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sdftosvg

SDF to SVG

Build Status

This is a javascript package for rendering SDF chemical structure files as SVGs.

sdftosvg is built with PubChem SDF files in mind, because PubChem includes extra helpful annotations in their structure files.

Examples

HBCDD Lindane PFOS

Command Line Usage

$ sdftosvg ./input.sdf ./output.svg

Command Line Arguments

  Usage: convert [options] <input> <output>
 
  Options:
 
    -h, --help                     output usage information
    -V, --version                  output the version number
    -w, --width <n>                Output width
    -h, --height <n>               Output height
    -b, --background <background>  Background color
 

NPM Package Usage

var renderer = require('sdftosvg');
 
// Convert SDF as string to SVG 
var fs = require('fs');
var sdf = fs.readFileSync('./pcb-138.sdf');
renderer.renderSdfToSvg(sdf, {}, function(svg) {
  console.log(svg);
});
 
// Convert SDF file to SVG file 
renderer.renderSdfToSvgFile('./pcb-138.sdf', './pcb-138.svg');

Methods

renderSdfToSvg(sdf, options, callback)

Renders an SDF string to an SVG string.

  • sdf: string containing SDF file contents
  • options: options object, defined below
  • callback: function called after rendering that is given output SVG as a string

renderSdfToSvgFile(inputFile, outputFile, options)

Renders an SDF file to an SVG file.

  • inputFile: path to input SDF file
  • outputFile: path to save output SVG file
  • options: options object, defined below

Options

The options object can contain the following keys:

  • width: output width, in pixels

  • height: output height, in pixels

  • atomRadius: radius of atom circles

  • bondStrokeWidth: stroke width of bond lines

  • backgroundColor: background color

  • colors: object mapping chemical abbreviations to colors. By default, sdftosvg uses the JMol color scheme. For example, to override:

    {
      "C": "red",
      "O": "blue",
      "H": "green"
    }

Todo

A number of features remain to be added:

  • Allow specifying custom color scheme on the command line.
  • Allow further customization of output