With the FragBuilder library out as a preprint from PeerJ and the library available at https://github.com/jensengroup/fragbuilder, I’m going to make a couple of blog posts to get you started using FragBuilder. You can access the manual via the GitHub page linked above.

This post will guide you through the installation of the FragBuilder library.

Figure 1: Example of peptide model made using the FragBuilder library

✅ Requirements

FragBuilder will run on most Linux distributions with a recent Python 2.x interpreter.

You need to have the following installed:

  1. NumPy
  2. Open Babel with Python bindings
  3. Git (to clone FragBuilder from GitHub)

📦 Installing FragBuilder

Use git to download (clone) the repository:

git clone git://github.com/jensengroup/fragbuilder

This will create a folder named fragbuilder. There’s no compilation needed, so it’s ready to go.

To use FragBuilder in your Python scripts, export the path to the library:

export PYTHONPATH=/home/andersx/dev/fragbuilder:$PYTHONPATH

You can add this to your ~/.bashrc file so it’s set every time you log in.

🧪 Testing Your Installation

Fire up Python and try importing the module:

$ python

Python 2.7.3 (default, Sep 26 2013, 20:03:06)
[GCC 4.6.3] on linux2
Type "help", "copyright", "credits" or "license" for more information.

>>> import fragbuilder
>>> print fragbuilder.__version__
1.0

If there are no errors, FragBuilder is working 🎉

🔧 Installing Dependencies

1. NumPy

Use your package manager:

Ubuntu/Debian:

sudo apt-get install python-numpy

Fedora/Red Hat:

su
yum install python-numpy

More info: http://www.scipy.org/install.html

2. Open Babel with Python Bindings

Ubuntu/Debian:

sudo apt-get install python-openbabel

Fedora/Red Hat:

su
yum install python-openbabel

Note:

If you run into issues (e.g. dihedral angles limited to 179.96°), you may want to compile Open Babel yourself.

I wrote a guide here:
Compiling Open Babel with Python
Official instructions:
http://openbabel.org/docs/dev/Installation/install.html

3. Git

Ubuntu/Debian:

sudo apt-get install git

Fedora/Red Hat:

su
yum install git

You’ll use Git to download FragBuilder and optionally submit patches.

That’s it! If you run into issues, feel free to leave a comment or question.