rubabel 0.1.0

data/lib/rubabel/molecule.rb

@@ -0,0 +1,305 @@
+require 'openbabel'
+require 'rubabel'
+require 'rubabel/atom'
+require 'rubabel/bond'
+
+class OpenBabel::OBMol
+  def upcast
+    Rubabel::Molecule.new(self)
+  end
+end
+
+module Rubabel
+  # yet to implement: 
+  class Molecule
+    include Enumerable
+
+    # the OpenBabel::OBmol object
+    attr_accessor :ob
+
+    class << self
+      def from_file(file, type=nil)
+        Rubabel.read_file(file, type)
+      end
+
+      def from_string(string, type=:smi)
+        Rubabel.read_string(string, type)
+      end
+    end
+
+    DEFAULT_OUT_TYPE = :can
+
+    def initialize(obmol, obconv=nil)
+      @obconv = obconv
+      @ob = obmol
+    end
+
+    # returns a list of atom indices matching the patterns (corresponds to
+    # the OBSmartsPattern::GetUMapList() method).  Note that the original
+    # GetUMapList returns atom *numbers* (i.e., the index + 1).  This method
+    # returns the zero indexed indices.
+    def smarts_indices(smarts_or_string)
+      pattern = smarts_or_string.is_a?(Rubabel::Smarts) ? smarts_or_string : Rubabel::Smarts.new(smarts_or_string)
+      pattern.ob.match(@ob)
+      pattern.ob.get_umap_list.map {|atm_indices| atm_indices.map {|i| i - 1 } }
+    end
+
+    # yields atom arrays matching the pattern.  returns an enumerator if no
+    # block is given
+    def each_match(smarts_or_string, &block)
+      block or return enum_for(__method__, smarts_or_string)
+      _atoms = self.atoms
+      smarts_indices(smarts_or_string).each do |ar|
+        block.call(_atoms.values_at(*ar))
+      end
+    end
+
+    # returns an array of matching atom sets.  Consider using each_match.
+    def matches(smarts_or_string)
+      each_match(smarts_or_string).map.to_a
+    end
+
+    def matches?(smarts_or_string)
+      # TODO: probably a more efficient way to do this using API
+      smarts_indices(smarts_or_string).size > 0
+    end
+
+    def charge
+      @ob.get_total_charge
+    end
+
+    def charge=(v)
+      @ob.set_total_charge(v)
+    end
+
+    def spin
+      @ob.get_total_spin_multiplicity
+    end
+
+    # returns an array of OpenBabel::OBRing objects.
+    def ob_sssr
+      @ob.get_sssr.to_a
+    end
+
+    def exact_mass
+      @ob.get_exact_mass
+    end
+
+    def mol_wt
+      @ob.get_mol_wt
+    end
+
+    alias_method :avg_mass, :mol_wt
+
+    def exact_mass
+      @ob.get_exact_mass
+    end
+
+    #def conformers
+      # Currently returns an object of type
+      # SWIG::TYPE_p_std__vectorT_double_p_std__allocatorT_double_p_t_t
+      #vec = @ob.get_conformers
+    #end
+
+    def add_h!
+      @ob.add_hydrogens
+    end
+    #alias_method :add_h!, :add_hydrogens!
+
+    # creates a new molecule (currently writes to smiles and uses babel
+    # commandline to get hydrogens at a given pH; this is because no pH model
+    # in ruby bindings currently).
+    def add_h_at_ph(ph=7.4)
+      # write the file with the molecule
+      self.write_file("tmp.smi")
+      system "#{Rubabel::CMD[:babel]} -i smi tmp.smi -p #{ph} -o can tmp.can"
+      Molecule.from_file("tmp.can")
+    end
+    #alias_method :add_h!, :add_hydrogens!
+
+    def remove_h!
+      @ob.delete_hydrogens
+    end
+
+    def separate!
+      @ob.separate
+    end
+
+    # returns a string representation of the molecular formula.  Not sensitive
+    # to add_h!
