rubabel 0.3.0 → 0.4.0

checksums.yaml

@@ -0,0 +1,7 @@
+---
+SHA1:
+  metadata.gz: 6e50e4f083ed06992600b2b86767d0d3a2b00fcf
+  data.tar.gz: e2b4f65a73450c8336b31d650c3c4bfff6981942
+SHA512:
+  metadata.gz: a1e131cbc6b178f52ea340acc11ca1b48b606846cdfe3f21609e9578c7b7ecbd9f5590655c988a1098bc7356e9089a930c5570dc359df09f6384f4349d69c65f
+  data.tar.gz: e626626e6f236810a4e46e41bdcf63da8927e8bfe0bc2d8b271c915ba2fc48dc898012eccf0c535f2b5c95dd1281e3be2c1d99c27c53f9779811613da191629b

data/.gitignore

@@ -0,0 +1,49 @@
+# rcov generated
+coverage
+coverage.data
+
+# rdoc generated
+rdoc
+
+# yard generated
+doc
+.yardoc
+
+# bundler
+.bundle
+
+# jeweler generated
+pkg
+
+# Have editor/IDE/OS specific files you need to ignore? Consider using a global gitignore: 
+#
+# * Create a file at ~/.gitignore
+# * Include files you want ignored
+# * Run: git config --global core.excludesfile ~/.gitignore
+#
+# After doing this, these files will be ignored in all your git projects,
+# saving you from having to 'pollute' every project you touch with them
+#
+# Not sure what to needs to be ignored for particular editors/OSes? Here's some ideas to get you started. (Remember, remove the leading # of the line)
+#
+# For MacOS:
+#
+#.DS_Store
+
+# For TextMate
+#*.tmproj
+#tmtags
+
+# For emacs:
+#*~
+#\#*
+#.\#*
+
+# For vim:
+.*.swp
+
+# For redcar:
+#.redcar
+
+# For rubinius:
+#*.rbc

data/Gemfile

@@ -0,0 +1,4 @@
+source 'https://rubygems.org'
+
+# Specify your gem's dependencies in rubabel.gemspec
+gemspec

data/Rakefile

@@ -1,36 +1,4 @@
-# encoding: utf-8
-
-require 'rubygems'
-require 'rake'
-
-require 'jeweler'
-Jeweler::Tasks.new do |gem|
-  # gem is a Gem::Specification... see http://docs.rubygems.org/read/chapter/20 for more options
-  gem.name = "rubabel"
-  gem.homepage = "http://github.com/princelab/rubabel"
-  gem.license = "MIT"
-  gem.summary = %Q{Ruby interface to the OpenBabel ruby bindings similar to pybel}
-  gem.description = %Q{Ruby interface to the openbabel ruby bindings (or the openbabel gem).  The
-interface attempts to be a ruby-ish analogue of pybel.}
-  gem.email = "jtprince@gmail.com"
-  gem.authors = ["John T. Prince"]
-  [
-    ["openbabel", "~> 2.3.1.2"],
-    ["andand", "~> 1.3.3"],
-    ["mini_magick", "~> 3.4"]
-  ].each do |args|
-    gem.add_dependency(*args)
-  end
-
-  [
-    ["rspec", "~> 2.13.0"], 
-    ["rdoc", "~> 3.12"], 
-    ["jeweler", "~> 1.8.3"]
-  ].each do |args|
-    gem.add_development_dependency(*args)
-  end
-end
-Jeweler::RubygemsDotOrgTasks.new
+require "bundler/gem_tasks"
 
 require 'rspec/core'
 require 'rspec/core/rake_task'

data/VERSION

@@ -1 +1 @@
-0.3.0
+0.3.1

data/lib/rubabel.rb

@@ -1,3 +1,4 @@
+require 'rubabel/version'
 require 'openbabel'
 require 'rubabel/molecule'
 

data/lib/rubabel/atom.rb

@@ -141,9 +141,10 @@ module Rubabel
     end
     alias_method :charge=, :formal_charge=
 
-    def heavy_valence
-      @ob.get_heavy_valence
-    end
+    # not recognizing get_heavy_valence right now for some reason
+    #def heavy_valence
+    #  @ob.get_heavy_valence
+    #end
 
     def hetero_valence
       @ob.get_hetero_valence
@@ -165,31 +166,75 @@ module Rubabel
       @ob.get_partial_charge
     end
 
