Class: Molecules::Calc

Inherits:
Tap::Task
  • Object
show all
Defined in:
lib/molecules/calc.rb

Overview

:startdoc::manifest a mass calculator Calculates the mass of a molecule or empirical formula. The options can be used to alter the output (precision, mass calculation method etc.) You may enter compound formulae, or a list of formulae. In addition, polypeptides can be specified using the one-letter residue codes:

% tap -- molecules/calc H2O
  I[17:09:00]   18.0105646863 Da H2O

% tap -- molecules/calc H2O -u kg
  I[13:35:59]    2.99072e-026 kg H2O

% tap -- molecules/calc 'C3H5NO + H2O' C50H73N15O11 -p 2
  I[17:08:21]           89.05 Da C3H5NO + H2O
  I[17:08:21]         1059.56 Da C50H73N15O11

% tap -- molecules/calc :RPPGFSPFR
  I[13:35:02]         1059.56 Da :RPPGFSPFR

Furthermore, if a unimod path is specified in the configurations, unimod modifcations may be specified by name as the polypeptide termini. Use ‘%’ signs as in a SQL query to shorten the name:

% tap -- molecules/calc 'Acetyl:RPPGFSPFR:Hydroxyl%' --unimod-path <...>
  I[13:33:25]         1059.56 Da Acetyl:RPPGFSPFR:Hydroxyl%

The unimod path must point to an sqlite3 ActiveUnimod database, and sqlite3-ruby must be installed for this feature to work.

* ActiveUnimod[http://bioactive.rubyforge.org/]
* sqlite3-ruby[http://rubyforge.org/projects/sqlite-ruby/]

Constant Summary collapse

WATER = 
EmpiricalFormula.parse "H2O"
HYDROGEN = 
EmpiricalFormula.parse "H"
HYDROXIDE = 
EmpiricalFormula.parse "OH"

Instance Method Summary collapse

Instance Method Details

#find_mod(code_name) ⇒ Object

Attempts to find and instantiate an EmpiricalFormula for a unimod modification matching code_name.



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# File 'lib/molecules/calc.rb', line 71

def find_mod(code_name)
  raise "no unimod_path was specified" if unimod_path == nil
  require 'sqlite3' unless Object.const_defined?(:SQLite3)
  
  results = []
  db = SQLite3::Database.new(unimod_path)
  db.execute(mod_query(code_name)) do |row|
    results << row
  end
  db.close
  
  case results.length
  when 1 then EmpiricalFormula.parse_simple(results[0][1])
  when 0 then raise "could not find modification: #{code_name}"
  else raise "multiple modifications found for: #{code_name} (#{results.collect {|result| result[0]}.join(', ')})"
  end
end

#mod_query(code_name) ⇒ Object

Formulates a query for a modification matching code_name for the unimod database. If the code_name contains a ‘%’ then the query will use a LIKE syntax, otherwise the code_name will be searced for exactly.



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# File 'lib/molecules/calc.rb', line 64

def mod_query(code_name)
  # should do a rails-like escape on code_name

  "SELECT code_name, composition FROM modifications WHERE code_name #{code_name.include?('%') ? 'LIKE' : '='} '#{code_name}'"
end

#process(*formulae) ⇒ Object

Returns an array of the calculated masses, in the correct unit.



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# File 'lib/molecules/calc.rb', line 94

def process(*formulae)
  formulae.collect do |formula_str|
    formula = EmpiricalFormula.parse(formula_str) do |str|
      case str
      when /^(.*?):([A-Z]+):?(.*)$/
        peptide = Libraries::Polypeptide.new($2) + WATER
        peptide += find_mod($1) unless $1.to_s.empty? 
        peptide += find_mod($3) unless $3.to_s.empty?
        peptide
      else nil
      end
    end

    mass = formula.mass do |element|
      case type
      when :monoisotopic then element.mass
      when :average then element.std_atomic_weight.value
      else raise "unknown mass type: #{type}"
      end
    end

    mass = Unit.new(mass, "Da").convert_to(units)
    unless precision == nil
      mass = Unit.new( Utils.round(mass.scalar, precision), units) 
    end
    
    log mass, composition ? formula : formula_str

    mass
  end
end