+    def formula
+      @ob.get_formula
+    end
+
+    # returns just the smiles string :smi (not the id)
+    def smiles
+      to_s(:smi)
+    end
+
+    # returns just the smiles string (not the id)
+    def csmiles
+      to_s(:can)
+    end
+
+    # equal if their canonical SMILES strings (including ID) are equal.  This
+    # may become more rigorous in the future
+    def ==(other)
+      self.write_string(:can) == other.write_string(:can)
+    end
+
+    # iterates over the molecule's Rubabel::Atom objects
+    def each_atom(&block)
+      # could use the C++ iterator in the future
+      block or return enum_for(__method__)
+      iter = @ob.begin_atoms
+      atom = @ob.begin_atom(iter)
+      while atom
+        block.call atom.upcast
+        atom = @ob.next_atom(iter)
+      end
+    end
+    alias_method :each, :each_atom
+
+    # iterates over the molecule's Rubabel::Bond objects
+    def each_bond(&block)
+      # could use the C++ iterator in the future
+      block or return enum_for(__method__)
+      iter = @ob.begin_bonds
+      obbond = @ob.begin_bond(iter)
+      while obbond
+        block.call obbond.upcast
+        obbond = @ob.next_bond(iter)
+      end
+      self
+    end
+
+    # returns the array of bonds.  Consider using #each_bond
+    def bonds
+      each_bond.map.to_a
+    end
+
+    # returns the array of atoms. Consider using #each
+    def atoms
+      each_atom.map.to_a
+    end
+
+    def dim
+      @ob.get_dimension
+    end
+
+    #def each_bond(&block)
+
+    # TODO: implement
+    #def calc_desc(descnames=[])
+    #end
+
+    # TODO: implement
+    # list of supported descriptors. (Not Yet Implemented!)
+    #def descs
+    #end
+
+    # TODO: implement
+    #def fingerprint(type='FP2')
+    #end
+    #alias_method :calc_fp, :fingerprint
+
+    def split(*bonds)
+      bonds.each do |bond|
+        unless @ob.delete_bond(bond.ob, false)
+          raise "#{bond.inspect} not deleted!" 
+        end
+      end
+      frags = @ob.separate.map(&:upcast)
+      bonds.each {|bond| @ob.add_bond(bond.ob) }
+      frags
+    end
+
+    alias_method :separate, :split
+
+    # emits smiles without the trailing tab, newline, or id.  Use write_string
+    # to get the default OpenBabel behavior (ie., tabs and newlines).
+    def to_s(type=DEFAULT_OUT_TYPE)
+      string = write_string(type)
+      case type
+      when :smi, :smiles, :can
+        # remove name with openbabel options in the future
+        string.split(/\s+/).first
+      else
+        string
+      end
+    end
+
+    # sensitive to add_h!
+    def num_atoms() @ob.num_atoms  end
+    def num_bonds() @ob.num_bonds  end
+    def num_hvy_atoms() @ob.num_hvy_atoms  end
+    def num_residues() @ob.num_residues  end
+    def num_rotors() @ob.num_rotors  end
+
+    # If filename_or_type is a symbol, then it will return a string of that type.
+    # If filename_or_type is a string, will write to the filename
+    # given no args, returns a DEFAULT_OUT_TYPE string
+    def write(filename_or_type=:can)
+      if filename_or_type.is_a?(Symbol)
+        write_string(filename_or_type)
+      else
+        write_file(filename_or_type)
+      end
+    end
+
+    def write_string(type=DEFAULT_OUT_TYPE)
+      @obconv ||= OpenBabel::OBConversion.new
+      @obconv.set_out_format(type.to_s)
+      @obconv.write_string(@ob)
+    end
+
+    # writes to the file based on the extension
+    def write_file(filename)
+      type = Rubabel.filetype(filename)
+      File.write(filename, write_string(type))
+    end
+
+    def inspect
+      "#<Mol #{to_s}>"
+    end
+
+  end
+end
+
+# NOTES TO SELF:
+=begin
+~/tools/openbabel-rvmruby1.9.3/bin/babel -L descriptors
+abonds    Number of aromatic bonds
+atoms    Number of atoms
+bonds    Number of bonds
+cansmi    Canonical SMILES
+cansmiNS    Canonical SMILES without isotopes or stereo
+dbonds    Number of double bonds
+formula    Chemical formula
+HBA1    Number of Hydrogen Bond Acceptors 1 (JoelLib)
+HBA2    Number of Hydrogen Bond Acceptors 2 (JoelLib)
+HBD    Number of Hydrogen Bond Donors (JoelLib)
+InChI    IUPAC InChI identifier
+InChIKey    InChIKey
+L5    Lipinski Rule of Five
+logP    octanol/water partition coefficient
+MR    molar refractivity
+MW    Molecular Weight filter
+nF    Number of Fluorine Atoms
+s    SMARTS filter
+sbonds    Number of single bonds
+smarts    SMARTS filter
+tbonds    Number of triple bonds
+title    For comparing a molecule's title
+TPSA    topological polar surface area
+
+# why can't I find any descriptors????