-    # permanently removes a hydrogen by properly incrementing the
-    # spin_multiplicity (and deleting a hydrogen if one is explicitly attached
-    # to the atom).  If called with cnt=2 a carbene or nitrene can be made
-    # (giving a spin_multiplicity of 3).  Makes no effort to ensure that the
-    # proper number of hydrogens already exist to be deleted, just alters the
-    # spin_multiplicity and deletes the right number of hydrogens if they are
-    # available to be deleted.  Adds one charge to the atom.
-    def remove_an_h!(add_charge=true)
-      new_spin = 
-        case @ob.get_spin_multiplicity
-        when 0 then 2
-        when 2 then 3
+    # doesn't take into account pH (use Molecule#do_without_hydrogens)
+    def do_without_hydrogens(&block)
+      _obmol = @ob.get_parent
+      had_hydrogens = _obmol.has_hydrogens_added
+      _obmol.delete_hydrogens(self.ob) if had_hydrogens
+      reply = block.call(had_hydrogens)
+      _obmol.add_hydrogens(self.ob) if had_hydrogens
+      reply
+    end
+
+    # doesn't take into account pH (use Molecule#do_with_hydrogens)
+    def do_with_hydrogens(&block)
+      _obmol = @ob.get_parent
+      had_hydrogens = _obmol.has_hydrogens_added
+      _obmol.add_hydrogens(self.ob) unless had_hydrogens
+      reply = block.call(had_hydrogens)
+      _obmol.delete_hydrogens(self.ob) unless had_hydrogens
+      reply
+    end
+
+    def remove_a_proton!(add_placeholder_hydrogens=false)
+      remove_a_hydrogen!(0, add_placeholder_hydrogens)
+    end
+
+    def remove_a_hydrogen!(with_num_electrons=1, add_placeholder_hydrogens=false)
+      self.dec_implicit_valence!
+      case with_num_electrons
+      when 0
+        self.charge -= 1
+      when 1
+        raise NotImplementedError, "not doing free radicals just yet"
+      when 2
+        self.charge += 1
+      end
+      if @ob.explicit_hydrogen_count > 0
+        _obmol = @ob.get_parent
+        each do |atom|
+          if atom.hydrogen?
+            _obmol.delete_atom(atom.ob, false)
+            break
+          end
         end
-      @ob.set_spin_multiplicity(new_spin)
-      atoms.each do |atom|
-        if atom.hydrogen?
-          self.mol.delete_atom(atom)
-          break
+      else
+        if add_placeholder_hydrogens
+          @ob.get_parent.add_hydrogens(@ob)
         end
       end
-      # add the charge
-      (self.charge = charge + 1) if add_charge
       self
     end
 
+    # removes a proton with its electrons from an atom.
+    # This gives precisely the same molecule as if the molecule were input by
+    # smiles.  csmiles, formula, exact_mass, valence, implicit_valence, etc.
+    #
+    #     mol = Rubabel["CC"]
+    #     mol[1].remove_a_hydride!
+    #     mol == Rubabel["C[CH2+]"]  # in all characteristics
+    #
+    # Note, however, that with explicit hydrogens, the <b>partial charge</b>
+    # is not matching up, even though every other property seems to be.  I'm
+    # not sure why this is.
+    #
+    #     mol == Rubabel["C[CH2+]"].add_h!
+    #     mol[1].remove_a_hydride!
+    #     mol == Rubabel["C[CH2+]"].add_h!  # identical except in partial charge!
+    def remove_a_hydride!(add_placeholder_hydrogens=false)
+      remove_a_hydrogen!(2, add_placeholder_hydrogens)
+    end
+
     # philosophy on equality: there are *so* many ways for two atoms to be
     # different that we can never really ensure that "equivalence" is met
     # without calling ~20 methods.  We narrowly define equivalence so it is
@@ -250,10 +295,32 @@ module Rubabel
       @ob.get_type
     end
 
+    # Returns the current number of explicit connections.  Don't confuse this for
+    # implicit_valence.
     def valence
       @ob.get_valence
     end
 
