rubabel 0.1.0 → 0.1.1

data/spec/rubabel/atom_spec.rb

@@ -4,6 +4,21 @@ require 'rubabel/molecule'
 require 'rubabel/atom'
 
 describe Rubabel::Atom do
+
+  it 'can be created given an element symbol' do
+    hydrogen = Rubabel::Atom[:h]
+    hydrogen.el.should == :h
+    hydrogen.id.should == 0
+
+    carbon = Rubabel::Atom[:c]
+    carbon.el.should == :c
+    carbon.id.should == 0
+
+    chlorine = Rubabel::Atom[:cl, 3]
+    chlorine.el.should == :cl
+    chlorine.id.should == 3
+  end
+
   describe 'working with a complex molecule' do
 
     before do
@@ -24,6 +39,15 @@ describe Rubabel::Atom do
       end
     end
 
+
+    it '#mol retrieves the parent molecule' do
+      @atom.mol.should == @mol
+
+      # no parent molecule 
+      h = Rubabel::Atom[:h]
+      h.mol.should be_nil
+    end
+
     it 'can get the bonds' do
       @atom.each_bond do |bond|
         bond.should be_a(Rubabel::Bond)
@@ -31,6 +55,9 @@ describe Rubabel::Atom do
       @atom.bonds.size.should == 4
     end
 
+    it 'can add a bond' do
+    end
+
     it 'can get the neighboring atoms' do
       @atom.id.should == 0
       @atom.atomic_num.should == 6
@@ -42,6 +69,14 @@ describe Rubabel::Atom do
       @atom.atoms.size.should == 4
     end
 
+    it '#get_bond can retrieve a particular bond based on the atom' do
+      other = @mol.atoms[3]
+      bond = @atom.get_bond(other)
+      bond.atoms.map(&:id).should == [0,3]
+      other = @mol.atoms[15]  # these are not connected
+      @atom.get_bond(other).should be_nil
+    end
+
     it '#coords gets the coordinates' do
       @atom.coords
     end

data/spec/rubabel/molecule/fragmentable_spec.rb

@@ -0,0 +1,51 @@
+require 'spec_helper'
+
+require 'rubabel'
+
+describe Rubabel::Molecule::Fragmentable do
+  describe 'the :co rule' do
+
+    describe 'water loss' do
+
+      it ':h2oloss' do
+        mol = Rubabel["NCCC(O)CC"]
+        fragments = mol.fragment( rules: [:h2oloss] )
+        fragments.flatten(1).map(&:csmiles).sort.should == ["CC=CCC[NH3+]", "CCC=CC[NH3+]", "O", "O"]
+      end
+
+      it ':h2oloss [does not allow bad chemistry]' do
+        # lone pair and double bond resonance ?
+        mol = Rubabel["NCC(O)CC"]
+        fragments = mol.fragment( rules: [:h2oloss] )
+        fragments.flatten(1).map(&:csmiles).sort.should == ["CC=CC[NH3+]", "O"]
+
+        mol = Rubabel["NC(O)CC"] 
+        fragments = mol.fragment( rules: [:h2oloss] )
+        fragments.flatten(1).map(&:csmiles).sort.should == []
+      end
+    end
+
+    describe 'backbone cleavage' do
+
+      it 'cleaves beside alcohols yielding aldehydes' do
+        mol = Rubabel["NCCC(O)CC"]
+        mol.correct_for_ph!
+        total_mass = mol.add_h!.mass
+
+        pieces = mol.fragment(rules: [:co])
+        pieces.size.should == 2
+        pieces.map(&:size).should == [2,2]
+        pieces.flatten(1).map(&:csmiles).should == ["CC[NH3+]", "CCC=O", "C(C=O)C[NH3+]", "CC"]
+        pieces.each do |pair|
+          pair.map(&:mass).reduce(:+).should == total_mass
+        end
+      end
+
+      xit 'does not cleave esters' do
+        mol = Rubabel["NCCC(=O)OC"]
+        pieces = mol.fragment( rules: [:co] )
+        pieces.should be_empty
+      end
+    end
+  end
+end

