rubabel 0.1.0

data/reference/bond_methods.txt

@@ -0,0 +1,79 @@
+Visit=
+Visit
+set_idx
+set_id
+set_bo
+set_bond_order
+set_begin
+set_end
+set_parent
+set_length
+set
+set_ksingle
+set_kdouble
+set_ktriple
+set_aromatic
+set_wedge
+set_hash
+set_wedge_or_hash
+set_up
+set_down
+set_in_ring
+set_closure
+unset_hash
+unset_wedge
+unset_up
+unset_down
+unset_aromatic
+unset_kekule
+get_idx
+get_id
+get_bo
+get_bond_order
+get_flags
+get_begin_atom_idx
+get_end_atom_idx
+get_begin_atom
+get_end_atom
+get_nbr_atom
+get_parent
+get_equib_length
+get_length
+get_nbr_atom_idx
+find_smallest_ring
+is_aromatic
+is_in_ring
+is_rotor
+is_amide
+is_primary_amide
+is_secondary_amide
+is_tertiary_amide
+is_ester
+is_carbonyl
+is_single
+is_double
+is_triple
+is_ksingle
+is_kdouble
+is_ktriple
+is_closure
+is_up
+is_down
+is_wedge
+is_hash
+is_wedge_or_hash
+is_cis_or_trans
+is_double_bond_geometry
+clear
+do_transformations
+get_title
+set_title
+has_data
+delete_data
+clone_data
+data_size
+get_all_data
+get_data
+begin_data
+end_data
+

data/reference/get_methods.rb

@@ -0,0 +1,52 @@
+module ObjectSpace
+  class << self
+    include Enumerable
+    alias_method :each, :each_object
+  end
+  def self.modules
+    self.select {|obj| obj.is_a?(Module) }
+  end
+end
+
+class Dog
+end
+
+before = ObjectSpace.modules
+
+require 'openbabel'
+
+after = ObjectSpace.modules
+
+modules = (after - before).reject {|mod| mod.to_s =~ /SWIG/i }
+
+class Object
+  def arity_hash
+    uniq = self.methods - (Object.new.methods + Object.methods)
+    Hash[ uniq.map do |name|
+      [name.to_s, self.method(name).arity]
+    end
+    ]
+  end
+end
+
+modules.each do |mod|
+  obj_hash = 
+    if mod.respond_to?(:allocate) 
+      begin
+        obj = mod.allocate
+        obj.arity_hash
+      rescue
+        {}
+      end
+    else
+      {}
+    end
+  klss_hash = mod.arity_hash
+  if (obj_hash.size + klss_hash.size) > 0
+    puts "*" * 50
+    puts mod
+    puts "*" * 50
+    puts obj_hash.map {|pair| pair.join(" ") }
+    puts klss_hash.map {|pair| pair.join(" ") }
+  end
+end

