Wednesday, September 16, 2015

Generating 2D SVG Images of MOL Files using RDKit Transparent Background

The latest release of RDKit (2015-03) can generate SVG images with several lines of codes but by default the generated SVG image has a white background. The investigations on sources didn't solve my problem as I couldn't find any option for setting background to transparent background.

An example of SVG image generation can be found on RDKit blog post called New Drawing Code.

In [3] shows the SVG image generation and it returns the SVG file content in XML. When you open this file in a text editor, you'll see there is a rect element with a style attribute having fill #ffffff which is white. If you make this none, the whole SVG background becomes transparent.

So, if you obtain the SVG file content as XML from using moltosvg function in the blog post, just use the following function to make its background transparent.

import xml.etree.ElementTree as ET

def transparentsvg(svg):
    # Make the white background transparent
    tree = ET.fromstring(svg)
    rect = tree.find('rect')
    rect.set('style', rect.get('style').replace('#ffffff', 'none'))
    # Recover some missing attributes for correct browser rendering
    tree.set('version', '1.1')
    tree.set('xmlns', '')
    tree.set('xmlns:rdkit', '')
    tree.set('xmlns:xlink', '')
    return '<?xml version="1.0" encoding="UTF-8"?>' + ET.tostring(tree).strip()

You can write this to an SVG file easily

svg = transparentsvg(svg)
with open('path/to/svg/file', 'w') as f:

Install Cairo Graphics and PyCairo on Ubuntu 14.04 / Linux Mint 17

Cairo is a 2D graphics library implemented as a library written in the C programming language but if you'd like to use Python programming language, you should also install Python bindings for Cairo.

This guide will go through installation of Cairo Graphics library version 1.14.2 (most recent) and py2cairo Python bindings version 1.10.1 (also most recent).

1. Install Cairo

It's very easy with the following repository. Just add it, update your packages and install.

sudo add-apt-repository ppa:ricotz/testing
sudo apt-get update
sudo apt-get install libcairo2-dev

2. Install py2cairo

cd ~
git clone git://

See what's your prefix

python -c "import sys; print sys.prefix"

Install dependencies

sudo apt-get install automake pkg-config libtool


cd ~/py2cairo
./ --prefix=/usr
sudo make
sudo make install

3. Verify

>>> import cairo
>>> cairo.cairo_version_string()
>>> cairo.version

Now, you can use up-to-date versions of these softwares in your computer.

Install RDKit 2015-03 Build on Ubuntu 14.04 / Linux Mint 17

RDKit is an open source toolkit for cheminformatics. It has many functionalities to work with chemical files.

Follow the below guide to install RDKit 2015-03 build on an Ubuntu 14.04 / Linux Mint 17 computer. Since Ubuntu packages don’t have the latest RDKit for trusty, you have to build RDKit from its source.

1. Install Dependencies

sudo apt-get install flex bison build-essential python-numpy cmake python-dev sqlite3 libsqlite3-dev libboost1.54-all-dev

2. Download the Build

cd /usr/local
sudo wget
sudo tar -xzf RDKit_2015_03_1.tgz
sudo mv rdkit-Release_2015_03_1/ rdkit
cd rdkit/
sudo mkdir build

3. Set Environment Variables

vim ~/.bashrc
# Enter following three lines at the end of .bashrc
export RDBASE="/usr/local/rdkit"
source ~/.bashrc

4. Download InChi API (Optional, remove the arg in the next step if you skip)

sudo bash

5. Build

cd $RDBASE/build
sudo make
sudo make install

6. Verify

>>> import rdkit
>>> rdkit.rdBase.rdkitVersion

Please comment if you have any issue with this installation.