rubabel 0.1.0 → 0.1.1

data/lib/rubabel/molecule_data.rb

@@ -0,0 +1,89 @@
+require 'openbabel'
+
+module Rubabel
+  # A hash-like interface for dealing with tag data in molecules inspired by
+  # the MoleculeData implementation in pybel.  This does not actually hash the
+  # data, it just reads it from the OBMol object each time and acts like a
+  # hash.
+  class MoleculeData
+    include Enumerable
+
+    OB_PAIR_DATA_TYPE = OpenBabel::OBPairData.new.get_data_type
+    OB_COMMENT_DATA_TYPE = OpenBabel::OBCommentData.new.get_data_type
+
+    DATA_TYPES = [OB_PAIR_DATA_TYPE, OB_COMMENT_DATA_TYPE]
+
+    attr_accessor :obmol
+
+    def initialize(obmol)
+      @obmol = obmol
+    end
+
+    def pair_data(&block)
+      block or return enum_for(__method__)
+      # TODO: should do this with an ob iterator
+      @obmol.get_data.each do |ob_gd|
+        if DATA_TYPES.include?( ob_gd.get_data_type )
+          block.call( OpenBabel.to_pair_data( ob_gd ) )
+        end
+      end
+    end
+
+    def each(&block)
+      block or return enum_for(__method__)
+      pair_data.each do |pd|
+        block.call [pd.get_attribute, pd.get_value]
+      end
+    end
+
+    def to_a
+      each.to_a
+    end
+
+    def size
+      pair_data.to_a.size
+    end
+    alias_method :length, :size
+
+    def [](key)
+      pair_data.find {|pd| pd.get_attribute == key }.get_value
+    end
+
+    # returns the val
+    def []=(key,val)
+      if key?(key)
+        OpenBabel.to_pair_data(@obmol.get_data(key)).set_value(val)
+        val
+      else
+        pd = OpenBabel::OBPairData.new
+        pd.set_attribute(key)
+        pd.set_value(val)
+        @obmol.clone_data(pd)
+        val
+      end
+    end
+
+    def key?(key)
+      pair_data.any? {|pd| pd.get_attribute == key }
+    end
+
+    def keys
+      pair_data.map(&:get_attribute)
+    end
+
+    def values
+      pair_data.map(&:get_value)
+    end
+
+    def delete(key, &block)
+      if key?(key)
+        val = self[key]
+        @obmol.delete_data( @obmol.get_data(key) )
+        val
+      else
+        block ? block.call : nil
+      end
+    end
+
+  end
+end

data/reference/arity_method_list.txt

@@ -1,6 +1,6 @@
-**************************************************
+############################################################
 OpenBabel
-**************************************************
+############################################################
 to_angle_data -1
 to_atom_class_data -1
 to_chiral_data -1
@@ -82,312 +82,396 @@ compare_ring_size -1
 smarts_lex_replace -1
 AliasDataType 0
 tanimoto -1
-**************************************************
-OpenBabel::VectorUnsignedInt
-**************************************************
-to_a -1
-slice -1
-each -1
-select -1
-reject_bang -1
-delete_if -1
-delete_at -1
-__delete_2__ -1
-push -1
-<< -1
-reject -1
-at -1
-[] -1
-[]= -1
-shift -1
-unshift -1
-map_bang -1
-__delete__ -1
-entries -1
-sort 0
-sort_by 0
-grep 1
-count -1
-find -1
-detect -1
-find_index -1
-find_all 0
-collect 0
-map 0
-flat_map 0
-collect_concat 0
-inject -1
-reduce -1
-partition 0
-group_by 0
-first -1
-all? 0
-any? 0
-one? 0
-none? 0
-min 0
-max 0
-minmax 0
-min_by 0
-max_by 0
-minmax_by 0
-member? 1
-each_with_index -1
-reverse_each -1
-each_entry -1
-each_slice 1
-each_cons 1
-each_with_object 1
-zip -1
-take 1
-take_while 0
-drop 1
-drop_while 0
-cycle -1
-chunk -1
-slice_before -1
-**************************************************
-OpenBabel::VectorInt
-**************************************************
-to_a -1
-slice -1
-each -1
-select -1
-reject_bang -1
-delete_if -1
-delete_at -1
-__delete_2__ -1
-push -1
-<< -1
-reject -1
-at -1
-[] -1
-[]= -1
-shift -1
-unshift -1
-map_bang -1
-__delete__ -1
-entries -1
-sort 0
-sort_by 0
-grep 1
-count -1
-find -1
-detect -1
-find_index -1
-find_all 0
-collect 0
-map 0
-flat_map 0
-collect_concat 0
-inject -1
-reduce -1
-partition 0
-group_by 0
-first -1
-all? 0
-any? 0
-one? 0
-none? 0
-min 0
-max 0
-minmax 0
-min_by 0
-max_by 0
-minmax_by 0
-member? 1
-each_with_index -1
-reverse_each -1
-each_entry -1
-each_slice 1
-each_cons 1
-each_with_object 1
-zip -1
-take 1
-take_while 0
-drop 1
-drop_while 0
-cycle -1
-chunk -1
-slice_before -1
-**************************************************
-OpenBabel::OBTorsion
-**************************************************
-clear -1
-empty -1
-add_torsion -1
-set_angle -1
-set_data -1
+############################################################
+OpenBabel::OBMol
+############################################################
+add -1
+reserve_atoms -1
+create_atom -1
+create_bond -1
+create_residue -1
+destroy_atom -1
+destroy_bond -1
+destroy_residue -1
+add_atom -1
+insert_atom -1
+add_bond -1
+add_residue -1
+new_atom -1
+new_bond -1
+new_residue -1
+delete_atom -1
+delete_bond -1
+delete_residue -1
+begin_modify -1
+end_modify -1
+get_mod -1
+increment_mod -1
+decrement_mod -1
+get_flags -1
+get_title -1
+num_atoms -1
+num_bonds -1
+num_hvy_atoms -1
+num_residues -1
+num_rotors -1
+get_atom -1
+get_atom_by_id -1
+get_first_atom -1
+get_bond_by_id -1
+get_bond -1
+get_residue -1
+get_internal_coord -1
+get_torsion -1
 get_angle -1
-get_bond_idx -1
-get_size -1
-get_bc -1
-get_ads -1
-is_proton_rotor -1
-**************************************************
-OpenBabel::OBSymmetryData
-**************************************************
-set_data -1
-set_point_group -1
-set_space_group -1
-get_point_group -1
-get_space_group -1
-set_attribute -1
-set_origin -1
-get_attribute -1
-get_data_type -1
-get_value -1
-get_origin -1
-**************************************************
-OpenBabel::OBConformerData
