spec/rubabel/atom_spec.rb in rubabel-0.1.0 vs spec/rubabel/atom_spec.rb in rubabel-0.1.1

@@ -2,10 +2,25 @@
 
 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
       @mol = Rubabel::Molecule.from_file( TESTFILES + '/cholesterol.sdf' )
       @atom = @mol.atoms.first
@@ -22,25 +37,45 @@
       it "has #{methd}" do
         @atom.send(methd).should == exp
       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)
       end
       @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
       @atom.type.should == 'C3'
       @atom.each_atom do |nbr_atom|
         nbr_atom.should be_a(Rubabel::Atom)
         nbr_atom.ob.equal?(@atom.ob).should be_false
       end
       @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