molecule_spec.rb in rubabel-0.3.0

- old
+ new

@@ -20,14 +20,14 @@
       mol.title.should == ''
     end
   end
 
   #xit 'can add a hydrogen to the formula' do
-    #mol = Rubabel["CCC"]
-    #p mol.formula
-    #mol.add_hydrogen_to_formula!
-    #p mol.formula
+  #mol = Rubabel["CCC"]
+  #p mol.formula
+  #mol.add_hydrogen_to_formula!
+  #p mol.formula
   #end
 
   describe 'png output' do
     it 'creates a png image (corresponds to the svg)' do
       mol = Rubabel["NCC(=O)O"]
@@ -75,18 +75,18 @@
     (mol1 == mol3).should be_false
   end
 
   specify '#[] retrieves atom by index' do
     mol = Rubabel["NCO"]
-    mol[0].el.should == :n
-    mol[1].el.should == :c
-    mol[2].el.should == :o
-    mol[-1].el.should == :o
-    mol[-2].el.should == :c
+    mol[0].el.should == :N
+    mol[1].el.should == :C
+    mol[2].el.should == :O
+    mol[-1].el.should == :O
+    mol[-2].el.should == :C
     ar = mol[1..-1]
-    ar.first.el.should == :c
-    ar.last.el.should == :o
+    ar.first.el.should == :C
+    ar.last.el.should == :O
     ar.size.should == 2
   end
 
   specify 'num_atoms gives the number of atoms which can vary with hydrogens added' do
     mol = Rubabel["CCC"]
@@ -98,38 +98,48 @@
   specify 'num_atoms(true) gives the number including implied hydrogens' do
     mol = Rubabel["CCC"]
     mol.num_atoms(true).should == 11
   end
 
-  describe 'adding an atom' do
-    it 'can be added but not attached' do
+  describe 'adding or associating atoms' do
+
+    it 'can associate atoms with the molecule' do
       mol = Rubabel["CCO"]
-      atom = mol.add_atom!(:n)
-      atom.el.should == :n
-      atom = mol.add_atom!(8)
-      atom.el.should == :o
+      nitrogen = mol.associate_atom!(:N)
+      nitrogen.el.should == :N
+      oxygen = mol.associate_atom!(8)
+      oxygen.el.should == :O
       mol.csmiles.should == "CCO.N.O"
+
+      oxygen_aromatic = mol.associate_atom!(:O)
+      mol.csmiles.should == "CCO.N.O.O"
     end
 
-    it "can be added and attached by el symbol or atomic number" do 
+    it "can be added and attached by element symbol or atomic number" do 
       mol = Rubabel["CCO"]
       first_carbon = mol[0]
-      mol.add_atom!(:n, first_carbon)
+      mol.add_atom!(:N, 1, first_carbon)
       mol.csmiles.should == "NCCO"
 
-      mol.add_atom!(16, first_carbon)
+      mol.add_atom!(16, 1, first_carbon)
       mol.csmiles.should == "NC(CO)S"
     end
 
   end
-  
-  specify '#<< adds atom to the last atom and returns the mol' do
+
+  specify '#<< adds atom to the last atom and returns the added atom' do
     mol = Rubabel::Molecule.new
+    reply = (mol << :N)
     # by element symbol or atomic number
-    reply = (mol << :n << :c)
-    reply.should be_a(Rubabel::Molecule)
-    reply.csmiles.should == 'CN'
+    reply = (mol << :N << :C)
+    reply.should be_a(Rubabel::Atom)
+    reply.el.should == :C
+
+    # properly handles aromaticity
+    mol.atoms.last.aromatic?.should be_false
+    mol << :c # aromatic specifier in SMILES
+    mol.atoms.last.aromatic?.should be_true
   end
 
   specify '#dup duplicates the molecule' do
     mol = Rubabel["CCO"]
     dup_mol = mol.dup
@@ -141,28 +151,28 @@
   specify '#add_atom! with a Rubabel::Atom'
 
   describe '#add_bond! adds a bond (and updates atoms)' do
     specify 'given two atoms' do
       mol = Rubabel["CCO"]
-      atom = mol.add_atom!(0)
+      atom = mol.associate_atom!(0)
       mol.add_bond!(mol[1], atom)
       mol.csmiles.should == '*C(O)C'
     end
   end
 
   specify '#atom(id) retrieves atom by id num' do
     mol = Rubabel["CCO"]
-    o = mol.find {|a| a.el == :o }
+    o = mol.find {|a| a.el == :O }
     mol.atom(o.id).id.should == o.id
   end
 
   specify '#swap! can swap atoms around' do
     mol = Rubabel["NCC(=O)O"]
     carboxy_carbon = mol.atoms.find {|atom| atom.type == 'Cac' }
     single_bonded_oxygen = mol.atoms.find {|atom| atom.type == 'O.co2' && atom.get_bond(carboxy_carbon).bond_order == 1 }
     nit_carbon = mol.atoms.find {|atom| atom.atoms.any? {|nbr| nbr.type == 'N3' } }
-    nitrogen = mol.atoms.find {|atom| atom.el == :n }
+    nitrogen = mol.atoms.find {|atom| atom.el == :N }
     swapped = mol.swap!(nit_carbon, nitrogen, carboxy_carbon, single_bonded_oxygen)
     swapped.should == mol
     swapped.csmiles.should == 'NC(=O)CO'
   end
 
@@ -313,10 +323,10 @@
   end
 
   describe 'breaking a molecule' do
     before(:each) do
       @mol =  Rubabel::Molecule.from_string("NC(=O)CO")
-      @n = @mol.find {|a| a.el == :n }
+      @n = @mol.find {|a| a.el == :N }
     end
 
     it 'num_atoms, atoms and each_atom are sensitive to #add_h!' do
       @mol.num_atoms.should == 5
       @mol.atoms.size.should == 5