-**************************************************
-set_dimension -1
-set_energies -1
-set_forces -1
-set_velocities -1
-set_displacements -1
-set_data -1
+get_formula -1
+get_spaced_formula -1
+get_mol_wt -1
+get_exact_mass -1
+get_total_charge -1
+get_total_spin_multiplicity -1
 get_dimension -1
-get_energies -1
-get_forces -1
-get_velocities -1
-get_displacements -1
-get_data -1
-set_attribute -1
-set_origin -1
-get_attribute -1
-get_data_type -1
-get_value -1
-get_origin -1
-**************************************************
-OpenBabel::OBUnitCell
-**************************************************
-set_data -1
-set_offset -1
-set_space_group -1
-set_lattice_type -1
-fill_unit_cell -1
-get_a -1
-get_b -1
-get_c -1
-get_alpha -1
-get_beta -1
-get_gamma -1
-get_offset -1
-get_space_group -1
-get_space_group_name -1
-get_lattice_type -1
-get_cell_vectors -1
-get_cell_matrix -1
-get_ortho_matrix -1
-get_orientation_matrix -1
-get_fractional_matrix -1
-fractional_to_cartesian -1
-cartesian_to_fractional -1
-wrap_cartesian_coordinate -1
-wrap_fractional_coordinate -1
-get_space_group_number -1
-get_cell_volume -1
-set_attribute -1
-set_origin -1
-get_attribute -1
-get_data_type -1
-get_value -1
-get_origin -1
-**************************************************
-OpenBabel::OBRingData
-**************************************************
-set_data -1
-push_back -1
-get_data -1
-begin_rings -1
-end_rings -1
-begin_ring -1
-next_ring -1
-set_attribute -1
-set_origin -1
-get_attribute -1
-get_data_type -1
-get_value -1
-get_origin -1
-**************************************************
-OpenBabel::OBVirtualBond
-**************************************************
-get_bgn -1
-get_end -1
-get_order -1
-get_stereo -1
-set_attribute -1
-set_origin -1
-get_attribute -1
-get_data_type -1
-get_value -1
-get_origin -1
-**************************************************
-OpenBabel::OBSetData
-**************************************************
-add_data -1
-set_data -1
-get_data -1
-get_begin -1
-get_end -1
+get_coordinates -1
+get_sssr -1
+get_lssr -1
+automatic_formal_charge -1
+automatic_partial_charge -1
+set_title -1
+set_formula -1
+set_energy -1
+set_dimension -1
+set_total_charge -1
+set_total_spin_multiplicity -1
+set_internal_coord -1
+set_automatic_formal_charge -1
+set_automatic_partial_charge -1
+set_aromatic_perceived -1
+set_sssrperceived -1
+set_lssrperceived -1
+set_ring_atoms_and_bonds_perceived -1
+set_atom_types_perceived -1
+set_ring_types_perceived -1
+set_chains_perceived -1
+set_chirality_perceived -1
+set_partial_charges_perceived -1
+set_hybridization_perceived -1
+set_implicit_valence_perceived -1
+set_kekule_perceived -1
+set_closure_bonds_perceived -1
+set_hydrogens_added -1
+set_corrected_for_ph -1
+set_aromatic_corrected -1
+set_spin_multiplicity_assigned -1
+set_flags -1
+unset_aromatic_perceived -1
+unset_sssrperceived -1
+unset_ring_types_perceived -1
+unset_partial_charges_perceived -1
+unset_implicit_valence_perceived -1
+unset_hydrogens_added -1
+unset_flag -1
+renumber_atoms -1
+set_coordinates -1
+to_inertial_frame -1
+translate -1
+rotate -1
+kekulize -1
+perceive_kekule_bonds -1
+new_perceive_kekule_bonds -1
+delete_hydrogens -1
+delete_non_polar_hydrogens -1
+delete_hydrogen -1
+add_hydrogens -1
+add_polar_hydrogens -1
+strip_salts -1
+separate -1
+get_next_fragment -1
+convert_dative_bonds -1
+correct_for_ph -1
+assign_spin_multiplicity -1
+set_is_pattern_structure -1
+center -1
+set_torsion -1
+find_sssr -1
+find_lssr -1
+find_ring_atoms_and_bonds -1
+find_chiral_centers -1
+find_children -1
+find_largest_fragment -1
+contig_frag_list -1
+align -1
+connect_the_dots -1
+perceive_bond_orders -1
+find_angles -1
+find_torsions -1
+get_gtdvector -1
+get_givector -1
+get_gidvector -1
+has_2d -1
+has_3d -1
+has_non_zero_coords -1
+has_aromatic_perceived -1
+has_sssrperceived -1
+has_lssrperceived -1
+has_ring_atoms_and_bonds_perceived -1
+has_atom_types_perceived -1
+has_ring_types_perceived -1
+has_chirality_perceived -1
+has_partial_charges_perceived -1
+has_hybridization_perceived -1
+has_implicit_valence_perceived -1
+has_kekule_perceived -1
+has_closure_bonds_perceived -1
+has_chains_perceived -1
+has_hydrogens_added -1
+has_aromatic_corrected -1
+is_corrected_for_ph -1
+has_spin_multiplicity_assigned -1
+is_chiral -1
+empty -1
+num_conformers -1
+set_conformers -1
+add_conformer -1
+set_conformer -1
+copy_conformer -1
+delete_conformer -1
+get_conformer -1
+set_energies -1
+get_energies -1
+get_energy -1
+begin_conformer -1
+next_conformer -1
+get_conformers -1
+begin_atoms -1
+end_atoms -1
+begin_bonds -1
+end_bonds -1
+begin_residues -1
+end_residues -1
+begin_atom -1
+next_atom -1
+begin_bond -1
+next_bond -1
+begin_residue -1
+next_residue -1
+begin_internal_coord -1
+next_internal_coord -1
+clear -1
+do_transformations -1
+has_data -1
 delete_data -1
-set_attribute -1
-set_origin -1
-get_attribute -1
-get_data_type -1
-get_value -1
-get_origin -1
-**************************************************
-OpenBabel::OBPairData
-**************************************************
-set_value -1
-set_attribute -1
-set_origin -1
-get_attribute -1
-get_data_type -1
-get_value -1
-get_origin -1
-**************************************************
-OpenBabel::OBExternalBondData
-**************************************************
-set_data -1
+clone_data -1
+data_size -1
+get_all_data -1
 get_data -1
-set_attribute -1
-set_origin -1
-get_attribute -1
-get_data_type -1
-get_value -1
-get_origin -1
+begin_data -1
+end_data -1
+class_description -1
 **************************************************
-OpenBabel::OBExternalBond
+OpenBabel::OBMol (DIFFERENT????)