+    # maximum number of connections expected for this atom
+    def implicit_valence
+      @ob.get_implicit_valence
+    end
+
+    # set the maximum number of connections expected for this atom
+    def implicit_valence=(val)
+      @ob.set_implicit_valence(val)
+    end
+
+    # increase by one the maximum number of connections expected for this atom
+    def inc_implicit_valence!
+      @ob.increment_implicit_valence
+    end
+
+    # decrease by one the maximum number of connections expected for this atom
+    def dec_implicit_valence!
+      @ob.decrement_implicit_valence
+    end
+
     def vector
       @ob.get_vector
     end
@@ -297,6 +364,13 @@ module Rubabel
       @ob.implicit_hydrogen_count + @ob.explicit_hydrogen_count
     end
 
+    def implicit_hydrogen_count
+      @ob.implicit_hydrogen_count
+    end
+
+    def explicit_hydrogen_count
+      @ob.explicit_hydrogen_count
+    end
     alias_method :num_h, :hydrogen_count
 
     def double_bond?
@@ -342,6 +416,5 @@ module Rubabel
       end.compact.join(" ") << ">"
     end
 
-
   end
 end

data/lib/rubabel/molecule.rb

@@ -227,6 +227,25 @@ module Rubabel
     end
     alias_method :h_added?, :hydrogens_added?
 
+    # ensures that hydrogens are added before an operation, but returns the
+    # molecule to the original hydrogen or no hydrogen state when finished.
+    # returns whatever was returned by the block.
+    def do_with_hydrogens(ph=nil, polaronly=false, &block)
+      hydr_added = @ob.has_hydrogens_added
+      add_h!(ph, polaronly) unless hydr_added
+      reply = block.call
+      @ob.delete_hydrogens unless hydr_added
+      reply
+    end
+
+    def do_without_hydrogens(ph=nil, polaronly=false, &block)
+      hydr_added = @ob.has_hydrogens_added
+      @ob.delete_hydrogens if hydr_added
+      reply = block.call
+      add_h!(ph, polaronly) if hydr_added
+      reply
+    end
+
     # returns self.  Corrects for ph if ph is not nil.  NOTE: the reversal of
     # arguments from the OpenBabel api.
     def add_h!(ph=nil, polaronly=false)
@@ -278,10 +297,12 @@ module Rubabel
     #    #alias_method :add_h!, :add_hydrogens!
 
     # returns self
-    def remove_h!
+    def delete_hydrogens!
       @ob.delete_hydrogens
       self
     end
+    alias_method :remove_h!, :delete_hydrogens!
+    alias_method :remove_hydrogens!, :delete_hydrogens!
 
     # returns just the smiles string :smi (not the id)
     def smiles
@@ -671,22 +692,6 @@ module Rubabel
       end
       distance_matrix.max
     end
-
-    # adds 1 hydrogen to the formula and returns self
-    def add_hydrogen_to_formula!
-      string = @ob.get_formula
-      substituted = false
-      new_string = string.sub(/H(\d*)/) { substituted=true; "H#{$1.to_i+1}" }
-      unless substituted
-        new_string = string.sub("^(C?\d*)") { $1 + 'H' }
-      end
-      puts 'HERE'
-      p string
-      p new_string
-      #@ob.set_formula(new_string)
-      self
-    end
-
   end
 end
 

data/lib/rubabel/molecule/fragmentable.rb

@@ -58,11 +58,12 @@ module Rubabel
         nmol = self.dup
         ncarbon = nmol.atom(carbon.id)
         noxygen = nmol.atom(oxygen.id)
+
+        is_carboxyl = noxygen.carboxyl_oxygen?
+        
         nmol.delete_bond(ncarbon, noxygen)
-        ncarbon.remove_an_h!
-        #noxygen.ob.set_spin_multiplicity  1
-        noxygen.spin = 1
-        noxygen.charge = -1
+        ncarbon.remove_a_hydride!
+        noxygen.remove_a_proton! 
         nmol.split
       end
 