data/spec/rubabel/molecule_data_spec.rb

@@ -0,0 +1,76 @@
+require 'spec_helper'
+
+require 'rubabel/molecule_data'
+require 'rubabel'
+
+describe Rubabel::MoleculeData do
+
+  before(:each) do
+    sdf = TESTFILES + "/Samples.sdf"
+    @mol = Rubabel::Molecule.from_file( sdf )
+  end
+
+  it 'is initialized with an OpenBabel molecule' do
+    md = Rubabel::MoleculeData.new(@mol.ob)
+    md.should be_a(Rubabel::MoleculeData)
+  end
+
+  describe 'hash-like behavior' do
+    subject { Rubabel::MoleculeData.new(@mol.ob) }
+
+    it '#each' do
+      enum = subject.each
+      enum.should be_a(Enumerator)
+      pair = enum.next
+      pair.should == ["NAME", "2Ferrocene"]
+    end
+
+    it '#to_a' do
+      subject.to_a.size.should == 2
+    end
+
+    it '#size & #length' do
+      subject.size.should == 2
+      subject.length.should == 2
+    end
+    
+    it '#[]' do
+      subject['NAME'].should == "2Ferrocene"
+    end
+
+    it '#[]=' do
+      # modify one:
+      subject['NAME'] = 'PEPPER'
+      subject.size.should == 2
+      # create_a new one:
+      subject['jtp_special'] = 'sauce'
+      subject.size.should == 3
+      string = subject.obmol.upcast.write(:sdf)
+      string.should =~ /jtp_special/
+      string.should =~ /sauce/
+      string.should =~ /PEPPER/
+    end
+
+    it '#key?' do
+      subject.key?('NAME').should be_true
+      subject.key?('bananas').should be_false
+    end
+
+    it '#keys' do
+      subject.keys.should == ["NAME", "OpenBabel Symmetry Classes"]
+    end
+
+    it '#values' do
+      subject.values.should == ["2Ferrocene", "8 4 9 4 4 4 4 4 4 4 4 4 5 3 6 2 7 1 5 3 6 2 5 3 7 1 5 3 6 2 6 2"]
+    end
+
+    it '#delete' do
+      key = "OpenBabel Symmetry Classes"
+      subject.delete(key).should =~ /8 4 9/
+      subject.key?(key).should be_false
+      subject.size.should == 1
+      subject.delete("nonsense").should be_nil
+      subject.delete("nonsense") { 'wow' }.should == 'wow'
+    end
+  end
+end

data/spec/rubabel/molecule_spec.rb

@@ -3,6 +3,13 @@ require 'spec_helper'
 require 'rubabel/molecule'
 
 describe Rubabel::Molecule do
+  describe 'creation' do
+    it 'can be made with Rubabel[]' do
+      mol = Rubabel["CC(O)O"]
+      mol.csmiles.should == "CC(O)O"
+    end
+  end
+
   before(:each) do
     @mol = Rubabel::Molecule.from_file( TESTFILES + '/cholesterol.sdf' )
   end
@@ -18,6 +25,14 @@ describe Rubabel::Molecule do
     end
   end
 
+  it '#dup creates an entirely new molecule based on the first' do
+    another = @mol.dup
+    # this is a deep copy all the way.  Even the atoms are duplicated so that
+    # they can be modified in one and do not affect the other at all.
+    @mol.atoms.first.charge = 1
+    @mol.charge.should_not == another.charge
+  end
+
   it '#each iterates through each atom in id order' do
     cnt = 0
     @mol.each do |atom|
@@ -29,6 +44,14 @@ describe Rubabel::Molecule do
     @mol.atoms.size.should == 74
   end
 
+  it '#hydrogens_added?' do
+    @mol.hydrogens_added?.should be_false
+    @mol.atoms.size.should == 33
+    @mol.add_h!
+    @mol.atoms.size.should == 74
+    @mol.hydrogens_added?.should be_true
+  end
+
   it 'calculates #ob_sssr (smallest set of smallest rings)' do
     ar = @mol.ob_sssr
     ar.should be_an(Array)
@@ -36,6 +59,106 @@ describe Rubabel::Molecule do
     ar.first.should be_a(OpenBabel::OBRing)
   end
 
