rubabel

Ruby interface to the OpenBabel ruby bindings (or the openbabel gem). The interface attempts to be a ruby-ish analogue of pybel. Works with ruby 1.9 and 2.0.

Examples

The Chemistry Toolkit Rosetta Wiki has a lot of examples you can check out.

Creating a molecule

From a string

“by require ‘rubabel’

by default, reads in smiles strings

serine = Rubabel[C(C(C(=O)O)N)O]

more formally:

serine = Rubabel::Molecule.from_string(“C(C(C(=O)O)N)O”)

also any other format openbabel supports, for example inchi

serine = Rubabel[InChI=1S/C3H7NO3/c4-2(1-5)3(6)7/h2,5H,1,4H2,(H,6,7), :inchi]

from the internet:

mol = Rubabel[some_molecule, Rubabel.format_from_mime(some_mime_type)]

Find out all the formats Rubabel supports (hash is format key pointing to the description):

hash = Rubabel.in_formats hash = Rubabel.out_formats

“

From a file

Reading multiple entries from a file:

“by Rubabel.foreach(“file.sdf”) do |mol| puts mol.exact_mass end

“

Foreach returns an enumerator that can be chained:

“by

return an array of every unique atom type in the file

uniq_atom_types = Rubabel.foreach(“file.mol”).flat_map {|mol| mol.map(&:type) }.uniq

“

Read a single molecule from a file (reads only the first molecule)

“by mol = Rubabel::Molecule.from_file(“file.sdf”)

handles gzipped files seamlessly:

mol = Rubabel::Molecule.from_file(“file.sdf.gz”) mol = Rubabel.molecule_from_file(“file.sdf”) # alternative

explicit format for uninformative/wrong extensions:

mol = Rubabel::Molecule.from_file(“file”, :sdf)

“

Writing/Drawing

create string output

“by mol = Rubabel[OCC] # ethanol

mol.to_s # canonical smiles -> “CCO” mol.csmiles # same thing

mol.to_s(:smi) # smiles -> “OCC” mol.smiles # same thing

“

For inclusion in a file with standard smiles formatting (SMILES\tID\n):

“by can_smiles_string = mol.write_string # -> “CCO\t\n” mol.title = “ethanol” can_smiles_string = mol.write(:can) # -> “CCO\tethanol\n”

“

Other formats in the same manner:

“by pdb_string = mol.write(:pdb)

“

Write to a file directly (single molecule only; depends on file extension for type):

“by

write to a smiles file

mol.write(“file.smi”) mol.write_file(“file.smi”)

“

Write multiple molecules to a file:

“by File.open(“somefile.pdb”, ‘w’) do |out| molecules.each {|mol| out.print mol.write(:pdb) } end

“

Drawing

If you write to svg or png (png uses mini_magick to convert from svg) then the molecule is automatically drawn in 2D:

“by mol = Rubabel[NCC(O)C(=O)O] mol.write(“file.svg”)

must have imagemagick (‘convert’ command) and mini_magick gem installed

mol.write(“file.png”)

“

Searching and Splitting

each_match, matches, matches?, smarts_indices all take the same input (SMARTS string or object and optional boolean specifying uniqueness of results):

“by mol = Rubabel[NCC(O)C(=O)O] mol.each_match(“CO”) do |match| # match is just an array of atoms that matched match.first.el # => :C match.last.el # => :O end

matches returns all the matches in an array

all_matches = mol.matches(“CO”)

all the match routines take a boolean to alter uniqueness

all_matches = mol.matches(“CO”, false) # some matches may not be uniq

“

Have some bonds to break?, split makes new molecules split from that bond(s)

“by bonds = mol.matches(“CO”).map {|c, o| c.get_bond(o) } mol.split(bonds) # splits between every carbon single bonded to oxygen

“

Add, delete, modify atoms/bonds

Adding

“by mol = Rubabel[OCC]

adds a carbon, then an oxygen to the previous carbon

mol « 6 « 8 # #

Maruku could not parse this XML/HTML: 
<Mol "OCCCO">
mol

add an ethyl group specifically to second atom (the first carbon)

mol = Rubabel[OCC] mol[1] « :C « :C

add a vinyl group to second carbon (use method notation and parenthesis

because we are going to specify 2 arguments (the bond order):

( mol[1] « :C).«(:C, 2)

“

Deleting

“by

delete an atom:

mol = Rubabel[NCO] mol.delete(mol[0])

mol.to_s -> #
Maruku could not parse this XML/HTML: 
<Mol CO>

delete a bond:

bond = mol[0].get_bond(mol[1]) mol.delete(bond)

mol.to_s -> #
Maruku could not parse this XML/HTML: 
<Mol C.O>

“

Modifying

Can easily change the bond order:

“by mol = Rubabel[CC] bond = mol[0].get_bond(mol[1]) # get the bond you want bond = mol[0].bonds.first # alternate way to get at bonds

bond += 2 # now it is a triple bond bond.dec! # now a double bond bond -= 1 # now a single bond bond.inc!(2) # back to a triple bond

“

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 openbabel instructions[https://github.com/amaunz/openbabel-gem]. On ubuntu/debian:

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

“

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

“sh 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). Some versions have this fixed already, apparently.
  3. make sure you have the right dependencies to compile

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’:

“sh

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

“

See also

MIT License. See LICENSE for further details.