A broswer-side protein viewer library leveraging three.js
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README.md

ProteinViewer V0.1

A light weight easy using JavaScript protein display library based on three.js

Import two JavaScript files in your webpage to use ProteinViewer:

<script src="https://cdnjs.cloudflare.com/ajax/libs/three.js/r70/three.min.js"></script>

<script src="http://renchusong.github.io/ProteinViewer/js/ptviewer.js"></script>

See Demo Code as a fast tutorial. Visit Online Demo Page to get an intuition about ProteinViewer.

ProteinViewerWrapper

The wrapper class to load json data and append proteins according to their format.

Json data format:

{

	"atoms":[

		{"x" : -12.7110, "y" : -76.6390, "z" : 20.3000, "type" : 0, "ID" : "A44"},

		{"x" : -14.6360, "y" : -73.3960, "z" : 19.7790, "type" : 0, "ID" : "A45"},

		{"x" : -15.7110, "y" : -70.6390, "z" : 18.3000, "type" : 1, "ID" : "A46"},

		{"x" : -16.6360, "y" : -68.3960, "z" : 17.7790, "type" : 1, "ID" : "A47"},

		...

		{"x" : -13.2180, "y" : -72.1640, "z" : 16.4780, "type" : 0, "ID" : "B46"},

		{"x" : -14.7430, "y" : -69.8440, "z" : 13.8510, "type" : 0, "ID" : "B47"},

		...

	]
}

"x", "y", "z": Protein node position

"type": 0 is line, 1 is slice, and 2 is roll

"ID": First character identifies protein, following number records order

API:

ProteinViewerWrapper(width, height, DOMObj, data, [lineRadius, planeWidth, splitThreshold]):

Append a protein viewing canvas to DOMObj, with width and height specified. data is a json object following the format above.

lineRadius specifies the radius of line geometry

planeWidth specifies the width of slice / roll

splitThreshold specifies the distance above which to be considered as non-connected segments within one protein

ProteinViewer

Customizable protein viewing class.

API:

ProteinViewer(width, height, DOMObj, [sceneMinX, sceneMaxX, sceneMinY, sceneMaxY]):

Append an empty protein viewing canvas to DOMObj, with width and height specified. Optional parameters can specify the range of camera, default to [-width / 2, width / 2] * [-height / 2, height / 2].

appendProtein(x, y, z, data, [color, scale, lineRadius, planeWidth]):

Append a protein to the canvas.

x, y, z specifies the center location of the protein.

data follows the following format:

[

	{"x" : -12.7110, "y" : -76.6390, "z" : 20.3000, "type" : 0},

	{"x" : -14.6360, "y" : -73.3960, "z" : 19.7790, "type" : 0},

	{"x" : -15.7110, "y" : -70.6390, "z" : 18.3000, "type" : 1},

	{"x" : -16.6360, "y" : -68.3960, "z" : 17.7790, "type" : 1},

	...

]

color is a hex number, e.g, 0xff0000

scale is used to scaling the protein proportionally.

lineRadius defines the radius of line and thickness of slice / roll. Default to 1.0.

planeWidth defines the width of the slice / roll. Default to 6.0.

hideProtein(index):

Hide the index_{th} added protein.

showProtein(index):

Show the index_{th} added protein.

changeProteinColor(index, newColor):

Change the index_{th} protein's color to newColor (hex value).

moveProteinTo(index, x, y, z):

Move the index_{th} protein to new location (x, y, z)

moveProtein(index, dx, dy, dz):

Move the index_{th} protein by (dx, dy, dz)

rotateProteinTo(index, rx, ry, rz):

Rotate the index_{th} protein to the direction of (rx, ry, rz) radians in three axes.

rotateProtein(index, rdx, rdy, rdz):

Rotate the index_{th} protein in three axes of (rx, ry, rz) radians.

sceneRotateTo(theta, phi):

Rotate the whole scene to the direction of (theta, phi) radians in polar coordinate system.

sceneRotate(rdx, rdy):

Rotate the whole scene in three axes of (rdx, rdy) radians relative to current direction.

Converting pdb file to json file

Supporting pdb format is our future work. Currently we provide a tool to convert pdb file to json file.

See more at PDB2JSON