data/reference/mol_methods.txt

@@ -0,0 +1,183 @@
+#<OpenBabel::OBMol:0x00000000b71c90>
+---
+- add
+- reserve_atoms
+- create_atom
+- create_bond
+- create_residue
+- destroy_atom
+- destroy_bond
+- destroy_residue
+- add_atom
+- insert_atom
+- add_bond
+- add_residue
+- new_atom
+- new_bond
+- new_residue
+- delete_atom
+- delete_bond
+- delete_residue
+- begin_modify
+- end_modify
+- get_mod
+- increment_mod
+- decrement_mod
+- get_flags
+- get_title
+- num_atoms
+- num_bonds
+- num_hvy_atoms
+- num_residues
+- num_rotors
+- get_atom
+- get_atom_by_id
+- get_first_atom
+- get_bond_by_id
+- get_bond
+- get_residue
+- get_internal_coord
+- get_torsion
+- get_angle
+- get_formula
+- get_spaced_formula
+- get_mol_wt
+- get_exact_mass
+- get_total_charge
+- get_total_spin_multiplicity
+- get_dimension
+- get_coordinates
+- get_sssr
+- get_lssr
+- automatic_formal_charge
+- automatic_partial_charge
+- set_title
+- set_formula
+- set_energy
+- set_dimension
+- set_total_charge
+- set_total_spin_multiplicity
+- set_internal_coord
+- set_automatic_formal_charge
+- set_automatic_partial_charge
+- set_aromatic_perceived
+- set_sssrperceived
+- set_lssrperceived
+- set_ring_atoms_and_bonds_perceived
+- set_atom_types_perceived
+- set_ring_types_perceived
+- set_chains_perceived
+- set_chirality_perceived
+- set_partial_charges_perceived
+- set_hybridization_perceived
+- set_implicit_valence_perceived
+- set_kekule_perceived
+- set_closure_bonds_perceived
+- set_hydrogens_added
+- set_corrected_for_ph
+- set_aromatic_corrected
+- set_spin_multiplicity_assigned
+- set_flags
+- unset_aromatic_perceived
+- unset_sssrperceived
+- unset_ring_types_perceived
+- unset_partial_charges_perceived
+- unset_implicit_valence_perceived
+- unset_hydrogens_added
+- unset_flag
+- renumber_atoms
+- set_coordinates
+- to_inertial_frame
+- translate
+- rotate
+- kekulize
+- perceive_kekule_bonds
+- new_perceive_kekule_bonds
+- delete_hydrogens
+- delete_non_polar_hydrogens
+- delete_hydrogen
+- add_hydrogens
+- add_polar_hydrogens
+- strip_salts
+- separate
+- get_next_fragment
+- convert_dative_bonds
+- correct_for_ph
+- assign_spin_multiplicity
+- set_is_pattern_structure
+- center
+- set_torsion
+- find_sssr
+- find_lssr
+- find_ring_atoms_and_bonds
+- find_chiral_centers
+- find_children
+- find_largest_fragment
+- contig_frag_list
+- align
+- connect_the_dots
+- perceive_bond_orders
+- find_angles
+- find_torsions
+- get_gtdvector
+- get_givector
+- get_gidvector
+- has_2d
+- has_3d
+- has_non_zero_coords
+- has_aromatic_perceived
+- has_sssrperceived
+- has_lssrperceived
+- has_ring_atoms_and_bonds_perceived
+- has_atom_types_perceived
+- has_ring_types_perceived
+- has_chirality_perceived
+- has_partial_charges_perceived
+- has_hybridization_perceived
+- has_implicit_valence_perceived
+- has_kekule_perceived
+- has_closure_bonds_perceived
+- has_chains_perceived
+- has_hydrogens_added
+- has_aromatic_corrected
+- is_corrected_for_ph
+- has_spin_multiplicity_assigned
+- is_chiral
+- empty
+- num_conformers
+- set_conformers
+- add_conformer
+- set_conformer
+- copy_conformer
+- delete_conformer
+- get_conformer
+- set_energies
+- get_energies
+- get_energy
+- begin_conformer
+- next_conformer
+- get_conformers
+- begin_atoms
+- end_atoms
+- begin_bonds
+- end_bonds
+- begin_residues
+- end_residues
+- begin_atom
+- next_atom
+- begin_bond
+- next_bond
+- begin_residue
+- next_residue
+- begin_internal_coord
+- next_internal_coord
+- clear
+- do_transformations
+- has_data
+- delete_data
+- clone_data
+- data_size
+- get_all_data
+- get_data
+- begin_data
+- end_data

data/spec/rubabel/atom_spec.rb

@@ -0,0 +1,49 @@
+require 'spec_helper'
+
+require 'rubabel/molecule'
+require 'rubabel/atom'
+
+describe Rubabel::Atom do
+  describe 'working with a complex molecule' do
+
+    before do
+      @mol = Rubabel::Molecule.from_file( TESTFILES + '/cholesterol.sdf' )
+      @atom = @mol.atoms.first
+      @mol_h =  Rubabel::Molecule.from_file( TESTFILES + '/cholesterol.sdf' )
+      @mol_h.add_h!
+      @atom_with_h = @mol_h.atoms.first
+    end
+
+    attributes = {
+      charge: 0,
+      id: 0,
+      spin: 0,
+    }.each do |methd, exp|
+      it "has #{methd}" do
+        @atom.send(methd).should == exp
+      end
+    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 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 '#coords gets the coordinates' do
+      @atom.coords
+    end
+  end
+end