+>> require 'openbabel'
+=> true
+>> OpenBabel::OBDescriptor.find_type("logP")
+=> nil
+>> OpenBabel::OBDescriptor.find_type("MR")
+=> nil
+
+=end
+

data/lib/rubabel/pm.rb

@@ -0,0 +1,38 @@
+
+class Object
+  ANSI_BOLD       = "\033[1m"
+  ANSI_RESET      = "\033[0m"
+  ANSI_LGRAY    = "\033[0;37m"
+  ANSI_GRAY     = "\033[1;30m"
+
+  # Print object's methods
+  def pm(*options)
+    methods = self.methods
+    methods -= Object.methods unless options.include? :more
+    filter = options.select {|opt| opt.kind_of? Regexp}.first
+    methods = methods.select {|name| name =~ filter} if filter
+
+    data = methods.sort.collect do |name|
+      method = self.method(name)
+      if method.arity == 0
+        args = "()"
+      elsif method.arity > 0
+        n = method.arity
+        args = "(#{(1..n).collect {|i| "arg#{i}"}.join(", ")})"
+      elsif method.arity < 0
+        n = -method.arity
+        args = "(#{(1..n).collect {|i| "arg#{i}"}.join(", ")}, ...)"
+      end
+      klass = $1 if method.inspect =~ /Method: (.*?)#/
+      [name, args, klass]
+    end
+    max_name = data.collect {|item| item[0].size}.max
+    max_args = data.collect {|item| item[1].size}.max
+    data.each do |item| 
+      print " #{ANSI_BOLD}#{item[0].rjust(max_name)}#{ANSI_RESET}"
+      print "#{ANSI_GRAY}#{item[1].ljust(max_args)}#{ANSI_RESET}"
+      print "   #{ANSI_LGRAY}#{item[2]}#{ANSI_RESET}\n"
+    end
+    data.size
+  end
+end

data/lib/rubabel/smarts.rb

@@ -0,0 +1,27 @@
+require 'openbabel'
+
+module Rubabel
+  class Smarts
+    
+    attr_accessor :ob
+
+    def initialize(string)
+      @string = string
+      @ob = OpenBabel::OBSmartsPattern.new
+      unless @ob.init(string)
+        raise ArgumentError, "#{string} not a valid SMARTS string"
+      end
+    end
+
+    def to_s
+      # would like to do the above, but just getting this:
+      # #<SWIG::TYPE_p_std__string:0x000000022ecd70
+      # @obsmarts.get_smarts.to_s
+      @string
+    end
+
+    def inspect
+      "<Rubabel::Smarts #{to_s}>"
+    end
+  end
+end

data/reference/OBConversion_methods.txt

@@ -0,0 +1,47 @@
+get_in_stream
+get_out_stream
+set_in_stream
+set_out_stream
+set_in_and_out_formats
+set_in_format
+set_out_format
+get_in_format
+get_out_format
+get_in_filename
+get_in_pos
+get_in_len
+get_title
+get_aux_conv
+set_aux_conv
+is_option
+get_options
+add_option
+remove_option
+set_options
+copy_options
+get_supported_input_format
+get_supported_output_format
+convert
+full_convert
+add_chem_object
+get_chem_object
+is_last
+is_first_input
+set_first_input
+get_output_index
+set_output_index
+set_more_files_to_come
+set_one_object_only
+set_last
+is_last_file
+get_count
+write
+write_string
+write_file
+close_out_file
+read
+read_string
+read_file
+open_in_and_out_files
+report_number_converted
+num_input_objects

data/reference/arity_method_list.txt

@@ -0,0 +1,3553 @@
+**************************************************
+OpenBabel
+**************************************************
+to_angle_data -1
+to_atom_class_data -1
+to_chiral_data -1
+to_comment_data -1
+to_conformer_data -1
+to_external_bond_data -1
+to_grid_data -1
+to_matrix_data -1
+to_nasa_thermo_data -1
+to_pair_data -1
+to_rate_data -1
+to_rotamer_list -1
+to_rotation_data -1
+to_serial_nums -1
+to_set_data -1
+to_symmetry_data -1
+to_torsion_data -1
+to_unit_cell -1
+to_vector_data -1
+to_vibration_data -1
+to_virtual_bond -1
+double_multiply -1
+double_add -1
+double_modulus -1
+rotate_coords -1
+calc_rms -1
+<< -1
++ -1
+- -1
+/ -1
+* -1
+dot -1
+cross -1
+vector_angle -1
+calc_torsion_angle -1
+point_2plane_signed -1
+point_2plane -1
+point_2plane_angle -1
+point_2line -1
+VZero 0
+VX 0
+VY 0
+VZ 0
+obrelease_version -1
+obErrorLog 0
+obErrorLog= 1
+Residue 0
+Residue= 1
+ElemDesc 0
+ElemDesc= 1
+ResNo 0
+ResNo= 1
+ElemNo 0
+ElemNo= 1
+throw_error -1
+cartesian_to_internal -1
+internal_to_cartesian -1
+new_extension -1
+etab 0
+etab= 1
+ttab 0
+ttab= 1
+isotab 0