+  describe 'masses' do
+    subject { Rubabel::Molecule.from_string("C(=O)COC(=O)C[NH3+]") }
+    it '#mol_wt (or #avg_mass)' do
+      subject.mol_wt.should be_within(0.000001).of(118.11121999999999)
+    end
+
+    it '#exact_mass' do
+      subject.exact_mass.should be_within(0.00000001).of(118.05041812003999)
+    end
+
+    it '#mass is the exact mass adjusted for electron gain/loss' do
+      subject.mass.should be_within(0.00000001).of(118.04986952003999)
+    end
+  end
+
+  describe 'getting other descriptors' do
+    # can't figure this out yet
+  end
+
+  describe 'pH' do
+
+    subject { Rubabel::Molecule.from_string("NCC(=O)OCC(=O)O") }
+
+    it '#correct_for_ph! neutral' do
+      subject.correct_for_ph!.to_s.should == '[O-]C(=O)COC(=O)C[NH3+]'
+    end
+
+    it '#correct_for_ph!(1.4) [low]' do
+      subject.correct_for_ph!(1.4).to_s.should == 'OC(=O)COC(=O)C[NH3+]'
+    end
+
+    it '#correct_for_ph!(11.0) [high]' do
+      subject.correct_for_ph!(11.0).to_s.should == '[O-]C(=O)COC(=O)CN'
+    end
+
+    it '#correct_for_ph!(nil) [gives neutral molecule]' do
+      subject.correct_for_ph!.to_s.should == '[O-]C(=O)COC(=O)C[NH3+]'
+      subject.correct_for_ph!(nil).to_s.should == "NCC(=O)OCC(=O)O"
+    end
+
+    it '#neutral! [can be set neutral again]' do
+      subject.correct_for_ph!
+      subject.to_s.should == '[O-]C(=O)COC(=O)C[NH3+]'
+      subject.h_added?.should == false
+      subject.neutral!.to_s.should == "NCC(=O)OCC(=O)O"
+      subject.h_added?.should == false
+    end
+
+    it '#neutral! [preserves hydrogens added state]' do
+      subject.correct_for_ph!
+      subject.add_h!
+      subject.to_s.should == '[O-]C(=O)COC(=O)C[NH3+]'
+      subject.h_added?.should == true
+      subject.neutral!.to_s.should == "NCC(=O)OCC(=O)O"
+      subject.h_added?.should == true
+    end
+
+    it '#add_h!(11.0) [can correct for ph if given a ph]' do
+      subject.add_h!(11.0).to_s.should == '[O-]C(=O)COC(=O)CN'
+    end
+
+  end
+
+  it 'can calculate a molecular fingerprint (for similarity calcs)' do
+    # this just returns the std::vector object at the moment
+    fp = @mol.ob_fingerprint
+    # this is an array of unsigned ints that really need to be coerced into
+    # bits for further usefulness.
+    fp.to_a.should == [0, 604110848, 16777216, 0, 2147483648, 4210688, 0, 2097152, 16, 16809984, 0, 0, 1, 37756928, 32, 0, 524296, 1028, 8388612, 131072, 1073741824, 512, 1048584, 16384, 1026, 0, 0, 524288, 0, 2048, 16777248, 0]
+    lambda { @mol.ob_fingerprint("WACKY") }.should raise_error
+  end
+
+  it 'can calculate the tanimoto similarity' do
+    # oo way to call:
+    @mol.tanimoto(@mol).should == 1.0
+    mol2 = Rubabel::Molecule.from_string("CCC(O)OCCC")
+    # class way to call this
+    t = Rubabel::Molecule.tanimoto(@mol, mol2)
+    # actual: 0.11363636363636363
+    t.should be < 0.2
+    t.should be > 0.0
+  end
+
+  describe '3D' do
+    before(:each) do
+      # cholesterol
+      @mol = Rubabel::Molecule.from_string("OC[C@H]1OC(O)[C@H](O)[C@@H](O)[C@@H]1O")
+    end
+
+    it 'can be turned into a 3D molecule' do
+      # this is only as good as the Builder is good.  For instance, it fails
+      # to get all the stereo centers of cholesterol (but it does warn on
+      # this, although I don't know how to capture the warnings (can't get
+      # with stdout or stderr??))
+      @mol.ob.has_3d.should be_false
+      @mol.make_3d!
+      @mol.ob.has_3d.should be_true 
+    end
+  end
+
   describe 'breaking a molecule' do
     before(:each) do
       @mol =  Rubabel::Molecule.from_string("NC(=O)CO")
@@ -61,13 +184,20 @@ describe Rubabel::Molecule do
       @mol.each_bond.map.to_a.size.should == 9
     end
 
