but I'm not sure how...

Part of https://github.com/DefinitelyTyped/DefinitelyTyped

I understand that the Type definitions for Big.js can be added with:
npm install --save-dev @types/big.js

Yes, but I don't want to include a dependency on another 3rd party library if it's somewhat easily avoidable.

Ribocode

…path

…e-pair fallback

Ribocode update for alignment

agdturner added 6 commits December 20, 2025 17:25

Ribocode extension

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Ribocode extension

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Ribocode extension

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Merge pull request #2 from agdturner/ribocode

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Ribocode

Ribocode extension

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Merge pull request #3 from agdturner/ribocode

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Ribocode extension removed color as this is too project specific.

agdturner added 16 commits December 20, 2025 18:10

Add/update package-lock.json

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Merge pull request #4 from agdturner/ribocode

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Add/update package-lock.json

Regenerate lock file and add big.js

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Recreate package-lock.json in molstar

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Merge branch 'ribocode-slola:master' into ribocode

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Merge pull request #5 from agdturner/ribocode

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Ribocode

Code style changes to pass test

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Merge branch 'ribocode' of https://github.com/agdturner/molstar into …

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Merge branch 'ribocode-slola:master' into ribocode

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Merge pull request #6 from agdturner/ribocode

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Ribocode

Code style changes to pass test

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Merge pull request #7 from agdturner/ribocode

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Code style changes to pass test

big.js types

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Merge pull request #8 from agdturner/ribocode

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big.js types

big.js types workaround

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added composite compiler option

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dsehnal reviewed Dec 21, 2025

View reviewed changes

agdturner added 2 commits January 6, 2026 17:04

provided a second way to re-align atoms when loading from a file

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Merge pull request #10 from agdturner/ribocode

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Ribocode

dsehnal mentioned this pull request Jan 19, 2026

TM-Align performances #1745

Closed

agdturner added 7 commits July 31, 2026 16:34

Fix centroid mapping for ribocode alignment transform

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Fix chain alignment rigid transform translation and add regression test

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fix(alignment): revert rigid-translation regression in chain realign …

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…path

Add shared atom-type fallback for alignment selectors

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Initialised variables that needed it

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fix(alignment): apply translation in equal-count path and guard singl…

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…e-pair fallback

Merge pull request #11 from agdturner/ribocode

b1fa886

Ribocode update for alignment

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agdturner commented Dec 20, 2025

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arose commented Dec 20, 2025

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