+isotab= 1
+aromtyper 0
+aromtyper= 1
+atomtyper 0
+atomtyper= 1
+chainsparser 0
+chainsparser= 1
+resdat 0
+resdat= 1
+NoId 0
+get_rmat -1
+ob_make_rmat -1
+qtrfit -1
+superimpose -1
+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
+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_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
+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
+get_data -1
+set_attribute -1
+set_origin -1
+get_attribute -1
+get_data_type -1
+get_value -1
+get_origin -1
+**************************************************
+OpenBabel::OBExternalBond
+**************************************************
+get_idx -1
+get_atom -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
+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
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+data_size -1
+get_all_data -1
+get_data -1
+begin_data -1
+end_data -1
+class_description -1
+**************************************************
+OpenBabel::OBInternalCoord
+**************************************************
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+_a -1
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+_b -1
+_c= -1
+_c -1
+_dst= -1
+_dst -1
+_ang= -1
+_ang -1
+_tor= -1
+_tor -1
+**************************************************
+OpenBabel::OBDescriptor
+**************************************************
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+first_line -1
+begin -1
+end -1
+**************************************************
+OpenBabel::FastSearchIndexer
+**************************************************
+add -1
+**************************************************
+OpenBabel::FastSearch
+**************************************************
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+read_index -1
+find -1
+find_match -1
+find_similar -1
+get_fingerprint -1
+get_index_header -1
+**************************************************
+OpenBabel::FptIndexHeader
+**************************************************
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+nEntries= -1
+nEntries -1
+words= -1
+words -1
+fpid= -1
+fpid -1
+datafilename= -1
+datafilename -1
+**************************************************
+OpenBabel::OBFingerprint
+**************************************************
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+list_as_string -1
+first_line -1
+begin -1
+end -1
+**************************************************
+OpenBabel::OBAtomClassData
+**************************************************
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+set_attribute -1
+set_origin -1
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+get_value -1
+get_origin -1
+**************************************************
+OpenBabel::AliasData
+**************************************************
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+get_data_type -1
+get_value -1
+get_origin -1
+revert_to_alias_form -1
+**************************************************
+OpenBabel::OBMolRingIter
+**************************************************
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+ring_id -1
+_path= -1
+_path -1
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+get_root_atom -1
+is_member -1
+is_in_ring -1
+set_parent -1
+get_parent -1
+find_center_and_normal -1
+**************************************************
+OpenBabel::OBMolPairIter
+**************************************************
+good -1
+inc -1
+__ref__ -1
+**************************************************
+OpenBabel::OBMolTorsionIter
+**************************************************
+good -1
+inc -1
+__ref__ -1
+**************************************************
+OpenBabel::OBMolAngleIter
+**************************************************
+good -1
+inc -1
+__ref__ -1
+**************************************************
+OpenBabel::OBResidueAtomIter
+**************************************************