-    it 'can be split into multiple molecules' do
+    it 'can be split into multiple molecules [unaffecting self]' do
+      num_bonds_before = @mol.num_bonds
+      num_atoms_before = @mol.num_atoms
+
       reply = @mol.split(@mol.bonds.first, @mol.bonds.last)
+
       reply.should be_a(Array)
       reply.size.should == 3
+      @mol.num_bonds.should == num_bonds_before
+      @mol.num_atoms.should == num_atoms_before
       csmiles = reply.map(&:csmiles)
       csmiles.sort.should == %w(N CC=O O).sort
     end
+
   end
 
   describe 'matching patterns (SMARTS)' do

data/spec/rubabel_spec.rb

@@ -48,19 +48,49 @@ describe Rubabel do
     end
   end
 
-  describe '::read_file and ::read_string' do
+  describe '::molecule_from_file and ::molecule_from_string' do
     before(:each) do 
       @samples = TESTFILES + "/Samples.sdf"
     end
 
     it 'return a single molecule (the first one in the file)' do
-      mol_f = Rubabel.read_file(@samples)
-      mol_s = Rubabel.read_string(IO.read(@samples), :sdf)
+      mol_f = Rubabel.molecule_from_file(@samples)
+      mol_s = Rubabel.molecule_from_string(IO.read(@samples), :sdf)
       [mol_f, mol_s].each {|mol| mol.should be_a(Rubabel::Molecule) }
       mol_f.should == mol_s
     end
   end
 
+  describe 'can deal with .gz files properly' do
+    before(:each) do 
+      @gz_file = TESTFILES + "/Samples.sdf.gz"
+    end
+
+    it 'can get the file format' do
+      # non-existant file okay
+      Rubabel.format_from_ext("silly.sdf.gz").should == :sdf
+      Rubabel.format_from_ext(@gz_file).should == :sdf
+      Rubabel.foreach(@gz_file) do |mol|
+        mol.should be_a(Rubabel::Molecule)
+      end
+    end
+
+  end
+
+  describe 'format from extension' do
+
+    it 'determines format from extension' do
+      Rubabel.format_from_ext( TESTFILES + "/Samples.sdf" ).should == :sdf
+      Rubabel.format_from_ext( TESTFILES + "/Samples.non_existent" ).should be_nil
+    end
+
+    it 'determines format from mime-type' do
+      Rubabel.format_from_mime( "chemical/x-mdl-sdfile" ).should == :sdf
+      Rubabel.format_from_mime( "chemical/wierdness" ).should be_nil
+    end
+
+  end
+
   #describe 'an atom in it' do
   #end
 end

data/spec/spec_helper.rb

@@ -1,4 +1,5 @@
 require 'rspec'
+require 'stringio'
 
 # Requires supporting files with custom matchers and macros, etc,
 # in ./support/ and its subdirectories.
@@ -10,3 +11,26 @@ RSpec.configure do |config|
 end
 
 TESTFILES = File.dirname(__FILE__) + "/testfiles"
+
+module Kernel
+  # from: http://thinkingdigitally.com/archive/capturing-output-from-puts-in-ruby/
+  def capture_stdout
+    out = StringIO.new
+    $stdout = out
+    yield
+    return out.string
+  ensure
+    $stdout = STDOUT
+  end
+
+  def capture_stderr
+    out = StringIO.new
+    $stderr = out
+    yield
+    return out.string
+  ensure
+    $stderr = STDERR
+  end
+
+
+end