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https://github.com/arpitnarechania/d3-molecule

D3 based interactive visualization library + tool to make render atoms and molecules learning chemical bonding in a fun way.
https://github.com/arpitnarechania/d3-molecule

atoms-in-molecules chemical-bonding chemoinformatics d3 interactive-visualizations javascript molecules open-source

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D3 based interactive visualization library + tool to make render atoms and molecules learning chemical bonding in a fun way.

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Project Title: d3-molecule


d3-molecule is an open-source library for learning Chemical Bonding in an interactive way.




Screenshot





Version History



Version

Date

Brief Description

Author(s)



v1.0.0

2017/03/01

Initial creation

[email protected]



v1.0.3

2017/03/01

Update Readme

[email protected]



v1.1.1

2017/12/31

Update Readme

[email protected]



v2.0.0

2018/02/07

Visualize organic chemical structures based on IUPAC conventions

[email protected];      [email protected]





Usage and Features


    

  • Clicking the atom selects it
    • 

  • Clicking on 2 atoms, joins them by a bond
    • 

  • Clicking on a bond, toggles the bond type
    • 

  • Clicking on a view port, locks and unlocks it from movement
    • 

  • Double clicking a bond, removes it
    • 

  • Double clicking an atom, removes it and its bonds
    • 

  • Lock/ Unlock atoms to their position if needed.
    • 

  • Hide/ Show atoms if needed.
    • 

  • Drag and Resizing of molemethaneculecule container
    • 

  • Option to Export molecule as a PNG image
    • 

  • Configurable forces, constants of force directed graph for the molecule
    • 

  • Configurable style parameters for canvas, atoms, bonds
    • 

  • Visualize organic chemical structures based on IUPAC conventions.
    • 





Features WIP


    

  • Molecule Reaction components
    • 

  • Loading examples directly from standard notations like SMILE
    • 

  • 3-D support
    • 



Check out an example here. Demo




Installation


Download d3-molecule using npm.


npm install d3-molecule --save-dev

cd d3-molecule

npm install



To use this library then, simply include d3.js, jquery, Molecule.js and Molecule.css:


<script src="/path/to/jquery.min.js"></script>

<script src="/path/to/d3.min.js"></script>

<link href="/path/to/dist/css/Molecule.css">

<script src="/path/to/dist/js/Molecule.js"></script>




Basic Usage


To use this library, you must create a container element and instantiate a new Molecule:


<div id="container"></div>


Data


var data = {

    "nodes": [

      {

        "id": 0,

        "atom": "Mg",

        "charge":""

        "size": 24

      },

      {

        "id": 1,

        "atom": "Cl",

        "charge":""

        "size": 35

      },

      {

        "id": 2,

        "atom": "Cl",

        "charge":""

        "size": 35

      }

    ],

    "links": [

      {

        "source": 0,

        "target": 1,

        "bond": 1

      },

      {

        "source": 0,

        "target": 2,

        "bond": 1

      }

    ]

  }



Setting chart parameters


    var options = {

        domElement: "#container",

        uniqueId: 1,

        width: 500, 

        height: 500,

        borderThickness: 1,

        borderColor: "#ffffff",

        background: "#ffffff",

        charge: -1000,

        friction: 0.9,

        alpha: 0.1,

        theta: 0.8,

        linkStrength: 1,

        gravity: 0.1,

        maxAtomRadius: 6,

        colorScheme:["#2AA9CC", "#FCF78A"],

        bondThickness: 2,

        bondColor: "#000000",

        atomBorderThickness: 2,

        atomBorderColor: "#000000",

        atomTextColor: "#000000",

        atomSizeBasis: "Atomic Radius",

        boundingBox: true,

        borderRadiusX: 5,

        borderRadiusY: 5,

        detailedTooltips: true

    };



    var molecule = new Molecule(data,options);

    molecule.render();





Options



Option

Description

Type

Example



domElement

The DOM element to append the molecule to

string

'#container'



uniqueId

A Unique ID in case multiple molecules are added (as in the demo)

number

1



width

Width of the svg container

number

500



height

Height of the svg container

number

500



borderThickness

Thickness of the border of the svg container

number

1



borderColor

Color of the border of the svg container

string

'#000000'



background

Background color of the svg container

string

'#FFFFFF'



charge

The Repulsion/ Attraction force between atoms

number

-1000



friction

The friction parameter of a force directed graph

number

0.9



alpha

The alpha parameter of a force directed graph

number

0.1



theta

The theta parameter of a force directed graph

number

0.8



linkStrength

The linkStrength parameter of a force directed graph

number

1



gravity

The gravity parameter of a force directed graph

number

0.1



maxAtomRadius

Radius of the biggest atom in the molecule

number

6



colorScheme

Color scheme of the atoms

list

["#2AA9CC", "#FCF78A"]



bondThickness

Bond thickness

number

1



bondColor

Bond Color

string

'#000000'



atomBorderThickness

Atom border thickness

string

1



atomBorderColor

Atom border color

string

'#000000'



atomTextColor

Atom text color

string

'#000000'



atomSizeBasis

Basis on which the atom circle svgs be rendered

string

'Atomic Radius'



boundingBox

If the molecule should be constrained inside the svg container

boolean

true



borderRadiusX

SVG container's border (X) parameter

number

5



borderRadiusY

SVG container's border (Y) parameter

number

5



detailedTooltips

If detailed info about the element to be shown on hover or not

boolean

true





Bond Types include :-


    

  • Single
    • 

  • Double
    • 

  • Triple
    • 

  • Quadruple
    • 

  • Wedged
    • 

  • Wavy
    • 

  • Dotted
    • 

  • Dashed (Stripes)
    • 

  • Dashed (Gradient)
    • 

  • Arc
    • 





Test (WIP)


    

  • Unit test cases in the testrunner.html
    • 

  • Start a simple HTTP server and go to http://localhost:/testrunner.html
    • 

  • The test cases will run for the demo example
    • 





Author


Arpit Narechania

[email protected]






New Feature of Organic Compounds (added on Jan-2018)


    

  • The new module IUPACname.js adds functionality of searching organic compounds using IUPAC names.
    • 

  • This library allows you to add the side groups including methyl, ethyl and propyl on the main chain.
    • 

  • Note that the library doesn't cover all names for organic compounds.
    • 





Types of organic compounds:



Organic Compounds



Alkanes



Alkenes



Alkynes



Alkyl halides



Alcohols



Ethers



Aldehydes



Ketones



Carboxylic Acids



Esters



Amines



Amides





Limitations for IUPAC name search:


    

  • The maximum number of carbon is 12.
    • 

  • The double bond, triple bond, -OH, -C=O- are at the end of the main chain.
    • 

  • The amide is always primary amide.
    • 

  • More diverse functionality will be updated.
    • 





Examples for using organic compounds



Organic Compounds

Example



Alkanes

methane, 2-methyl-4-ethyloctane



Alkenes

ethene,2-methyl-4-ethyloctene



Alkynes

ethyne,2-methyl-4-ethyloctyne



Alkyl halides

3-fluoro-4-ethyloctyne



Alcohols

ethanol



Ethers

ethyl methyl ether



Aldehydes

3-methylbutanal



Ketones

propanone



Carboxylic Acids

ethanoic acid



Esters

methyl propanoate



Amines

ethyl methyl amine



Amides

butamide





Author for Organic Compounds






License


MIT (https://opensource.org/licenses/MIT.)