data/spec/rubabel/bond_spec.rb

@@ -0,0 +1,19 @@
+require 'spec_helper'
+
+require 'rubabel/molecule'
+require 'rubabel/bond'
+
+describe Rubabel::Bond do
+  subject { Rubabel::Molecule.from_file( TESTFILES + '/cholesterol.sdf' ).bonds.first }
+
+  it 'is a Rubabel::Bond' do
+    subject.should be_a(Rubabel::Bond)
+  end
+
+  it 'knows what atoms it includes' do
+    subject.each_atom do |atom|
+      atom.should be_a(Rubabel::Atom)
+    end
+    subject.atoms.size.should == 2
+  end
+end

data/spec/rubabel/molecule_spec.rb

@@ -0,0 +1,91 @@
+require 'spec_helper'
+
+require 'rubabel/molecule'
+
+describe Rubabel::Molecule do
+  before(:each) do
+    @mol = Rubabel::Molecule.from_file( TESTFILES + '/cholesterol.sdf' )
+  end
+
+  attributes = {
+    charge: 0,
+    formula: "C27H46O",
+    dim: 2,
+    spin: 1,
+  }.each do |methd, exp|
+    it "has #{methd}" do
+      @mol.send(methd).should == exp
+    end
+  end
+
+  it '#each iterates through each atom in id order' do
+    cnt = 0
+    @mol.each do |atom|
+      atom.id.should == cnt
+      cnt += 1
+    end
+    @mol.atoms.size.should == 33
+    @mol.add_h!
+    @mol.atoms.size.should == 74
+  end
+
+  it 'calculates #ob_sssr (smallest set of smallest rings)' do
+    ar = @mol.ob_sssr
+    ar.should be_an(Array)
+    # in the future should be Rubabel::Ring
+    ar.first.should be_a(OpenBabel::OBRing)
+  end
+
+  describe 'breaking a molecule' do
+    before(:each) do
+      @mol =  Rubabel::Molecule.from_string("NC(=O)CO")
+    end
+
+    it 'num_atoms, atoms and each_atom are sensitive to #add_h!' do
+      @mol.num_atoms.should == 5
+      @mol.atoms.size.should == 5
+      @mol.each_atom.map.to_a.size.should == 5
+      @mol.add_h!
+      @mol.num_atoms.should == 10
+      @mol.atoms.size.should == 10
+      @mol.each_atom.map.to_a.size.should == 10
+    end
+
+    it 'num_bonds, bonds and each_bond are also sensitive to #add_h!' do
+      @mol.num_bonds.should == 4
+      @mol.bonds.size.should == 4
+      @mol.each_bond.map.to_a.size.should == 4
+      @mol.add_h!
+      @mol.num_bonds.should == 9
+      @mol.bonds.size.should == 9
+      @mol.each_bond.map.to_a.size.should == 9
+    end
+
+    it 'can be split into multiple molecules' do
+      reply = @mol.split(@mol.bonds.first, @mol.bonds.last)
+      reply.should be_a(Array)
+      reply.size.should == 3
+      csmiles = reply.map(&:csmiles)
+      csmiles.sort.should == %w(N CC=O O).sort
+    end
+  end
+
+  describe 'matching patterns (SMARTS)' do
+    before(:each) do
+      @mol =  Rubabel::Molecule.from_string("NC(=O)O")
+    end
+
+    it 'can match smarts patterns' do
+      smarts_pattern = 'C=O'
+      ar = @mol.matches(smarts_pattern)
+      ar.should be_a(Array)
+      ar.size.should == 1
+      ar.first.map(&:type).should == %w(Cac O.co2)
+
+      # reverse order of smiles gives reverse order
+      ar = @mol.matches(smarts_pattern.reverse)
+      ar.first.map(&:type).should == %w(Cac O.co2).reverse
+    end
+
+  end
+end