data/lib/rubabel/version.rb

@@ -0,0 +1,3 @@
+module Rubabel
+  VERSION = "0.4.0"
+end

data/rubabel.gemspec

@@ -0,0 +1,39 @@
+# coding: utf-8
+lib = File.expand_path('../lib', __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+require 'rubabel/version'
+
+Gem::Specification.new do |spec|
+  spec.name          = "rubabel"
+  spec.version       = Rubabel::VERSION
+  spec.authors       = ["John T. Prince"]
+  spec.email         = ["jtprince@gmail.com"]
+  spec.description   = %q{Ruby interface to the OpenBabel ruby bindings similar to pybel}
+  spec.summary       = %q{Ruby interface to the openbabel ruby bindings (or the openbabel gem).  The
+interface attempts to be a ruby-ish analogue of pybel.}
+  spec.homepage      = "http://github.com/princelab/rubabel"
+  spec.license       = "MIT"
+
+  spec.files         = `git ls-files`.split($/)
+  spec.executables   = spec.files.grep(%r{^bin/}) { |f| File.basename(f) }
+  spec.test_files    = spec.files.grep(%r{^(test|spec|features)/})
+  spec.require_paths = ["lib"]
+
+  [
+    ["openbabel", "~> 2.3.1.2"],
+    ["andand", "~> 1.3.3"],
+    ["mini_magick", "~> 3.6.0"]
+  ].each do |args|
+    spec.add_dependency(*args)
+  end
+  [
+    ["bundler", "~> 1.3"],
+    ["rspec", "~> 2.13.0"], 
+    ["rdoc", "~> 3.12"], 
+    ["jeweler", "~> 1.8.3"],
+    ["simplecov"],
+    ["rake"]
+  ].each do |args|
+    spec.add_development_dependency(*args)
+  end
+end

data/spec/chemistry_toolkit_rosetta/chemistry_toolkit_rosetta_spec.rb

@@ -28,8 +28,8 @@ describe 'Chemistry Toolkit Rosetta Wiki' do
     (png1.size - png2.size < delta)
   end
 
-  def pngs_have_same_header(png1, png2, check_length=60)
-     png1[0..check_length] == png2[0..check_length]
+  def pngs_have_same_header(png1, png2, check_length=18)
+     png1[0,check_length] == png2[0,check_length]
   end
 
   before(:each) do
@@ -269,7 +269,7 @@ describe 'Chemistry Toolkit Rosetta Wiki' do
     File.unlink('3016_highlighted.rubabel.png')
   end
 
-  xspecify 'Align the depiction using a fixed substructure' do
+  specify 'Align the depiction using a fixed substructure' do
     # http://ctr.wikia.com/wiki/Align_the_depiction_using_a_fixed_substructure
 		#TODO
 	end

data/spec/rubabel/atom_spec.rb

@@ -45,24 +45,127 @@ describe Rubabel::Atom do
     (mol.atoms[0].eql?(mol2.atoms[0])).should_not be_true
   end
 
-  it 'removes hydrogens with proper charge accounting' do
-    mol = Rubabel["CC"]
-    mol.add_h!
-    mol.atoms[0].remove_an_h!
-    mol.formula.should == "C2H5"
-    mol.csmiles.should == 'C[CH2+]'
-    mol.exact_mass.round(5).should == 29.03913
-    mol.charge.should == 1
-
-    # can't seem to get working properly!!!
-    #mol.atoms[0].add_an_h!
-    #mol.formula.should == 'C2H6'
-    #mol.csmiles.should == 'CC'
-    #mol.charge.should == 0
-    ##fmol.atoms[0].charge -= 1
-    #mol.exact_mass.should == 323
+
+  describe 'removing protons and hydrides' do
+
+    def are_identical(obs, exp, atom_index)
+      [:formula, :csmiles, :charge, :exact_mass].each do |mol_prop|
+        exp_val = exp.send(mol_prop)
+        obs_val = obs.send(mol_prop)
+        exp_val.is_a?(Float) ? 
+          (obs_val.round(5).should == exp_val.round(5)) :
+          (obs_val.should == exp_val)
+      end
+      
+      [:formal_charge, :implicit_valence, :isotope, :spin, :valence, :partial_charge].each do |prop|
+        obs[atom_index].send(prop).should == exp.atoms[atom_index].send(prop)
+      end
+    end
+
+    context 'on a molecule with implicit hydrogens' do
+      subject { Rubabel["CC"] }
+
+      specify 'removing a hydride' do
+        subject[1].remove_a_hydride!
+        are_identical( subject, Rubabel["C[CH2+]"].remove_h!, 1)
+      end
+
+      specify 'removing a proton' do
+        subject[1].remove_a_proton!
+        are_identical( subject, Rubabel["C[CH2-]"].remove_h!, 1)
+      end
+    end
+
+    context 'on a molecule with explicit hydrogens' do
+      subject { Rubabel["CC"].add_h! }
+
+      specify 'removing a hydride' do
+        subject[1].remove_a_hydride!
+        are_identical( subject, Rubabel["C[CH2+]"].add_h!, 1)
+      end
+
+      specify 'removing a proton' do
+        subject[1].remove_a_proton!
+        are_identical( subject, Rubabel["C[CH2-]"].add_h!, 1)
+      end
+
+      # the :partial_charge is not matching up on these, not sure why!
+      specify 'the atom matches the partial_charge from atom made from smiles'
+    end
   end
 