 **************************************************
-get_idx -1
+add -1
+reserve_atoms -1
+create_atom -1
+create_bond -1
+create_residue -1
+destroy_atom -1
+destroy_bond -1
+destroy_residue -1
+add_atom -1
+insert_atom -1
+add_bond -1
+add_residue -1
+new_atom -1
+new_bond -1
+new_residue -1
+delete_atom -1
+delete_bond -1
+delete_residue -1
+begin_modify -1
+end_modify -1
+get_mod -1
+increment_mod -1
+decrement_mod -1
+get_flags -1
+get_title -1
+num_atoms -1
+num_bonds -1
+num_hvy_atoms -1
+num_residues -1
+num_rotors -1
 get_atom -1
+get_atom_by_id -1
+get_first_atom -1
+get_bond_by_id -1
 get_bond -1
-set_idx -1
-set_atom -1
-set_bond -1
-**************************************************
-OpenBabel::OBAtom
-**************************************************
-Visit= -1
-Visit -1
-duplicate -1
-set_idx -1
-set_id -1
-set_hyb -1
-set_atomic_num -1
-set_isotope -1
-set_implicit_valence -1
-increment_implicit_valence -1
-decrement_implicit_valence -1
-set_formal_charge -1
-set_spin_multiplicity -1
-set_type -1
-set_partial_charge -1
-set_coord_ptr -1
-set_vector -1
+get_residue -1
+get_internal_coord -1
+get_torsion -1
+get_angle -1
+get_formula -1
+get_spaced_formula -1
+get_mol_wt -1
+get_exact_mass -1
+get_total_charge -1
+get_total_spin_multiplicity -1
+get_dimension -1
+get_coordinates -1
+get_sssr -1
+get_lssr -1
+automatic_formal_charge -1
+automatic_partial_charge -1
+set_title -1
+set_formula -1
+set_energy -1
+set_dimension -1
+set_total_charge -1
+set_total_spin_multiplicity -1
+set_internal_coord -1
+set_automatic_formal_charge -1
+set_automatic_partial_charge -1
+set_aromatic_perceived -1
+set_sssrperceived -1
+set_lssrperceived -1
+set_ring_atoms_and_bonds_perceived -1
+set_atom_types_perceived -1
+set_ring_types_perceived -1
+set_chains_perceived -1
+set_chirality_perceived -1
+set_partial_charges_perceived -1
+set_hybridization_perceived -1
+set_implicit_valence_perceived -1
+set_kekule_perceived -1
+set_closure_bonds_perceived -1
+set_hydrogens_added -1
+set_corrected_for_ph -1
+set_aromatic_corrected -1
+set_spin_multiplicity_assigned -1
+set_flags -1
+unset_aromatic_perceived -1
+unset_sssrperceived -1
+unset_ring_types_perceived -1
+unset_partial_charges_perceived -1
+unset_implicit_valence_perceived -1
+unset_hydrogens_added -1
+unset_flag -1
+renumber_atoms -1
+set_coordinates -1
+to_inertial_frame -1
+translate -1
+rotate -1
+kekulize -1
+perceive_kekule_bonds -1
+new_perceive_kekule_bonds -1
+delete_hydrogens -1
+delete_non_polar_hydrogens -1
+delete_hydrogen -1
+add_hydrogens -1
+add_polar_hydrogens -1
+strip_salts -1
+separate -1
+get_next_fragment -1
+convert_dative_bonds -1
+correct_for_ph -1
+assign_spin_multiplicity -1
+set_is_pattern_structure -1
+center -1
+set_torsion -1
+find_sssr -1
+find_lssr -1
+find_ring_atoms_and_bonds -1
+find_chiral_centers -1
+find_children -1
+find_largest_fragment -1
+contig_frag_list -1
+align -1
+connect_the_dots -1
+perceive_bond_orders -1
+find_angles -1
+find_torsions -1
+get_gtdvector -1
+get_givector -1
+get_gidvector -1
+has_2d -1
+has_3d -1
+has_non_zero_coords -1
+has_aromatic_perceived -1
+has_sssrperceived -1
+has_lssrperceived -1
+has_ring_atoms_and_bonds_perceived -1
+has_atom_types_perceived -1
+has_ring_types_perceived -1
+has_chirality_perceived -1
+has_partial_charges_perceived -1
+has_hybridization_perceived -1
+has_implicit_valence_perceived -1
+has_kekule_perceived -1
+has_closure_bonds_perceived -1
+has_chains_perceived -1
+has_hydrogens_added -1
+has_aromatic_corrected -1
+is_corrected_for_ph -1
+has_spin_multiplicity_assigned -1
+is_chiral -1
+empty -1
+num_conformers -1
+set_conformers -1
+add_conformer -1
+set_conformer -1
+copy_conformer -1
+delete_conformer -1
+get_conformer -1
+set_energies -1
+get_energies -1
+get_energy -1
+begin_conformer -1
+next_conformer -1
+get_conformers -1
+begin_atoms -1
+end_atoms -1
+begin_bonds -1
+end_bonds -1
+begin_residues -1
+end_residues -1
+begin_atom -1
+next_atom -1
+begin_bond -1
+next_bond -1
+begin_residue -1
+next_residue -1
+begin_internal_coord -1
+next_internal_coord -1
+clear -1
+do_transformations -1
+has_data -1
+delete_data -1
+clone_data -1
+data_size -1
+get_all_data -1
+get_data -1
+begin_data -1
+end_data -1
+class_description -1
+############################################################
+OpenBabel::OBAtom
+############################################################
+Visit= -1
+Visit -1
+duplicate -1
+set_idx -1
+set_id -1
+set_hyb -1
+set_atomic_num -1
+set_isotope -1
+set_implicit_valence -1
+increment_implicit_valence -1
+decrement_implicit_valence -1
+set_formal_charge -1
+set_spin_multiplicity -1
+set_type -1
+set_partial_charge -1
+set_coord_ptr -1
+set_vector -1
 set_residue -1
 set_parent -1
 set_aromatic -1
@@ -517,414 +601,130 @@ get_data -1
 begin_data -1
 end_data -1
 class_description -1
+
 **************************************************
-OpenBabel::OBInternalCoord
-**************************************************
-_a= -1
-_a -1
-_b= -1
-_b -1
-_c= -1
-_c -1
-_dst= -1
-_dst -1
-_ang= -1
-_ang -1
-_tor= -1
-_tor -1
-**************************************************
-OpenBabel::OBDescriptor
+OpenBabel::OBBond
 **************************************************
-predict -1
-predict_and_save -1
-get_string_value -1
-compare -1
-order -1
-description -1
-type_id -1
-make_instance -1
-init -1
+Visit= -1
+Visit -1
+set_idx -1
+set_id -1
+set_bo -1
+set_bond_order -1
+set_begin -1
+set_end -1
+set_parent -1
+set_length -1
+set -1
+set_ksingle -1
+set_kdouble -1
+set_ktriple -1
+set_aromatic -1
+set_wedge -1
+set_hash -1
+set_wedge_or_hash -1
+set_up -1
+set_down -1
+set_in_ring -1
+set_closure -1
+unset_hash -1
+unset_wedge -1
+unset_up -1
+unset_down -1
+unset_aromatic -1
+unset_kekule -1
