= rubabel

Ruby interface to the openbabel ruby bindings (or the openbabel gem).  The
interface attempts to be a ruby-ish analogue of
{pybel}[http://openbabel.org/docs/current/UseTheLibrary/Python_PybelAPI.html].

== Examples

    Rubabel.foreach("file.sdf") do |mol|
      print mol.write  # -> canonical smiles: "smiles_string\tname\n"
      puts mol  # .to_s -> canonical smiles string with no name or newline
      puts mol.exact_mass
    end

    uniq_atom_types = Rubabel.foreach("file.mol").map(&:type).uniq

== Installing

First, many thanks to Andreas Maunz for packaging openbabel as a gem which makes this install quite painless.

=== Quick Install

On a POSIX system, make sure you have openbabel (including header files), cmake, curl, tar, sed and make {see openbabel instructions}[https://github.com/amaunz/openbabel-gem].  On ubuntu/debian:

    sudo apt-get install openbabel libopenbabel-dev cmake make curl

Then install the gem (which should install the openbabel gem, too):

    gem install rubabel

=== Building from Source

1. download openbabel 
2. swap out Init_OpenBabel for Init_openbabel in scripts/ruby/openbabel-ruby.cpp (see here[http://forums.openbabel.org/Ruby-Open-Babel-in-2-1-1-td957640.html]).  Some versions have this fixed already, apparently.
3. make sure you have the right {dependencies to compile}(http://openbabel.org/docs/2.3.1/Installation/install.html#compiling-open-babel)

Here's a complete example of compiling for a single user on Ubuntu 11.10 and probably will be generally forward compatible for some time.  This will compile bindings on whichever ruby comes up with '/usr/bin/env ruby':

    # install the dependencies:
    sudo apt-get install libeigen2-dev cmake libwxgtk2.8-dev libxml2-dev libcairo2-dev
    # unpack it:
    tar -xzvf openbabel-2.3.1.tar.gz
    # swap out buggy lines in ruby bindings:
    sed -i 's/Init_OpenBabel/Init_openbabel/g' openbabel-2.3.1/scripts/ruby/openbabel-ruby.cpp
    # make a separate build directory for building in:
    mkdir build-rvmruby1.9.3
    cd build-rvmruby1.9.3
    mkdir ~/tools
    cmake ../openbabel-2.3.1 -DRUBY_BINDINGS=ON -DCMAKE_INSTALL_PREFIX=~/tools/openbabel-rvmruby1.9.3
    make && make install

[I still need to make directions to install the gem on top of a build from source]
 
== Copyright

MIT License.  See LICENSE for further details.