+
+#  describe 'removing protons and hydrides' do
+#describe 'on molecule with implicit hydrogens' do
+#subject { Rubabel["CC"] }
+
+      #it 'behaves like an ethane carbanion' do
+        ##http://en.wikipedia.org/wiki/Carbanion
+        #ethane_carbanion = Rubabel["C[CH2-]"]
+        #ethane_carbanion.add_h! if subject.hydrogens_added?
+        #[:formula, :csmiles, :charge, :exact_mass].each do |mol_prop|
+          #ethane_carbanion.send(mol_prop).should == subject.send(mol_prop)
+        #end
+        #[:formal_charge, :implicit_valence, :isotope, :partial_charge, :spin, :valence].each do |prop|
+          #ethane_carbanion[1].send(prop).should == subject.atoms[altered_atom_idx].send(prop)
+        #end
+      #end
+    #end
+  #end
+
+    #xit "removes protons on molecule with implicit hydrogens" do
+      #mol = Rubabel["CC"]
+      #mol.atoms[1].remove_a_proton!
+      #include_examples "is ethane carbanion", mol
+    #end
+
+    #xit "removes protons on molecule with explicit H's" do
+      #mol = Rubabel["CC"]
+      #mol.add_h!
+      #mol.atoms[1].remove_a_proton!
+      #mol.formula.should == "C2H5-"
+      #mol.csmiles.should == '[CH2-]C'
+      #mol.exact_mass.round(5).should == 29.03913
+      #mol.charge.should == 1
+    #end
+  #end
+
+  #describe 'properly removing a hydride' do
+    #before do
+      #@ethane = Rubabel["CC"]
+    #end
+
+    #shared_examples "is ethenium" do |mol|
+      ## http://en.wikipedia.org/wiki/Ethenium
+      ## protonated ethylene
+      #ethenium = Rubabel["C[CH2+]"]
+      #ethenium.add_h! if mol.hydrogens_added?
+      #[:formula, :csmiles, :charge, :exact_mass].each do |mol_prop|
+        #ethenium.send(mol_prop).should == mol.send(mol_prop)
+      #end
+      #[:formal_charge, :implicit_valence, :isotope, :partial_charge, :spin, :valence].each do |prop|
+        #ethenium.send(prop).should == mol.send(prop)
+      #end
+    #end
+
+    #it "removes hydrides on molecule with implicit hydrogens" do
+      #@ethane.atoms[1].remove_a_hydride!
+      #include_examples "is ethenium", @ethane
+    #end
+
+    #xit "removes hydrides on molecule with explicit hydrogens" do
+      #@ethane = Rubabel["CC"]
+      #@ethane.add_h!
+      #@ethane.atoms[1].remove_a_hydride!
+      #@ethane.formula.should == "C2H5-"
+      #@ethane.csmiles.should == 'C[CH2-]'
+      #@ethane.exact_mass.round(5).should == 29.03913
+      #@ethane.charge.should == -1
+    #end
+  #end
+
+
+
   it 'can find atom identities with simple questions' do
     mol = Rubabel["NCC(O)CC(=O)"]
     (c_exp, o_exp) = mol.matches("C=O").first

data/spec/rubabel/molecule/fragmentable_spec.rb

@@ -54,23 +54,26 @@ describe Rubabel::Molecule::Fragmentable do
       # oxygen just steals the electron pair it is attached to.  This
       # typically results in a negatively charged oxygen and a positively
       # charged carbo-cation.
-      specify 'ether to ions (same for esters)' do
+      specify 'ether to ions' do
         mol = Rubabel["CCOCCN"]
         frag_set = mol.fragment(rules: [:oxe])
         frags = frag_set.first
         frags.first.csmiles.should == "C[CH2+]"
         frags.last.csmiles.should == '[O-]CC[NH3+]'
-        frags.first.formula.should == 'C2H5'
+        frags.first.formula.should == 'C2H5+'
         frags.last.formula.should == 'C2H7NO'
         frags.first.exact_mass.should be_within(1e-6).of(29.03912516)
         frags.last.exact_mass.should be_within(1e-6).of(61.052763849)
+      end
 