+get_idx -1
 get_id -1
-get_map -1
-default -1
-find_type -1
-filter_compare -1
-add_properties -1
-delete_properties -1
-get_values -1
-get_identifier -1
-get_plugin -1
-list_as_vector -1
-list -1
-list_as_string -1
-first_line -1
-begin -1
-end -1
-**************************************************
-OpenBabel::FastSearchIndexer
-**************************************************
-add -1
-**************************************************
-OpenBabel::FastSearch
-**************************************************
-read_index_file -1
-read_index -1
-find -1
-find_match -1
-find_similar -1
-get_fingerprint -1
-get_index_header -1
-**************************************************
-OpenBabel::FptIndexHeader
-**************************************************
-headerlength= -1
-headerlength -1
-nEntries= -1
-nEntries -1
-words= -1
-words -1
-fpid= -1
-fpid -1
-datafilename= -1
-datafilename -1
-**************************************************
-OpenBabel::OBFingerprint
-**************************************************
-default -1
-find_type -1
-tanimoto -1
-getbitsperint -1
-find_fingerprint -1
-get_plugin -1
-list_as_vector -1
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-end -1
-**************************************************
-OpenBabel::OBAtomClassData
-**************************************************
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-**************************************************
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-**************************************************
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-get_origin -1
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-**************************************************
-OpenBabel::OBMolRingIter
-**************************************************
-good -1
-inc -1
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-ring_id= -1
-ring_id -1
-_path= -1
-_path -1
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 is_in_ring -1
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-**************************************************
-OpenBabel::OBMolPairIter
-**************************************************
-good -1
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-**************************************************
-OpenBabel::OBMolTorsionIter
-**************************************************
-good -1
-inc -1
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-**************************************************
-OpenBabel::OBMolAngleIter
-**************************************************
-good -1
-inc -1
-__ref__ -1
-**************************************************
-OpenBabel::OBResidueAtomIter
-**************************************************
-good -1
-inc -1
-deref -1
-__ref__ -1
+is_rotor -1
+is_amide -1
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+data_size -1
+get_all_data -1
+get_data -1
+begin_data -1
+end_data -1
+class_description -1
+############################################################
+OpenBabel::OBBond
+############################################################
 Visit= -1
 Visit -1
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 set_idx -1
 set_id -1
-set_hyb -1
-set_atomic_num -1
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 get_idx -1
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-**************************************************
-OpenBabel::OBResidueIter
-**************************************************
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-**************************************************
-OpenBabel::OBAtomBondIter
-**************************************************
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 get_parent -1
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 get_length -1
@@ -955,116 +755,853 @@ is_cis_or_trans -1
 is_double_bond_geometry -1
 clear -1
 do_transformations -1
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 get_title -1
 set_title -1
 has_data -1
 delete_data -1
 clone_data -1
 data_size -1
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 get_all_data -1
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 begin_data -1
 end_data -1
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+
+
 **************************************************
-OpenBabel::OBAtomAtomIter
+OpenBabel::VectorUnsignedInt
 **************************************************
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+**************************************************
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+**************************************************
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+**************************************************
+OpenBabel::OBTorsion
+**************************************************
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+**************************************************
+OpenBabel::OBSymmetryData
+**************************************************
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+**************************************************
+OpenBabel::OBConformerData
+**************************************************
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+**************************************************
+OpenBabel::OBUnitCell
+**************************************************
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+**************************************************
+OpenBabel::OBRingData
+**************************************************
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+**************************************************
+OpenBabel::OBVirtualBond
+**************************************************
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+**************************************************
