Rcdk - The Ruby Interface for the Chemistry Development Kit (CDK)

RCDK makes it possible to use the Chemistry Development Kit (CDK) from Ruby. CDK is a Java library for chemical informatics.

Installation

Add this line to your application's Gemfile:

gem 'rcdk', "=0.4.1", :git => "https://github.com/HITS-SDBV/rcdk.git", :version => "v0.4.1"

And then execute:

$ bundle install

Usage

require 'rubygems'
require_gem 'rcdk'
require 'rcdk/util'
mol = RCDK::Util::Lang.read_smiles 'c1ccccc1'
puts mol.getAtomCount # =>6

Development

After checking out the repo, run bin/setup to install dependencies. Then, run rake test to run the tests. You can also run bin/console for an interactive prompt that will allow you to experiment.

To install this gem onto your local machine, run bundle exec rake install. To release a new version, update the version number in version.rb, and then run bundle exec rake release, which will create a git tag for the version, push git commits and tags, and push the .gem file to rubygems.org.

development environment with vagrant

You can use the provided vagrant environment to develop in the project:

git submodule update --init --recursive
cd vagrant
vagrant --extra-vars-file=../ansible_vars.yml --ansible-playbook=../ansible_site.yml --vmname=rcdk --cpus=2 --memory=4096 --nfs up
vagrant ssh

If the provision process appears to be hanging (e.g. does not make progress) you can temrinate the process (Ctrl+C) and provision again:

vagrant halt
vagrant --extra-vars-file=../ansible_vars.yml --ansible-playbook=../ansible_site.yml --vmname=rcdk --cpus=2 --memory=4096 --nfs up --provision

This will restart the provisioning process - and ansible will take care of finishing unfinished steps.

vagrant ssh

You are in the virtual machine and you can find this project mounted in /project You can start eclipse with

cd /project # this is important to set the proper ruby version and GEM_HOME
~/sw/eclipse/4.5/eclipse/eclipse

To shutdown (after logout) and resume use:

vagrant halt
vagrant --vmname=rcdk --cpus=2 --memory=4096 --nfs up

With every git pull, it might be necessary to update the submodule also; git status should show if it is necessary also, since the roles might be installed from ansible-galaxy in new versions, the 'old' ones need to be removed ansible-galaxy does not have a lock feature with versions yet

git submodule update
rm -r -- vagrant/ansible/roles/*/

Contributing

Bug reports and pull requests are welcome on GitHub at https://github.com/HITS-SDBV/rcdk. This project is intended to be a safe, welcoming space for collaboration, and contributors are expected to adhere to the Contributor Covenant code of conduct.

License

CDK is distributed under the GNU LGPL version 2.1 (see 'LICENSE'). It contains bytecode from the following sources: -Chemistry Development Kit (CDK), licensed under the LGPL: http://cdk.sf.net -OPSIN, licensed under the Artistic License: http://sourceforge.net/projects/oscar3-chem/ -Structure-CDK, licensed under the LGPL: http://sf.net/projects/structure