2. Installation

2.1. Dependencies

Python versions 2.6+ are recommended for CanTherm. Currently Python 3.x versions are incompatible with CanTherm.

CanTherm relies on a number of Python packages for certain functionality. The following lists the required Python packages that are not part of the Python standard library:

  • NumPy. Provides efficient array and matrix operations.
  • SciPy. Provides efficient linear algebra functions and special functions.
  • Cython v0.19+. C-extensions for Python
  • RDKit. Cheminformatics libraries and functions
  • Cairo. Cairo graphics rendering for Python for drawing reaction networks
  • Quantities. For converting between different scientific units
  • Argparse. For parsing input arguments when running scripts

You can install these dependencies on Linux in the following fashion.

sudo apt-get install python-numpy python-scipy python-cairo
sudo pip install cython>=0.19 quantities argparse

It is recommended that RDKit be installed manually with InChI capabilities on.

2.2. Installing CanTherm

Once you have obtained the required dependencies, CanTherm can be installed by first obtaining the RMG-Py source code by either downloading into a directory using git:

git clone git@github.com:ReactionMechanismGenerator/RMG-Py.git

or by downloading the zip file of the current RMG-Py master source code found here and unzipping into the appropriate directory.

Inside the root package directory for RMG-Py, execute the following make command:

make cantherm

The appropriate cythonization and compilation steps will now begin. When they are completed, you can run a test example by going into the examples folder to run a sample Cantherm job to verify the installation:

cd examples/cantherm/networks/acetyl+O2
python ../../../../cantherm.py input.py

This will allow you to use the cantherm.py as a Python script anytime you point to it.