+OpenBabel::OBSetData
+**************************************************
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+**************************************************
+OpenBabel::OBPairData
+**************************************************
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+**************************************************
+OpenBabel::OBExternalBondData
+**************************************************
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+**************************************************
+OpenBabel::OBExternalBond
+**************************************************
+get_idx -1
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+**************************************************
+OpenBabel::OBInternalCoord
+**************************************************
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+_dst= -1
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+**************************************************
+OpenBabel::OBDescriptor
+**************************************************
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+**************************************************
+OpenBabel::FastSearchIndexer
+**************************************************
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+**************************************************
+OpenBabel::FastSearch
+**************************************************
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+OpenBabel::FptIndexHeader
+**************************************************
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+**************************************************
+OpenBabel::OBFingerprint
+**************************************************
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+**************************************************
+OpenBabel::OBAtomClassData
+**************************************************
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+**************************************************
+OpenBabel::AliasData
+**************************************************
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+**************************************************
+OpenBabel::OBMolRingIter
+**************************************************
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+**************************************************
+OpenBabel::OBMolPairIter
+**************************************************
+good -1
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+**************************************************
+OpenBabel::OBMolTorsionIter
+**************************************************
+good -1
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+**************************************************
+OpenBabel::OBMolAngleIter
+**************************************************
+good -1
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+**************************************************
+OpenBabel::OBResidueAtomIter
+**************************************************
+good -1
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+deref -1
+__ref__ -1
+Visit= -1
+Visit -1
+duplicate -1
+set_idx -1
+set_id -1
+set_hyb -1
+set_atomic_num -1
+set_isotope -1
+set_implicit_valence -1
+increment_implicit_valence -1
+decrement_implicit_valence -1
+set_formal_charge -1
+set_spin_multiplicity -1
+set_type -1
+set_partial_charge -1
+set_vector -1
+set_coord_ptr -1
+set_residue -1
+set_parent -1
+set_aromatic -1
+unset_aromatic -1
+set_clockwise_stereo -1
+set_anti_clockwise_stereo -1
+set_positive_stereo -1
+set_negative_stereo -1
+unset_stereo -1
+set_in_ring -1
+set_chiral -1
+clear_coord_ptr -1
+get_formal_charge -1
+get_atomic_num -1
+get_isotope -1
+get_spin_multiplicity -1
+get_atomic_mass -1
+get_exact_mass -1
+get_idx -1
+get_index -1
+get_id -1
+get_coordinate_idx -1
+get_cidx -1
+get_valence -1
+get_hyb -1
+get_implicit_valence -1
+get_hvy_valence -1
+get_hetero_valence -1
+get_type -1
+get_x -1
+get_y -1
+get_z -1
+x -1
+y -1
+z -1
+get_coordinate -1
+get_vector -1
+get_partial_charge -1
+get_residue -1
+get_parent -1
+get_new_bond_vector -1
+get_bond -1
+get_next_atom -1
+begin_bonds -1
+end_bonds -1
+begin_bond -1
+next_bond -1
+begin_nbr_atom -1
+next_nbr_atom -1
+get_distance -1
+get_angle -1
+new_residue -1
+add_residue -1
+delete_residue -1
+add_bond -1
+insert_bond -1
+delete_bond -1
+clear_bond -1
+hto_methyl -1
+set_hyb_and_geom -1
+force_no_h -1
+has_no_hforced -1
+force_impl_h -1
+has_impl_hforced -1
+count_free_oxygens -1
+implicit_hydrogen_count -1
+explicit_hydrogen_count -1
+member_of_ring_count -1
+member_of_ring_size -1
+count_ring_bonds -1
+smallest_bond_angle -1
+average_bond_angle -1
+bosum -1
+kbosum -1
+has_residue -1
+is_hydrogen -1
+is_carbon -1
+is_nitrogen -1
+is_oxygen -1
+is_sulfur -1
+is_phosphorus -1
+is_aromatic -1
+is_in_ring -1
+is_in_ring_size -1
+is_heteroatom -1
+is_not_cor_h -1
+is_connected -1
+is_one_three -1
+is_one_four -1
+is_carboxyl_oxygen -1
+is_phosphate_oxygen -1
+is_sulfate_oxygen -1
+is_nitro_oxygen -1
+is_amide_nitrogen -1
+is_polar_hydrogen -1
+is_non_polar_hydrogen -1
+is_aromatic_noxide -1
+is_chiral -1
+is_axial -1
+is_clockwise -1
+is_anti_clockwise -1
+is_positive_stereo -1
+is_negative_stereo -1
+has_chirality_specified -1
+has_chiral_volume -1
+is_hbond_acceptor -1
+is_hbond_donor -1
+is_hbond_donor_h -1
+has_alpha_beta_unsat -1
+has_bond_of_order -1
+count_bonds_of_order -1
+has_non_single_bond -1
+has_single_bond -1
+has_double_bond -1
+has_aromatic_bond -1
+matches_smarts -1
+clear -1
+do_transformations -1
+class_description -1
+get_title -1
+set_title -1
+has_data -1
+delete_data -1
+clone_data -1
+data_size -1
+get_data -1