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+has_alpha_beta_unsat -1
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+data_size -1
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+get_all_data -1
+begin_data -1
+end_data -1
+**************************************************
+OpenBabel::OBResidueIter
+**************************************************
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+data_size -1
+get_data -1
+get_all_data -1
+begin_data -1
+end_data -1
+**************************************************
+OpenBabel::OBAtomBondIter
+**************************************************
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+**************************************************
+OpenBabel::OBAtomAtomIter
+**************************************************
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+begin_data -1
+end_data -1
+**************************************************
+OpenBabel::OBMolBondIter
+**************************************************
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+begin_data -1
+end_data -1
+**************************************************
+OpenBabel::OBMolBondBFSIter
+**************************************************
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+**************************************************
+OpenBabel::OBMolAtomBFSIter
+**************************************************
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+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::OBMolAtomDFSIter
+**************************************************
+good -1
+inc -1
+deref -1
+__ref__ -1
+next -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::OBMolAtomIter
+**************************************************
+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
+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::OBRotamerList
+**************************************************
+setup -1
+num_rotors -1
+num_rotamers -1
+add_rotamer -1
+add_rotamers -1
+get_reference_array -1
+begin_rotamer -1
+end_rotamer -1
+create_conformer_list -1
+expand_conformer_list -1
+set_current_coordinates -1
+set_base_coordinate_sets -1
+num_base_coordinate_sets -1
+get_base_coordinate_set -1
+num_atoms -1
+set_attribute -1
+set_origin -1
+get_attribute -1
+get_data_type -1
+get_value -1
+get_origin -1
+**************************************************
+OpenBabel::OBRotorKeys
+**************************************************
+clear -1
+num_keys -1
+add_rotor -1
+next -1
+get_key -1
+**************************************************
+OpenBabel::RotorDigit
+**************************************************
+set_size -1
+set_state -1
+get_state -1
+size -1
+next -1
+**************************************************
+OpenBabel::OBRotorList
+**************************************************
+clear -1
+size -1
+is_fixed_bond -1
+has_fixed_bonds -1
+remove_sym_vals -1
+setup -1
+set_fixed_bonds -1
+init -1
+set_quiet -1
+set_rot_atoms -1
+find_rotors -1
+set_eval_atoms -1
+assign_tor_vals -1
+begin_rotor -1
+next_rotor -1
+begin_rotors -1
+end_rotors -1
+identify_eval_atoms -1
+set_fix_atoms -1
+has_fixed_atoms -1
+ignore_symmetry_removal -1
+set_rot_atoms_by_fix -1
+**************************************************
+OpenBabel::OBRotor
+**************************************************
+set_bond -1
+set_idx -1
+set_dihedral_atoms -1
+set_rot_atoms -1
+set_torsion_values -1
+set_fixed_bonds -1
+set_to_angle -1
+set_rotor -1
+precompute -1
+precalc -1
+set -1
+get_bond -1
+size -1
+get_idx -1
+get_dihedral_atoms -1
+get_torsion_values -1
+get_fixed_bonds -1
+calc_torsion -1
+calc_bond_length -1
+begin_tor_increment -1
+end_tor_increment -1
+remove_sym_torsion_values -1
+set_delta -1
+get_delta -1
+get_fixed_atoms -1
+set_fixed_atoms -1
+get_eval_atoms -1
+set_eval_atoms -1
+get_rot_atoms -1
+get_resolution -1
+set_num_coords -1
+**************************************************
+OpenBabel::OBRotorRules