+      specify 'ester to ions' do
         mol = Rubabel["CCOC(=O)CCN"]
         frag_set = mol.fragment(rules: [:oxe])
         ff = frag_set.first
         ff.first.csmiles.should == 'C[CH2+]'
         ff.last.csmiles.should == '[O-]C(=O)CC[NH3+]'
-        ff.first.formula.should == "C2H5"
+        ff.first.formula.should == "C2H5+"
+
         ff.last.formula.should == "C3H7NO2"
         ff.first.exact_mass.should be_within(1e-6).of(29.03912516035)
         ff.last.exact_mass.should be_within(1e-6).of(89.04767846841)
@@ -81,10 +84,13 @@ describe Rubabel::Molecule::Fragmentable do
         frag_set = mol.fragment(rules: [:oxe])
         ff = frag_set.first
         ff.first.csmiles.should == 'CC[C+]=O'
-        ff.last.csmiles.should == '[O-]'
-        ff.first.formula.should == "C3H5O"
+        # this is a carboxylate oxygen that falls off
+        ff.last.csmiles.should == '[O-2]'
+        #ff.first.formula.should == "C3H5O"
+        ff.first.formula.should == "C3H5O+"
         ff.first.exact_mass.should be_within(1e-6).of(57.034039779909996)
-        ff.last.formula.should == "O"
+        #ff.last.formula.should == "O"
+        ff.last.formula.should == "O--"
       end
 
       specify 'phosphodiester' do
@@ -92,10 +98,13 @@ describe Rubabel::Molecule::Fragmentable do
         frag_set = mol.fragment(rules: [:oxepd])
         ff = frag_set.first
         ff.first.csmiles.should == '[O-]CCC' 
-        ff.last.csmiles.should == '[NH3+]CCO[P](=O)=O'
-        ff.first.formula.should == 'C3H7O'
+        #ff.last.csmiles.should == '[NH3+]CCO[P](=O)=O'
+        ff.last.csmiles.should == "[NH3+]CCOP(=O)=O"
+        #ff.first.formula.should == 'C3H7O'
+        ff.first.formula.should == 'C3H7O-'
         ff.first.exact_mass.should be_within(1e-6).of(59.049689844)
-        ff.last.formula.should == 'C2H7NO3P'
+        #ff.last.formula.should == 'C2H7NO3P'
+        ff.last.formula.should == 'C2H7NO3P+'
         ff.last.exact_mass.should be_within(1e-6).of(124.016354719)
 
         mol = Rubabel["CCCOP(=O)(OCC[N+](C)(C)C)[O-]"]
@@ -105,8 +114,8 @@ describe Rubabel::Molecule::Fragmentable do
         # other are allowed to cancel one another out!
         frag_set.size.should == 4
         mols = frag_set.flatten
-        mols.map(&:csmiles).should ==  ["CC[CH2+]", "[O-]P(=O)(OCC[N+](C)(C)C)[O-]", "CCCOP(=O)([O-])[O-]", "[CH2+]C[N+](C)(C)C", "[O-]CCC", "O=[P](=O)OCC[N+](C)(C)C", "CCCO[P](=O)=O", "[O-]CC[N+](C)(C)C"]
-        mols.map(&:formula).should == ["C3H7", "C5H13NO4P", "C3H7O4P", "C5H13N", "C3H7O", "C5H13NO3P", "C3H7O3P", "C5H13NO"]
+        mols.map(&:csmiles).should == ["CC[CH2+]", "[O-]P(=O)(OCC[N+](C)(C)C)[O-]", "CCCOP(=O)([O-])[O-]", "[CH2+]C[N+](C)(C)C", "[O-]CCC", "O=P(=O)OCC[N+](C)(C)C", "CCCOP(=O)=O", "[O-]CC[N+](C)(C)C"]
+        mols.map(&:formula).should == ["C3H7+", "C5H13NO4P-", "C3H7O4P--", "C5H13N++", "C3H7O-", "C5H13NO3P+", "C3H7O3P", "C5H13NO"]
         mols.map(&:exact_mass).zip([43.05477522449, 182.05821952995, 138.00819533273, 87.10479942171, 59.04968984405, 166.06330491039, 122.01328071317, 103.09971404127]) do |act, exp|
           act.should be_within(1e-6).of(exp)
         end
@@ -126,7 +135,8 @@ describe Rubabel::Molecule::Fragmentable do
         ll = frags.last
         ll.first.csmiles.should == 'CC=CC[NH3+]'
         ll.last.csmiles.should == 'O'
-        ff.first.formula.should == 'C4H10N'
+        #ff.first.formula.should == 'C4H10N'
+        ff.first.formula.should == 'C4H10N+'
         ff.first.exact_mass.should be_within(1e-6).of(72.0813243255)
       end
 
