atom.rb in rubabel-0.1.1

- old
+ new

@@ -1,6 +1,7 @@
 require 'matrix'
+require 'andand'
 
 require 'rubabel/bond'
 
 class OpenBabel::OBAtom
   def upcast
@@ -10,10 +11,25 @@
 
 module Rubabel
   class Atom
     include Enumerable
 
+    class << self
+      # takes an element symbol and creates that atom
+      def [](el_sym=:h, id=0)
+        ob_atom = OpenBabel::OBAtom.new
+        ob_atom.set_id(id)
+        ob_atom.set_atomic_num(Rubabel::EL_TO_NUM[el_sym])
+        self.new(ob_atom)
+      end
+    end
+
+    # returns the molecule that is parent of this atom
+    def mol
+      @ob.get_parent.andand.upcast
+    end
+
     # the OpenBabel::OBAtom object
     attr_accessor :ob
 
     def initialize(obatom)
       @ob = obatom
@@ -40,10 +56,20 @@
     # abbreviated name, properly capitalized and as a String
     def element
       NUM_TO_ELEMENT[atomic_num]
     end
 
+    # creates a bond and adds it to both atoms
+    def add_atom!(other)
+      obbond = OpenBabel::OBBond.new
+      obbond.set_begin(self.ob)
+      obbond.set_end(other.ob)
+      @ob.add_bond(obbond)
+      other.ob.add_bond(obbond)
+      self
+    end
+
     def each_bond(&block)
       block or return enum_for(__method__)
       iter = @ob.begin_bonds
       _bond = @ob.begin_bond(iter)
       while _bond
@@ -52,10 +78,15 @@
       end
     end
 
     alias_method :each, :each_bond
 
+    # retrieves the bond 
+    def get_bond(atom)
+      @ob.get_bond(atom.ob).andand.upcast
+    end
+
     # returns the bonds.  Consider using each_bond.
     def bonds
       each_bond.map.to_a
     end
 
@@ -90,10 +121,15 @@
     def formal_charge
       @ob.get_formal_charge
     end
     alias_method :charge, :formal_charge
 
+    def formal_charge=(val)
+      @ob.set_formal_charge(val)
+    end
+    alias_method :charge=, :formal_charge=
+
     def heavy_valence
       @ob.get_heavy_valence
     end
 
     def hetero_valence
@@ -129,9 +165,51 @@
     end
 
     def vector
       @ob.get_vector
     end
+
+    def hydrogen?() @ob.is_hydrogen end
+    def carbon?() @ob.is_carbon end
+    def nitrogen?() @ob.is_nitrogen end
+    def oxygen?() @ob.is_oxygen end
+    def sulfur?() @ob.is_sulfur end
+    def phosphorus?() @ob.is_phosphorus end
+    def aromatic?() @ob.is_aromatic end
+    def in_ring?() @ob.is_in_ring end
+    def in_ring_size?() @ob.is_in_ring_size end
+    def heteroatom?() @ob.is_heteroatom end
+    def not_c_or_h?() @ob.is_not_cor_h end
+    def connected?() @ob.is_connected end
+    def one_three?() @ob.is_one_three end
+    def one_four?() @ob.is_one_four end
+    def carboxyl_oxygen?() @ob.is_carboxyl_oxygen end
+    def phosphate_oxygen?() @ob.is_phosphate_oxygen end
+    def sulfate_oxygen?() @ob.is_sulfate_oxygen end
+    def nitro_oxygen?() @ob.is_nitro_oxygen end
+    def amide_nitrogen?() @ob.is_amide_nitrogen end
+    def polar_hydrogen?() @ob.is_polar_hydrogen end
+    def non_polar_hydrogen?() @ob.is_non_polar_hydrogen end
+    def aromatic_noxide?() @ob.is_aromatic_noxide end
+    def chiral?() @ob.is_chiral end
+    def axial?() @ob.is_axial end
+    def clockwise?() @ob.is_clockwise end
+    def anti_clockwise?() @ob.is_anti_clockwise end
+    def positive_stereo?() @ob.is_positive_stereo end
+    def negative_stereo?() @ob.is_negative_stereo end
+    def chirality_specified?() @ob.has_chirality_specified end
+    def chiral_volume?() @ob.has_chiral_volume end
+    def hbond_acceptor?() @ob.is_hbond_acceptor end
+    def hbond_donor?() @ob.is_hbond_donor end
+    def hbond_donor_h?() @ob.is_hbond_donor_h end
+
+    def carboxyl_carbon?
+      atoms.any?(&:carboxyl_oxygen?)
+    end
+
+#    # does this carbon hold a primary alcohol
+#    def primary_alcohol_carbon?
+#    end
 
     def coords
       Vector[@ob.x, @ob.y, @ob.z]
     end
 