+**************************************************
+set_filename -1
+get_rotor_increments -1
+quiet -1
+init -1
+get_size -1
+set_read_directory -1
+set_environment_variable -1
+parse_line -1
+**************************************************
+OpenBabel::OBRotorRule
+**************************************************
+is_valid -1
+get_reference_atoms -1
+set_delta -1
+get_delta -1
+get_torsion_vals -1
+get_smarts_string -1
+get_smarts_pattern -1
+**************************************************
+OpenBabel::OBBitVec
+**************************************************
+set_bit_on -1
+set_bit_off -1
+set_range_on -1
+set_range_off -1
+fold -1
+first_bit -1
+next_bit -1
+end_bit -1
+get_size -1
+count_bits -1
+empty -1
+is_empty -1
+resize -1
+resize_words -1
+bit_is_set -1
+bit_is_on -1
+from_vec_int -1
+from_string -1
+to_vec_int -1
+clear -1
+negate -1
+get_words -1
+add -1
+idx -1
+**************************************************
+OpenBabel::OBOp
+**************************************************
+default -1
+find_type -1
+op_options -1
+do_ops -1
+get_plugin -1
+list_as_vector -1
+list -1
+list_as_string -1
+first_line -1
+begin -1
+end -1
+**************************************************
+OpenBabel::OBBuilder
+**************************************************
+build -1
+set_keep_rings -1
+unset_keep_rings -1
+load_fragments -1
+get_new_bond_vector -1
+connect -1
+swap -1
+correct_stereo_bonds -1
+correct_stereo_atoms -1
+is_spiro_atom -1
+get_fragment -1
+add_nbrs -1
+**************************************************
+OpenBabel::OBForceField
+**************************************************
+default -1
+find_type -1
+find_force_field -1
+ignore_calculation -1
+vector_bond_derivative -1
+vector_distance_derivative -1
+vector_length_derivative -1
+vector_angle_derivative -1
+vector_oopderivative -1
+vector_torsion_derivative -1
+vector_subtract -1
+vector_add -1
+vector_divide -1
+vector_multiply -1
+vector_self_multiply -1
+vector_normalize -1
+vector_copy -1
+vector_length -1
+vector_distance -1
+vector_angle -1
+vector_torsion -1
+vector_oop -1
+vector_clear -1
+vector_dot -1
+vector_cross -1
+print_vector -1
+get_plugin -1
+list_as_vector -1
+list -1
+list_as_string -1
+first_line -1
+begin -1
+end -1
+**************************************************
+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
+**************************************************
+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
+set_parent -1
+get_parent -1
+find_center_and_normal -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_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::OBBond
+**************************************************
+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
+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
+**************************************************
+OpenBabel::OBResidue
+**************************************************
+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
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+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
+**************************************************
+OpenBabel::OBConversion
+**************************************************
+get_in_stream -1
+get_out_stream -1
+set_in_stream -1
+set_out_stream -1
+set_in_and_out_formats -1
+set_in_format -1
+set_out_format -1
+get_in_format -1
+get_out_format -1
+get_in_filename -1
+get_in_pos -1
+get_in_len -1
+get_title -1
+get_aux_conv -1
+set_aux_conv -1
+is_option -1
+get_options -1
+add_option -1
+remove_option -1
+set_options -1
+copy_options -1
+get_supported_input_format -1
+get_supported_output_format -1
+convert -1
+full_convert -1
+add_chem_object -1
+get_chem_object -1
+is_last -1
+is_first_input -1
+set_first_input -1
+get_output_index -1
+set_output_index -1
+set_more_files_to_come -1
+set_one_object_only -1
+set_last -1
+is_last_file -1
+get_count -1
+write -1
+write_string -1
+write_file -1
+close_out_file -1
+read -1
+read_string -1