@@ -138,7 +148,8 @@ describe Rubabel::Molecule::Fragmentable do
         frags = mol.fragment(rules: [:oxh])
         mols = frags.flatten
         mols.map(&:csmiles).should == ["C=CCC[NH3+]", "OO", "CC(=O)CC[NH3+]", "O", "CC=CC[NH3+]", "OO"]
-        mols.map(&:formula).should == ["C4H10N", "H2O2", "C4H10NO", "H2O", "C4H10N", "H2O2"]
+        mols.map(&:formula).should == ["C4H10N+", "H2O2", "C4H10NO+", "H2O", "C4H10N+", "H2O2"]
+        #mols.map(&:formula).should == ["C4H10N", "H2O2", "C4H10NO", "H2O", "C4H10N", "H2O2"]
         mols.map(&:exact_mass).zip([72.081324325, 34.005479304, 88.076238945, 18.010564684, 72.081324325, 34.005479304]) do |act, exp|
           act.should be_within(1e-6).of(exp)
         end
@@ -165,7 +176,8 @@ describe Rubabel::Molecule::Fragmentable do
         frags = mol.fragment(rules: [:oxh])
         mols = frags.flatten
         mols.map(&:csmiles).should == ["C=C=O", "OCCC[NH3+]", "CC(=O)O", "C=CC[NH3+]"]
-        mols.map(&:formula).should == ["C2H2O", "C3H10NO", "C2H4O2", "C3H8N"]
+        #mols.map(&:formula).should == ["C2H2O", "C3H10NO", "C2H4O2", "C3H8N"]
+        mols.map(&:formula).should == ["C2H2O", "C3H10NO+", "C2H4O2", "C3H8N+"]
         mols.map(&:exact_mass).zip([42.010564684, 76.076238945, 60.021129368000004, 58.065674261]) do |act,exp|
           act.should be_within(1e-6).of(exp)
         end

data/spec/rubabel/molecule_spec.rb

@@ -210,18 +210,6 @@ describe Rubabel::Molecule do
     ar.first.should be_a(OpenBabel::OBRing)
   end
 
-  describe 'making carbo-cations: spin_multiplicity and charges' do
-    # http://openbabel.org/docs/2.3.1/Features/Radicals.html
-    subject { mol = Rubabel["CC"] }
-    it 'can be turned into a carbocation' do
-      mol = subject
-      c = mol[0]
-      c.ob.set_spin_multiplicity 2
-      c.charge += 1
-      mol.csmiles.should == "C[CH2+]"
-    end
-  end
-
   describe 'masses' do
     subject { Rubabel["C(=O)COC(=O)C[NH3+]"] }
     it '#mol_wt (or #avg_mass)' do

data/spec/spec_helper.rb

@@ -1,3 +1,6 @@
+require 'simplecov'
+SimpleCov.start
+
 require 'rspec'
 require 'stringio'
 