+get_all_data -1
+begin_data -1
+end_data -1
+**************************************************
+OpenBabel::OBResidueIter
+**************************************************
+good -1
+inc -1
+deref -1
+__ref__ -1
+add_atom -1
+insert_atom -1
+remove_atom -1
+set_name -1
+set_num -1
+set_chain -1
+set_chain_num -1
+set_idx -1
+set_atom_id -1
+set_het_atom -1
+set_serial_num -1
+get_name -1
+get_num -1
+get_num_string -1
+get_num_atoms -1
+get_chain -1
+get_chain_num -1
+get_idx -1
+get_res_key -1
+get_atoms -1
+get_bonds -1
+get_atom_id -1
+get_serial_num -1
+get_amino_acid_property -1
+get_atom_property -1
+get_residue_property -1
+is_het_atom -1
+is_residue_type -1
+begin_atoms -1
+end_atoms -1
+begin_atom -1
+next_atom -1
+clear -1
+do_transformations -1
+class_description -1
+get_title -1
+set_title -1
+has_data -1
+delete_data -1
+clone_data -1
+data_size -1
+get_data -1
+get_all_data -1
+begin_data -1
+end_data -1
+**************************************************
+OpenBabel::OBAtomBondIter
+**************************************************
+good -1
+inc -1
+deref -1
+__ref__ -1
+Visit= -1
+Visit -1
+set_idx -1
+set_id -1
+set_bo -1
+set_bond_order -1
+set_begin -1
+set_end -1
+set_parent -1
+set_length -1
+set -1
+set_ksingle -1
+set_kdouble -1
+set_ktriple -1
+set_aromatic -1
+set_wedge -1
+set_hash -1
+set_wedge_or_hash -1
+set_up -1
+set_down -1
+set_in_ring -1
+set_closure -1
+unset_hash -1
+unset_wedge -1
+unset_up -1
+unset_down -1
+unset_aromatic -1
+unset_kekule -1
+get_idx -1
+get_id -1
+get_bo -1
+get_bond_order -1
+get_flags -1
+get_begin_atom_idx -1
+get_end_atom_idx -1
+get_begin_atom -1
+get_end_atom -1
+get_nbr_atom -1
+get_parent -1
+get_equib_length -1
+get_length -1
+get_nbr_atom_idx -1
+find_smallest_ring -1
+is_aromatic -1
+is_in_ring -1
+is_rotor -1
+is_amide -1
+is_primary_amide -1
+is_secondary_amide -1
+is_tertiary_amide -1
+is_ester -1
+is_carbonyl -1
+is_single -1
+is_double -1
+is_triple -1
+is_ksingle -1
+is_kdouble -1
+is_ktriple -1
+is_closure -1
+is_up -1
+is_down -1
+is_wedge -1
+is_hash -1
+is_wedge_or_hash -1
+is_cis_or_trans -1
+is_double_bond_geometry -1
+clear -1
+do_transformations -1
+class_description -1
+get_title -1
+set_title -1
+has_data -1
+delete_data -1
+clone_data -1
+data_size -1
+get_data -1
+get_all_data -1
+begin_data -1
+end_data -1
+**************************************************
+OpenBabel::OBAtomAtomIter
+**************************************************
+good -1
+inc -1
+deref -1
+__ref__ -1
+Visit= -1
+Visit -1
+duplicate -1
+set_idx -1
+set_id -1
+set_hyb -1
+set_atomic_num -1
+set_isotope -1
+set_implicit_valence -1
+increment_implicit_valence -1
+decrement_implicit_valence -1
+set_formal_charge -1
+set_spin_multiplicity -1
+set_type -1
+set_partial_charge -1
+set_vector -1
+set_coord_ptr -1
+set_residue -1
+set_parent -1
+set_aromatic -1
+unset_aromatic -1
+set_clockwise_stereo -1
+set_anti_clockwise_stereo -1
+set_positive_stereo -1
+set_negative_stereo -1
+unset_stereo -1
+set_in_ring -1
+set_chiral -1
+clear_coord_ptr -1
+get_formal_charge -1
+get_atomic_num -1
+get_isotope -1
+get_spin_multiplicity -1
+get_atomic_mass -1
+get_exact_mass -1
+get_idx -1
+get_index -1
+get_id -1
+get_coordinate_idx -1
+get_cidx -1
+get_valence -1
+get_hyb -1
+get_implicit_valence -1
+get_hvy_valence -1
+get_hetero_valence -1
+get_type -1
+get_x -1
+get_y -1
+get_z -1
+x -1
+y -1
+z -1
+get_coordinate -1
+get_vector -1
+get_partial_charge -1
+get_residue -1
+get_parent -1
+get_new_bond_vector -1
+get_bond -1
+get_next_atom -1
+begin_bonds -1
+end_bonds -1
+begin_bond -1
+next_bond -1
+begin_nbr_atom -1
+next_nbr_atom -1
+get_distance -1
+get_angle -1
+new_residue -1
+add_residue -1
+delete_residue -1
+add_bond -1
+insert_bond -1
+delete_bond -1
+clear_bond -1
+hto_methyl -1
+set_hyb_and_geom -1
+force_no_h -1
+has_no_hforced -1
+force_impl_h -1
+has_impl_hforced -1
+count_free_oxygens -1
+implicit_hydrogen_count -1
+explicit_hydrogen_count -1
+member_of_ring_count -1
+member_of_ring_size -1
+count_ring_bonds -1
+smallest_bond_angle -1
+average_bond_angle -1
+bosum -1
+kbosum -1
+has_residue -1
 is_hydrogen -1
 is_carbon -1
 is_nitrogen -1
@@ -1971,516 +2508,249 @@ OpenBabel::OBFFConstraints
 clear -1
 get_constraint_energy -1
 get_gradient -1
-setup -1
-set_factor -1
-add_ignore -1
-add_atom_constraint -1
-add_atom_xconstraint -1
-add_atom_yconstraint -1
-add_atom_zconstraint -1
-add_distance_constraint -1
-add_angle_constraint -1
-add_torsion_constraint -1
-delete_constraint -1
-get_factor -1
-size -1
-get_constraint_type -1
-get_constraint_value -1
-get_constraint_atom_a -1
-get_constraint_atom_b -1
-get_constraint_atom_c -1
-get_constraint_atom_d -1
-is_ignored -1
-is_fixed -1
-is_xfixed -1
-is_yfixed -1
-is_zfixed -1
-get_ignored_bit_vec -1
-get_fixed_bit_vec -1
-**************************************************
-OpenBabel::OBFFConstraint
-**************************************************
-factor= -1
-factor -1
-constraint_value= -1
-constraint_value -1
-rab0= -1
-rab0 -1
-rbc0= -1
-rbc0 -1
-type= -1
-type -1
-ia= -1
-ia -1
-ib= -1
-ib -1
-ic= -1
-ic -1
-id= -1
-id -1
-a= -1
-a -1
-b= -1
-b -1
-c= -1
-c -1
-d= -1
-d -1
-grada= -1
-grada -1
-gradb= -1
-gradb -1
-gradc= -1
-gradc -1
-gradd= -1
-gradd -1
-get_gradient -1
-**************************************************
-OpenBabel::OBFFCalculation4
-**************************************************
-d= -1
-d -1
-idx_d= -1
-idx_d -1
-pos_d= -1
-pos_d -1
-force_d= -1
-force_d -1
-c= -1
-c -1
-idx_c= -1
-idx_c -1
-pos_c= -1
-pos_c -1
-force_c= -1
-force_c -1
-energy= -1
-energy -1
-a= -1
-a -1
-b= -1
-b -1
-idx_a= -1
-idx_a -1
-idx_b= -1
-idx_b -1
-pos_a= -1
-pos_a -1
-pos_b= -1
-pos_b -1
-force_a= -1
-force_a -1
-force_b= -1
-force_b -1
-setup_pointers -1
-**************************************************
-OpenBabel::OBFFCalculation3
-**************************************************
-c= -1
-c -1
-idx_c= -1
-idx_c -1
-pos_c= -1
-pos_c -1
-force_c= -1
-force_c -1
-energy= -1
-energy -1
-a= -1
-a -1
-b= -1
-b -1
-idx_a= -1
-idx_a -1
-idx_b= -1
-idx_b -1
-pos_a= -1
-pos_a -1
-pos_b= -1
-pos_b -1
-force_a= -1
-force_a -1
-force_b= -1
-force_b -1
-setup_pointers -1
-**************************************************
-OpenBabel::OBFFCalculation2
-**************************************************
-energy= -1
-energy -1
-a= -1
-a -1
-b= -1
-b -1
-idx_a= -1
-idx_a -1
-idx_b= -1
-idx_b -1
-pos_a= -1
-pos_a -1
-pos_b= -1
-pos_b -1
-force_a= -1
-force_a -1
-force_b= -1
-force_b -1
-setup_pointers -1
-**************************************************
-OpenBabel::OBFFParameter
-**************************************************
-a= -1
-a -1
-b= -1
-b -1
-c= -1
-c -1
-d= -1
-d -1
-_a= -1
-_a -1
-_b= -1
-_b -1
-_c= -1
-_c -1
-_d= -1
-_d -1
-_ipar= -1
-_ipar -1
-_dpar= -1
-_dpar -1
-clear -1
-**************************************************
-OpenBabel::OBSSMatch
-**************************************************
-match -1
-**************************************************
-OpenBabel::OBSmartsMatcher
-**************************************************
-match -1
-**************************************************
-OpenBabel::OBSmartsPattern
-**************************************************
-init -1
-get_smarts -1
-empty -1
-is_valid -1
-num_atoms -1
-num_bonds -1
-get_bond -1
-get_atomic_num -1
-get_charge -1
-get_vector_binding -1
-match -1
-has_match -1
-restricted_match -1
-num_matches -1
-get_map_list -1
-begin_mlist -1
-end_mlist -1
-get_umap_list -1
-write_map_list -1
-**************************************************
-OpenBabel::OBRTree
-**************************************************
-get_atom_idx -1
-path_to_root -1
-**************************************************
-OpenBabel::OBRingSearch
-**************************************************
-sort_rings -1
-remove_redundant -1
-add_ring_from_closure -1
-save_unique_ring -1
-write_rings -1
-begin_rings -1
-end_rings -1
+setup -1
+set_factor -1
+add_ignore -1
+add_atom_constraint -1
+add_atom_xconstraint -1
+add_atom_yconstraint -1
+add_atom_zconstraint -1
+add_distance_constraint -1
+add_angle_constraint -1
+add_torsion_constraint -1
+delete_constraint -1
+get_factor -1
+size -1
+get_constraint_type -1
+get_constraint_value -1
+get_constraint_atom_a -1
+get_constraint_atom_b -1
+get_constraint_atom_c -1
+get_constraint_atom_d -1
+is_ignored -1
+is_fixed -1
+is_xfixed -1
+is_yfixed -1
+is_zfixed -1
+get_ignored_bit_vec -1
+get_fixed_bit_vec -1
 **************************************************
-OpenBabel::OBRing
+OpenBabel::OBFFConstraint
 **************************************************
-ring_id= -1
-ring_id -1
-_path= -1
-_path -1
-_pathset= -1
-_pathset -1
-size -1
-path_size -1
-is_aromatic -1
-set_type -1
-get_type -1
-get_root_atom -1
-is_member -1
-is_in_ring -1
-set_parent -1
-get_parent -1
-find_center_and_normal -1
+factor= -1
+factor -1
+constraint_value= -1
+constraint_value -1
+rab0= -1
+rab0 -1
+rbc0= -1
+rbc0 -1
+type= -1
+type -1
+ia= -1
+ia -1
+ib= -1
+ib -1
+ic= -1
+ic -1
+id= -1
+id -1
+a= -1
+a -1
+b= -1
+b -1
+c= -1
+c -1
+d= -1
+d -1
+grada= -1
+grada -1
+gradb= -1
+gradb -1
+gradc= -1
+gradc -1
+gradd= -1
+gradd -1
+get_gradient -1
 **************************************************
-OpenBabel::OBMol
+OpenBabel::OBFFCalculation4
 **************************************************
-add -1
-reserve_atoms -1
-create_atom -1
-create_bond -1
-create_residue -1
-destroy_atom -1
-destroy_bond -1
-destroy_residue -1
-add_atom -1
-insert_atom -1
-add_bond -1
-add_residue -1
-new_atom -1
-new_bond -1
-new_residue -1
-delete_atom -1
-delete_bond -1
-delete_residue -1
-begin_modify -1
-end_modify -1
-get_mod -1
-increment_mod -1
-decrement_mod -1
-get_flags -1
-get_title -1
-num_atoms -1
-num_bonds -1
-num_hvy_atoms -1
-num_residues -1
-num_rotors -1
-get_atom -1
-get_atom_by_id -1
-get_first_atom -1
-get_bond_by_id -1
-get_bond -1
-get_residue -1
-get_internal_coord -1
-get_torsion -1
-get_angle -1
-get_formula -1
-get_spaced_formula -1
-get_mol_wt -1
-get_exact_mass -1
-get_total_charge -1
-get_total_spin_multiplicity -1
-get_dimension -1
-get_coordinates -1
-get_sssr -1
-get_lssr -1
-automatic_formal_charge -1
-automatic_partial_charge -1
-set_title -1
-set_formula -1
-set_energy -1
-set_dimension -1
-set_total_charge -1
-set_total_spin_multiplicity -1
-set_internal_coord -1
-set_automatic_formal_charge -1
-set_automatic_partial_charge -1
-set_aromatic_perceived -1
-set_sssrperceived -1
-set_lssrperceived -1
-set_ring_atoms_and_bonds_perceived -1
-set_atom_types_perceived -1
-set_ring_types_perceived -1
-set_chains_perceived -1
-set_chirality_perceived -1
-set_partial_charges_perceived -1
-set_hybridization_perceived -1
-set_implicit_valence_perceived -1
-set_kekule_perceived -1
-set_closure_bonds_perceived -1
-set_hydrogens_added -1
-set_corrected_for_ph -1
-set_aromatic_corrected -1
-set_spin_multiplicity_assigned -1
-set_flags -1
-unset_aromatic_perceived -1
-unset_sssrperceived -1
-unset_ring_types_perceived -1
-unset_partial_charges_perceived -1
-unset_implicit_valence_perceived -1
-unset_hydrogens_added -1
-unset_flag -1
-renumber_atoms -1
-set_coordinates -1
-to_inertial_frame -1
-translate -1
-rotate -1
-kekulize -1
-perceive_kekule_bonds -1
-new_perceive_kekule_bonds -1
-delete_hydrogens -1
-delete_non_polar_hydrogens -1
-delete_hydrogen -1
-add_hydrogens -1
-add_polar_hydrogens -1
-strip_salts -1
-separate -1
-get_next_fragment -1
-convert_dative_bonds -1
-correct_for_ph -1
-assign_spin_multiplicity -1
