molecules 0.1.3 → 0.2.0

data/lib/molecules/calc.rb

@@ -1,4 +1,5 @@
-require 'molecules/empirical_formula'
+require 'tap/task'
+require 'molecules/empirical_formula'
 require 'molecules/libraries/polypeptide'
 
 # patch for ruby units
@@ -7,29 +8,37 @@ class Unit < Numeric # :nodoc:
   UNIT_DEFINITIONS['<dalton>'] = [%w{Da Dalton Daltons dalton daltons}, 1/6.0221415e26, :mass, %w{<kilogram>}]
 end
 Unit.setup
-
-module Molecules
-
-  # :startdoc::manifest a mass calculator
-  #
-  # Calculates the mass of a molecule.  Compound formulae are allowed and you may
-  # specify a list of formulae. The options can be used to alter the output (precision, 
-  # mass calculation method etc.)
-  #
-  #   % tap run -- molecules/calc H2O
-  #     I[17:08:00]   18.0105646863 Da H2O
+
+module Molecules
+
+  # :startdoc::task a mass calculator
+  #
+  # Calculates the mass of a molecule or formula. The options can be used to
+  # alter the output (precision,  mass calculation method etc.)
+  #
+  #   % tap run -- molecules/calc H2O --: dump
+  #   18.0106 Da
+  #   
+  #   % tap run -- molecules/calc "NH3 + H2O" --precision 2 --: dump
+  #   35.04 Da
+  #
+  # Units can carry prefixes (ex 'mm', 'kg').  See {Ruby Units}[http://ruby-units.rubyforge.org/ruby-units/]
+  # for more information.
+  #
+  #   % tap run -- molecules/calc H2O --units yg --precision 2 --: dump
+  #   29.91 yg
   #
-  #   % tap run -- molecules/calc H2O --units yg --precision 6
-  #     I[17:08:21]       29.907243 yg H2O
-  #
-  #   % tap run -- molecules/calc 'C3H5NO + H2O' C50H73N15O11 -p 2
-  #     I[17:08:53]           89.05 Da C3H5NO + H2O
-  #     I[17:08:53]         1059.56 Da C50H73N15O11
-  #
-  class Calc < Tap::Task
-  
-    config :type, :monoisotopic                             # the mass type calculated
-    config :precision, nil, :short => 'p'                   # the precision of the mass
+  # Note that Calc returns instances of Unit, which by default prints itself
+  # with a precison of 4.  To view the full-precision value, inspect the scalar
+  # value of the result.
+  #
+  #   % tap run -- molecules/calc H2O --: inspect -m scalar
+  #   18.0105646863
+  #
+  class Calc < Tap::Task
+  
+    config :type, :monoisotopic                             # the mass type calculated
+    config :precision, nil, :short => 'p'                   # the precision of the mass
     config :units, "Da", :short => 'u', &c.string           # the mass unit reported
     config :composition, false, :short => 'c', &c.flag      # reports the composition, not the formula
     
@@ -40,27 +49,23 @@ module Molecules
       EmpiricalFormula.parse(formula)
     end
     
-    # Returns an array of the calculated masses, in the correct unit.
-    def process(*formulae)
-      formulae.collect do |formula_str|
-        mass = parse(formula_str).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
+    # Returns an array of the calculated masses, in the correct unit.
+    def process(formula)
+      mass = parse(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.scalar} #{mass.units}", composition ? formula : formula_str
-
-        mass
-      end
+      mass = Unit.new(mass, "Da").convert_to(units)
+      unless precision == nil
+        mass = Unit.new( Utils.round(mass.scalar, precision), units) 
+      end
+
+      mass
     end
-    
-  end
+    
+  end
 end

data/lib/molecules/empirical_formula.rb

@@ -299,7 +299,7 @@ module Molecules
     # - Masses are calculated such that mathematical operations 
     #   are performed on the return of the block.
     # 
-    def mass(&block)
+    def mass(&block) # :yields: element
       if block_given? 
         mass = 0
         each {|e, n| mass = (yield(e) * n) + mass }

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification 
 name: molecules
 version: !ruby/object:Gem::Version 
-  version: 0.1.3
+  version: 0.2.0
 platform: ruby
 authors: 
 - Simon Chiang
@@ -9,7 +9,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2008-10-13 00:00:00 -06:00
+date: 2009-05-06 00:00:00 -06:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency 
@@ -30,7 +30,7 @@ dependencies:
     requirements: 
     - - ">="
       - !ruby/object:Gem::Version 
-        version: 0.10.8
+        version: 0.17.0
     version: 
 description: 
 email: simon.a.chiang@gmail.com
@@ -73,7 +73,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
 requirements: []
 
 rubyforge_project: bioactive
-rubygems_version: 1.2.0
+rubygems_version: 1.3.1
 signing_key: 
 specification_version: 2
 summary: A library of molecules for scientific calculations in Ruby.