metadata

@@ -1,20 +1,18 @@
 --- !ruby/object:Gem::Specification
 name: rubabel
 version: !ruby/object:Gem::Version
-  version: 0.3.0
-  prerelease: 
+  version: 0.4.0
 platform: ruby
 authors:
 - John T. Prince
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-03-21 00:00:00.000000000 Z
+date: 2013-06-07 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: openbabel
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
@@ -22,7 +20,6 @@ dependencies:
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
@@ -30,7 +27,6 @@ dependencies:
 - !ruby/object:Gem::Dependency
   name: andand
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
@@ -38,7 +34,6 @@ dependencies:
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
@@ -46,23 +41,34 @@ dependencies:
 - !ruby/object:Gem::Dependency
   name: mini_magick
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: '3.4'
+        version: 3.6.0
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: '3.4'
+        version: 3.6.0
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '1.3'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '1.3'
 - !ruby/object:Gem::Dependency
   name: rspec
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
@@ -70,7 +76,6 @@ dependencies:
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
@@ -78,7 +83,6 @@ dependencies:
 - !ruby/object:Gem::Dependency
   name: rdoc
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
@@ -86,7 +90,6 @@ dependencies:
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
@@ -94,7 +97,6 @@ dependencies:
 - !ruby/object:Gem::Dependency
   name: jeweler
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
@@ -102,24 +104,50 @@ dependencies:
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
         version: 1.8.3
-description: ! 'Ruby interface to the openbabel ruby bindings (or the openbabel gem).  The
-
-  interface attempts to be a ruby-ish analogue of pybel.'
-email: jtprince@gmail.com
+- !ruby/object:Gem::Dependency
+  name: simplecov
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: rake
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+description: Ruby interface to the OpenBabel ruby bindings similar to pybel
+email:
+- jtprince@gmail.com
 executables:
 - fragmenter.rb
 extensions: []
-extra_rdoc_files:
-- LICENSE
-- README.md
+extra_rdoc_files: []
 files:
 - .document
+- .gitignore
 - .rspec
+- Gemfile
 - LICENSE
 - README.md
 - Rakefile
@@ -136,6 +164,7 @@ files:
 - lib/rubabel/molecule_data.rb
 - lib/rubabel/pm.rb
 - lib/rubabel/smarts.rb
+- lib/rubabel/version.rb
 - reference/OBConversion_methods.txt
 - reference/arity_method_list.txt
 - reference/arity_method_list_CLASS.txt
@@ -144,6 +173,7 @@ files:
 - reference/fragmentation_rules_.pdf
 - reference/get_methods.rb
 - reference/mol_methods.txt
+- rubabel.gemspec
 - spec/chemistry_toolkit_rosetta/README.txt
 - spec/chemistry_toolkit_rosetta/benzodiazepine.sdf.gz
 - spec/chemistry_toolkit_rosetta/benzodiazepine.smi.gz
@@ -171,26 +201,51 @@ files:
 homepage: http://github.com/princelab/rubabel
 licenses:
 - MIT
+metadata: {}
 post_install_message: 
 rdoc_options: []
 require_paths:
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement
-  none: false
   requirements:
-  - - ! '>='
+  - - '>='
     - !ruby/object:Gem::Version
       version: '0'
 required_rubygems_version: !ruby/object:Gem::Requirement
-  none: false
   requirements:
-  - - ! '>='
+  - - '>='
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 1.8.23
+rubygems_version: 2.0.2
 signing_key: 
-specification_version: 3
-summary: Ruby interface to the OpenBabel ruby bindings similar to pybel
-test_files: []
+specification_version: 4
+summary: Ruby interface to the openbabel ruby bindings (or the openbabel gem).  The
+  interface attempts to be a ruby-ish analogue of pybel.
+test_files:
+- spec/chemistry_toolkit_rosetta/README.txt
+- spec/chemistry_toolkit_rosetta/benzodiazepine.sdf.gz
+- spec/chemistry_toolkit_rosetta/benzodiazepine.smi.gz
+- spec/chemistry_toolkit_rosetta/chemistry_toolkit_rosetta_spec.rb
+- spec/chemistry_toolkit_rosetta/key/3016_highlighted.rubabel.frozen.png
+- spec/chemistry_toolkit_rosetta/key/benzodiazepine_heavy_atom_counts.output.10.txt
+- spec/chemistry_toolkit_rosetta/key/benzodiazepine_ring_counts.output.10.txt
+- spec/chemistry_toolkit_rosetta/key/caffeine.frozen.png
+- spec/chemistry_toolkit_rosetta/key/rule5.10.sdf
+- spec/chemistry_toolkit_rosetta/tpsa.tab
+- spec/rubabel/atom_spec.rb
+- spec/rubabel/bond_spec.rb
+- spec/rubabel/molecule/fragmentable_spec.rb
+- spec/rubabel/molecule_data_spec.rb
+- spec/rubabel/molecule_spec.rb
+- spec/rubabel_spec.rb
+- spec/spec_helper.rb
+- spec/testfiles/7-oxocholesterol-d7.mol
+- spec/testfiles/7-oxocholesterol-d7.sdf
+- spec/testfiles/Samples.sdf
+- spec/testfiles/Samples.sdf.gz
+- spec/testfiles/cholesterol.mol
+- spec/testfiles/cholesterol.sdf
+- spec/testfiles/two.sdf
+has_rdoc: