README
= 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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- Rubyforge[http://rubyforge.org/projects/bioactive]
- Lighthouse[http://bahuvrihi.lighthouseapp.com/projects/13518-molecules/overview]
- Github[http://github.com/bahuvrihi/molecules/tree/master]
== 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[http://tap.rubyforge.org] 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[http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification] 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[http://rubyforge.org/projects/bioactive]. Use:
% gem install molecules
== Info
Copyright (c) 2006-2008, Regents of the University of Colorado. Developer:: {Simon Chiang}[http://bahuvrihi.wordpress.com], {Biomolecular Structure Program}[http://biomol.uchsc.edu/], {Hansen Lab}[http://hsc-proteomics.uchsc.edu/hansenlab/] Support:: CU Denver School of Medicine Deans Academic Enrichment Fund Licence:: MIT-Style