-set_is_pattern_structure -1
-center -1
-set_torsion -1
-find_sssr -1
-find_lssr -1
-find_ring_atoms_and_bonds -1
-find_chiral_centers -1
-find_children -1
-find_largest_fragment -1
-contig_frag_list -1
-align -1
-connect_the_dots -1
-perceive_bond_orders -1
-find_angles -1
-find_torsions -1
-get_gtdvector -1
-get_givector -1
-get_gidvector -1
-has_2d -1
-has_3d -1
-has_non_zero_coords -1
-has_aromatic_perceived -1
-has_sssrperceived -1
-has_lssrperceived -1
-has_ring_atoms_and_bonds_perceived -1
-has_atom_types_perceived -1
-has_ring_types_perceived -1
-has_chirality_perceived -1
-has_partial_charges_perceived -1
-has_hybridization_perceived -1
-has_implicit_valence_perceived -1
-has_kekule_perceived -1
-has_closure_bonds_perceived -1
-has_chains_perceived -1
-has_hydrogens_added -1
-has_aromatic_corrected -1
-is_corrected_for_ph -1
-has_spin_multiplicity_assigned -1
-is_chiral -1
-empty -1
-num_conformers -1
-set_conformers -1
-add_conformer -1
-set_conformer -1
-copy_conformer -1
-delete_conformer -1
-get_conformer -1
-set_energies -1
-get_energies -1
-get_energy -1
-begin_conformer -1
-next_conformer -1
-get_conformers -1
-begin_atoms -1
-end_atoms -1
-begin_bonds -1
-end_bonds -1
-begin_residues -1
-end_residues -1
-begin_atom -1
-next_atom -1
-begin_bond -1
-next_bond -1
-begin_residue -1
-next_residue -1
-begin_internal_coord -1
-next_internal_coord -1
+d= -1
+d -1
+idx_d= -1
+idx_d -1
+pos_d= -1
+pos_d -1
+force_d= -1
+force_d -1
+c= -1
+c -1
+idx_c= -1
+idx_c -1
+pos_c= -1
+pos_c -1
+force_c= -1
+force_c -1
+energy= -1
+energy -1
+a= -1
+a -1
+b= -1
+b -1
+idx_a= -1
+idx_a -1
+idx_b= -1
+idx_b -1
+pos_a= -1
+pos_a -1
+pos_b= -1
+pos_b -1
+force_a= -1
+force_a -1
+force_b= -1
+force_b -1
+setup_pointers -1
+**************************************************
+OpenBabel::OBFFCalculation3
+**************************************************
+c= -1
+c -1
+idx_c= -1
+idx_c -1
+pos_c= -1
+pos_c -1
+force_c= -1
+force_c -1
+energy= -1
+energy -1
+a= -1
+a -1
+b= -1
+b -1
+idx_a= -1
+idx_a -1
+idx_b= -1
+idx_b -1
+pos_a= -1
+pos_a -1
+pos_b= -1
+pos_b -1
+force_a= -1
+force_a -1
+force_b= -1
+force_b -1
+setup_pointers -1
+**************************************************
+OpenBabel::OBFFCalculation2
+**************************************************
+energy= -1
+energy -1
+a= -1
+a -1
+b= -1
+b -1
+idx_a= -1
+idx_a -1
+idx_b= -1
+idx_b -1
+pos_a= -1
+pos_a -1
+pos_b= -1
+pos_b -1
+force_a= -1
+force_a -1
+force_b= -1
+force_b -1
+setup_pointers -1
+**************************************************
+OpenBabel::OBFFParameter
+**************************************************
+a= -1
+a -1
+b= -1
+b -1
+c= -1
+c -1
+d= -1
+d -1
+_a= -1
+_a -1
+_b= -1
+_b -1
+_c= -1
+_c -1
+_d= -1
+_d -1
+_ipar= -1
+_ipar -1
+_dpar= -1
+_dpar -1
 clear -1
-do_transformations -1
-has_data -1
-delete_data -1
-clone_data -1
-data_size -1
-get_all_data -1
-get_data -1
-begin_data -1
-end_data -1
-class_description -1
 **************************************************
-OpenBabel::OBBond
+OpenBabel::OBSSMatch
 **************************************************
-Visit= -1
-Visit -1
-set_idx -1
-set_id -1
-set_bo -1
-set_bond_order -1
-set_begin -1
-set_end -1
-set_parent -1
-set_length -1
-set -1
-set_ksingle -1
-set_kdouble -1
-set_ktriple -1
-set_aromatic -1
-set_wedge -1
-set_hash -1
-set_wedge_or_hash -1
-set_up -1
-set_down -1
-set_in_ring -1
-set_closure -1
-unset_hash -1
-unset_wedge -1
-unset_up -1
-unset_down -1
-unset_aromatic -1
-unset_kekule -1
-get_idx -1
-get_id -1
-get_bo -1
-get_bond_order -1
-get_flags -1
-get_begin_atom_idx -1
-get_end_atom_idx -1
-get_begin_atom -1
-get_end_atom -1
-get_nbr_atom -1
-get_parent -1
-get_equib_length -1
-get_length -1
-get_nbr_atom_idx -1
-find_smallest_ring -1
+match -1
+**************************************************
+OpenBabel::OBSmartsMatcher
+**************************************************
+match -1
+**************************************************
+OpenBabel::OBSmartsPattern
+**************************************************
+init -1
+get_smarts -1
+empty -1
+is_valid -1
+num_atoms -1
+num_bonds -1
+get_bond -1
+get_atomic_num -1
+get_charge -1
+get_vector_binding -1
+match -1
+has_match -1
+restricted_match -1
+num_matches -1
+get_map_list -1
+begin_mlist -1
+end_mlist -1
+get_umap_list -1
+write_map_list -1
+**************************************************
+OpenBabel::OBRTree
+**************************************************
+get_atom_idx -1
+path_to_root -1
+**************************************************
+OpenBabel::OBRingSearch
+**************************************************
+sort_rings -1
+remove_redundant -1
+add_ring_from_closure -1
+save_unique_ring -1
+write_rings -1
+begin_rings -1
+end_rings -1
+**************************************************
+OpenBabel::OBRing
+**************************************************
+ring_id= -1
+ring_id -1
+_path= -1
+_path -1
+_pathset= -1
+_pathset -1
+size -1
+path_size -1
 is_aromatic -1
+set_type -1
+get_type -1
+get_root_atom -1
+is_member -1
 is_in_ring -1
-is_rotor -1
-is_amide -1
-is_primary_amide -1
-is_secondary_amide -1
-is_tertiary_amide -1
-is_ester -1
-is_carbonyl -1
-is_single -1
-is_double -1
-is_triple -1
-is_ksingle -1
-is_kdouble -1
-is_ktriple -1
-is_closure -1
-is_up -1
-is_down -1
-is_wedge -1
-is_hash -1
-is_wedge_or_hash -1
-is_cis_or_trans -1
-is_double_bond_geometry -1
-clear -1
-do_transformations -1
-get_title -1
-set_title -1
-has_data -1
-delete_data -1
-clone_data -1
-data_size -1
-get_all_data -1
-get_data -1
-begin_data -1
-end_data -1
-class_description -1
+set_parent -1
+get_parent -1
+find_center_and_normal -1
 **************************************************
 OpenBabel::OBResidue
 **************************************************