Installation

With npm:

npm install @rnacanvas/bases-layout

Usage

All exports of this package can be accessed using named imports.

// some example imports
import { stemmify } from '@rnacanvas/bases-layout';
import { Centroid, shift } from '@rnacanvas/bases-layout';
import { circularize, round } from '@rnacanvas/bases-layout';

Exports

Nucleobase

The Nucleobase interface defines the expected interface for nucleobases used throughout this package.

(Basically, nucleobases just have to have a getCenterPoint() method and a setCenterPoint() method.)

interface Nucleobase {
  getCenterPoint(): { x: number, y: number };

  setCenterPoint(p: { x: number, y: number }): void;
}

NucleobaseMock

The NucleobaseMock class is a simple class that just stores the coordinates of a center point (and is primarily used for testing purposes).

It is often possible, though, to improve the performance of layout operations on nucleobases by performing them on mock nucleobases first and then copying the final coordinates of the mock nucleobases to the actual nucleobases that one is working with.

let b = new NucleobaseMock({ centerPoint: { x: 92.3, y: -57.2 } });

b.getCenterPoint(); // { x: 92.3, y: -57.2 }

b.setCenterPoint({ x: 111.5, y: 63 });

Centroid

The Centroid class represents the centroid of a collection of nucleobases (where the centroid is defined as the "average" of the center points of all the bases).

Setting this will move the bases.

let bases = [
  new NucleobaseMock({ centerPoint: { x: 10, y: 22 } }),
  new NucleobaseMock({ centerPoint: { x: 2, y: 8 } }),
  new NucleobaseMock({ centerPoint: { x: 0, y: -12 } }),
];

let centroid = new Centroid(bases);

centroid.get(); // { x: 4, y: 6 }

// move the bases such that their centroid is now (33, 41)
centroid.set({ x: 33, y: 41 });

Direction

The Direction class represents the overall direction of an ordered collection of nucleobases (i.e., it is the direction of the vector that results from traversing the bases in order and adding the individual vectors connecting each consecutive pair of bases).

This is also equal to simply the direction of the vector from the first base to the last base.

This class expresses direction values in radians.

The set method of this class can also be used to rotate the target bases such that their overall direction becomes the specified direction.

let bases = [
  new NucleobaseMock({ centerPoint: { x: 124, y: 4134 } }),
  new NucleobaseMock({ centerPoint: { x: 8, y: 0 } }),
  new NucleobaseMock({ centerPoint: { x: 99, y: -2 } }),
  new NucleobaseMock({ centerPoint: { x: 551, y: 7 } }),
];

let direction = new Direction(bases);

direction.get(); // -1.4676981844274177

// rotates the target bases such their overall direction becomes 0.62
direction.set(0.62);

shift()

Shifts the target bases by the given displacement vector.

let bases = [
  new NucleobaseMock({ centerPoint: { x: 14, y: 12 } }),
  new NucleobaseMock({ centerPoint: { x: 140, y: 437 } }),
  new NucleobaseMock({ centerPoint: { x: -2, y: -88 } }),
];

shift(bases, { x: 38, y: -124 });

bases[0].getCenterPoint(); // { x: 52, y: -112 }
bases[1].getCenterPoint(); // { x: 178, y: 313 }
bases[2].getCenterPoint(); // { x: 36, y: -212 }

rotate()

Rotates the target bases by the given angle (specified in radians).

Bases are rotated in the direction of increasing direction angles (i.e., counterclockwise in the standard Cartesian coordinate system).

let bases = [
  new NucleobaseMock({ centerPoint: { x: 12, y: 100 } }),
  new NucleobaseMock({ centerPoint: { x: -58, y: -2 } }),
  new NucleobaseMock({ centerPoint: { x: 64, y: 800 } }),
];

let direction = new Direction(bases);
direction.get(); // 1.496646807136276

rotate(bases, Math.PI / 4);

direction.get(); // 2.282044970533724

straighten()

Arranges the target bases in a straight line, maintaining the original positions of the first and last bases and spacing the bases evenly.

let bases = [
  new NucleobaseMock({ centerPoint: { x: 81, y: 7 } }),
  new NucleobaseMock({ centerPoint: { x: 92, y: 12 } }),
  new NucleobaseMock({ centerPoint: { x: 401, y: -42 } }),
  new NucleobaseMock({ centerPoint: { x: -3819, y: 4829 } }),
];

straighten(bases);

linearize()

Arranges the target bases in a straight line (with the specified spacing between the center points of each consecutive pair of bases).

At present, this function will maintain the original centroid and overall direction (see the Direction class) of the target bases, though this might be subject to change in the future.

linearize(bases, { spacing: 20 });

arrange()

Arranges bases into stems and loops (based on the base-pairs present) with no attempt to avoid overlaps among bases.

This would correspond to a polygonal layout, as reported by Shapiro et al., 1982.

Pseudoknots are ignored according to the incremental range heuristic reported by Smit et al., 2008.

// an array of bases
var seq = [...'AUCGAUCGUAGCUAGGC'].map(() => new NucleobaseMock());

// the `parseDotBracket()` function can be imported
// from the `@rnacanvas/base-pairs` package
var basePairs = [...parseDotBracket(seq, '..(((.....))).')];

var options = { spacing: 10 };

arrange(seq, basePairs, options);

Options to the arrange() function include the following.

type Options = {
  // the spacing between consecutive bases in general
  // (is required)
  spacing: number;

  // the spacing between stacked base-pairs in stems
  // (defaults to `spacing`)
  basePairSpacing: number;

  // the spacing between consecutive bases in hairpin loops
  // (defaults to `spacing`)
  hairpinLoopSpacing: number;

  // the spacing between the first and last bases in the outermost loop
  // (defaults to `spacing`)
  terminiGap: number;
};