RDKit.rb

Cheminformatics for Ruby, powered by RDKit

Installation

Add this line to your application’s Gemfile:

gem "rdkit-rb"

Getting Started

Create a molecule

mol = RDKit::Molecule.from_smiles("c1ccccc1O")

Get the number of atoms

mol.num_atoms

Get substructure matches

mol.match(RDKit::Molecule.from_smarts("ccO"))

Get fragments

mol.fragments

Generate an SVG

mol.to_svg

Fingerprints

A number of fingerprints are supported.

RDKit

mol.rdkit_fingerprint

Morgan

mol.morgan_fingerprint

Pattern

mol.pattern_fingerprint

Atom pair

mol.atom_pair_fingerprint

Topological torsion

mol.topological_torsion_fingerprint

MACCS

mol.maccs_fingerprint

You can use a library like pgvector-ruby to find similar molecules. See an example.

Updates

Add or remove hydrogen atoms

mol.add_hs!
mol.remove_hs!

Standardize

mol.cleanup!
mol.normalize!
mol.neutralize!
mol.reionize!
mol.canonical_tautomer!
mol.charge_parent!
mol.fragment_parent!

Conversion

SMILES

mol.to_smiles

SMARTS

mol.to_smarts

CXSMILES

mol.to_cxsmiles

CXSMARTS

mol.to_cxsmarts

JSON

mol.to_json

Reactions

Create a reaction

rxn = RDKit::Reaction.from_smarts("[CH3:1][OH:2]>>[CH2:1]=[OH0:2]")

Generate an SVG

rxn.to_svg

History

View the changelog

Contributing

Everyone is encouraged to help improve this project. Here are a few ways you can help:

• Report bugs
• Fix bugs and submit pull requests
• Write, clarify, or fix documentation
• Suggest or add new features

To get started with development:

git clone https://github.com/ankane/rdkit-ruby.git
cd rdkit-ruby
bundle install
bundle exec rake vendor:all
bundle exec rake test