bin/fragmenter.rb in rubabel-0.2.1 vs bin/fragmenter.rb in rubabel-0.2.2

@@ -2,42 +2,66 @@
 
 require 'trollop'
 require 'rubabel'
 require 'rubabel/molecule/fragmentable'
 
+default_ph = 2.5
 
+Fragment = Struct.new(:frag, :id, :title, :mz, :mass, :charge, :smiles, :pairing)
+
 parser = Trollop::Parser.new do
   banner "usage: #{File.basename($0)} [OPTIONS|RULES] <SMARTS> ..."
   text "\noptions:"
-  opt :ph, "the pH to use (experimental option)", :default => Rubabel::Molecule::Fragmentable::DEFAULT_OPTIONS[:ph]
+  opt :ph, "the pH to use (experimental option)", :default => default_ph
+  opt :images, "print out svg images of fragments" 
+  opt :format, "format of the molecules", :default => 'smiles'
   #opt :uniq, "no repeated fragments", :default => false
   text "\nrules:"
   Rubabel::Molecule::Fragmentable::RULES.each do |rule|
     opt rule, rule.to_s.gsub("_",' ')
   end
   text "\nexample:"
-  text "fragmenter.rb -aecsoxn 'CCC(=O)OCCC' 'CCC(=O)OCCC(=O)O'"
+  text "fragmenter.rb -xeh 'CCC(=O)OCCC' 'CCC(=O)OCCC(=O)O'"
 end
 
-rules = parser.parse(ARGV)
-options = {rules: []}
-options[:ph] = rules.delete(:ph)
-options[:uniq] = rules.delete(:uniq)
-rules.each do |k,v|
-  options[:rules] << k if v && k.to_s !~ /_given/
-end
+options = parser.parse(ARGV)
+opts = {rules: []}
+opts[:uniq] = options.delete(:uniq)
+ph = options.delete(:ph)
+opts[:rules] = Rubabel::Molecule::Fragmentable::RULES.map do |rule|
+  rule if options["#{rule}_given".to_sym]
+end.compact
 
 if ARGV.size == 0
   parser.educate && exit
 end
 
-ARGV.each do |mol|
-  mol = Rubabel[mol]
+ARGV.each do |smiles|
+  mol = Rubabel[smiles, options[:format].to_sym]
   puts "\nmolecule: #{mol.csmiles}"
-  fragment_sets = mol.fragment(options)
-  fragment_sets.each do |frag_set|
-    puts ""
-    frag_set.each do |frag|
-      puts "#{frag.mass.round(5)} #{frag.csmiles}"
+  mol.correct_for_ph!(ph)
+  puts "at ph #{ph}: #{mol.csmiles}"
+  fragment_sets = mol.fragment(opts)
+  puts %w(mz mass charge title smiles pairing).join("\t")
+  frags = []
+  fragment_sets.each_with_index do |frag_set,i|
+    frag_set.each_with_index do |frag,j|
+      unless frag.charge == 0
+        mz = (frag.mass / frag.charge).round(5)
+      end
+
+      frag.title = "#{i}-#{j}pair_" + (mz ? "#{mz}_mz" : "#{frag.mass.round(3)}_Mass")
+      frag_obj = Fragment.new(frag, frag.title, frag.title, mz, frag.exact_mass, frag.charge, frag.csmiles, i)
+      frags << frag_obj
     end
+  end
+  frags = frags.sort_by {|frag| [-frag.charge, frag.mz] }
+  if options[:images]
+    frags.each do |frag|
+      fn = "#{frag.title}.png"
+      frag.frag.write(fn)
+    end
+  end
+  frags.each do |frag|
+    puts [:mz, :mass, :charge, :title, :smiles, :pairing].map {|cat| frag.send(cat) }.join("\t")
   end
 end