Molecules

A library of molecules for scientific calculations in Ruby.

Description

Molecules provides libraries of commonly used molecules (currently just amino acid residues and polypeptides). Library classes inherit from EmpiricalFormula which allows calculation of molecular composition and mass, as well as adding/subtraction of other molecules.

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Usage

require 'molecules'
include Molecules::Libraries
# Residue predefines all common amino acids
# as well as some uncommon ones.
r = Residue::A
r.name               # => "Alanine"
r.abbr               # => "Ala"
r.letter             # => "A"
r.side_chain.to_s    # => "CH(3)"
r.mass               # => 71.03711
r.immonium_ion_mass  # => 44.0500
# Polypeptide allows for creation of polypeptides
# from residue sequences.
p = Polypeptide.new("RPPGFSPFR")
p.to_s               # => "C(50)H(71)N(15)O(10)"
p.mass               # => 1041.5508
# Generic molecules may be specified with EmpiricalFormula.
caffeine = Molecules::EmpiricalFormula.parse("C8H10N4O2")
coffee = Molecules::EmpiricalFormula.parse("C8H10N4O2 + H2O")

Mass Calculator (tap task)

Molecules provides a mass calculator tap task. Tap is not required by molecules in general, but you get this bonus if you have tap installed:

% tap run -- molecules/calc H2O
  I[17:08:00]   18.0105646863 Da H2O

Known Issues

Polypeptide only allows common residues
No ‘Molecule’ class is defined, pending the potential addition of more molecule data (ex: SMILES data)
No mechanism for defining large libraries of molecules has been chosen. A database solution may be adopted to this end.

Installation

Molecules is available as a gem through RubyForge. Use:

% gem install molecules

Info

Developer: Simon Chiang, Biomolecular Structure Program, Hansen Lab
Support: CU Denver School of Medicine Deans Academic Enrichment Fund
Licence: MIT-Style