https://github.com/ardcore/fit_transform

Calculate and apply the optimal transformation matrix that minimizes the RMSD (root mean squared deviation) between two paired sets of points.
https://github.com/ardcore/fit_transform

cheminformatics kabsch molecular-modeling rmsd

Last synced: 26 days ago
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Calculate and apply the optimal transformation matrix that minimizes the RMSD (root mean squared deviation) between two paired sets of points.

• Host: GitHub
• URL: https://github.com/ardcore/fit_transform
• Owner: ardcore
• License: mpl-2.0
• Created: 2019-03-13T14:49:08.000Z (over 6 years ago)
• Default Branch: master
• Last Pushed: 2019-03-13T15:43:34.000Z (over 6 years ago)
• Last Synced: 2025-05-29T14:02:06.903Z (about 1 month ago)
• Topics: cheminformatics, kabsch, molecular-modeling, rmsd
• Language: JavaScript
• Size: 36.1 KB
• Stars: 4
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# fit_transform

## Problem

_Given two corresponding sets of 2D points A and B, find and apply an optimal transformation matrix to bring set A [as close as possible](https://en.wikipedia.org/wiki/Root-mean-square_deviation) to set B._

## Solution

- fit_transform implements full [Kabsch algorithm](https://en.wikipedia.org/wiki/Kabsch_algorithm) for datasets where `N >= 3`

- _closeness_ of sets is understood as RMSD

- this implementation focuses on 2D points only, but can be easily

  generalised to support more dimensions

## API

  - `fitTransform(A, B) -> A'` -- returns a transformed dataset

  - `kabsch(A, B) -> C` -- returns an optimal rotation matrix

## Installation

    npm install fit_transform

## Building and Testing

    yarn

    yarn build

    yarn test

    cd examples/

    python -m SimpleHTTPServer

## Examples

![Image showing fit_transform applied to a 2-point dataset](https://user-images.githubusercontent.com/49605/54288513-e546fb00-45a7-11e9-84f0-297dddcb2f8c.png)

![Image showing fit_transform applied to a 3-point dataset

](https://user-images.githubusercontent.com/49605/54288515-e546fb00-45a7-11e9-832c-c7950efe28bb.png)

![Image showing fit_transform applied to a 3-point dataset

](https://user-images.githubusercontent.com/49605/54288517-e5df9180-45a7-11e9-8e46-646377ad0ff0.png)

See also

[examples](https://github.com/ardcore/fit_transform/tree/master/examples)