GreenGroup/RMG-Py — pull request #135 by rwest (2013-07-31 21:46:44+00:00)
Title: Switch from OpenBabel to RDKit

This fork involves removing our dependence on OpenBabel and instead using RDKit.
RDKit is required already for any runs that use QM (highly recommended) and so we may as well make it a global requirement. Then, if we can remove needing OpenBabel as well, that cuts down our dependencies (and OpenBabel can be hard to install, with its Python bindings). RDKit is in Debian, so you should be able to just do `$ sudo apt-get install python-rdkit librdkit1 rdkit-data` on Ubuntu, and there's a nice homebrew recipe for MacOS X. See [rdkit instructions](http://www.rdkit.org/docs/index.html) for more help installing.

This fork should solve a number of bugs:

* #86 - Drawing of fused rings buggy
* #90 - molecule.fromSMILES(CC1=CC=CO1) gives "Unable to determine atom type for atom O."
* #121 - Furan inchi and SMILES cannot be resolved

It may also help in the future with

* #106 - Aromaticity detection problems in thermo?

NB1. Anything that is read in using RDKit (eg. from an InChI or SMILES) is Kekulized before making the RMG molecule.
This means if you input benzene as `SMILES="c1ccccc1"` it will be equivalent to `SMILES="C1=CC=CC=C1"`. This is how we fix issues #90 and #121, but it does make it harder if you *do* want aromatic things like benzene. If you want `B` type bonds, you have to input it as an adjacency list.
What *should* happen is that RMG detects aromaticity correctly on its own, and it doesn't matter how you input it, but that's issue #106 and not addressed here!

NB2. Before pushing to the webserver, make sure you have installed RDkit.

This is not quite ready to merge, but should be soon.