+read_file -1
+open_in_and_out_files -1
+report_number_converted -1
+num_input_objects -1
+register_format -1
+find_format -1
+format_from_ext -1
+format_from_mime -1
+get_next_format -1
+description -1
+register_option_param -1
+get_option_params -1
+get_default_format -1
+**************************************************
+OpenBabel::OBFormat
+**************************************************
+default -1
+find_type -1
+format_from_mime -1
+get_plugin -1
+list_as_vector -1
+list -1
+list_as_string -1
+first_line -1
+begin -1
+end -1
+**************************************************
+OpenBabel::OBMessageHandler
+**************************************************
+throw_error -1
+get_messages_of_level -1
+start_logging -1
+stop_logging -1
+set_max_log_entries -1
+get_max_log_entries -1
+clear_log -1
+set_output_level -1
+get_output_level -1
+set_output_stream -1
+get_output_stream -1
+start_error_wrap -1
+stop_error_wrap -1
+get_error_message_count -1
+get_warning_message_count -1
+get_info_message_count -1
+get_audit_message_count -1
+get_debug_message_count -1
+get_message_summary -1
+**************************************************
+OpenBabel::OBError
+**************************************************
+message -1
+get_method -1
+get_error -1
+get_explanation -1
+get_possible_cause -1
+get_suggested_remedy -1
+get_level -1
+**************************************************
+OpenBabel::OBPlugin
+**************************************************
+get_plugin -1
+list_as_vector -1
+list -1
+list_as_string -1
+first_line -1
+begin -1
+end -1
+**************************************************
+OpenBabel::CharPtrLess
+**************************************************
+call -1
+**************************************************
+OpenBabel::OBGridData
+**************************************************
+get_xaxis -1
+get_yaxis -1
+get_zaxis -1
+get_axes -1
+get_number_of_points -1
+get_number_of_steps -1
+get_values -1
+get_value -1
+get_unit -1
+get_min_value -1
+get_max_value -1
+get_origin_vector -1
+get_max_vector -1
+get_unrestricted -1
+get_num_symmetries -1
+set_number_of_points -1
+set_limits -1
+set_value -1
+set_values -1
+set_unit -1
+set_unrestricted -1
+set_num_symmetries -1
+set_attribute -1
+set_origin -1
+get_attribute -1
+get_data_type -1
+get_origin -1
+**************************************************
+OpenBabel::OBMatrixData
+**************************************************
+set_data -1
+get_data -1
+set_attribute -1
+set_origin -1
+get_attribute -1
+get_data_type -1
+get_value -1
+get_origin -1
+**************************************************
+OpenBabel::OBVectorData
+**************************************************
+set_data -1
+get_data -1
+set_attribute -1
+set_origin -1
+get_attribute -1
+get_data_type -1
+get_value -1
+get_origin -1
+**************************************************
+OpenBabel::OBRotationData
+**************************************************
+set_data -1
+get_rot_consts -1
+get_symmetry_number -1
+get_rotor_type -1
+set_attribute -1
+set_origin -1
+get_attribute -1
+get_data_type -1
+get_value -1
+get_origin -1
+**************************************************
+OpenBabel::OBElectronicTransitionData
+**************************************************
+set_data -1
+set_edipole -1
+set_rotatory_strengths_velocity -1
+set_rotatory_strengths_length -1
+get_wavelengths -1
+get_forces -1
+get_edipole -1
+get_rotatory_strengths_velocity -1
+get_rotatory_strengths_length -1
+set_attribute -1
+set_origin -1
+get_attribute -1
+get_data_type -1
+get_value -1
+get_origin -1
+**************************************************
+OpenBabel::OBOrbitalData
+**************************************************
+set_alpha_orbitals -1
+set_beta_orbitals -1
+set_homo -1
+set_open_shell -1
+is_open_shell -1
+get_alpha_homo -1
+get_beta_homo -1
+get_alpha_orbitals -1
+get_beta_orbitals -1
+load_closed_shell_orbitals -1
+load_alpha_orbitals -1
+load_beta_orbitals -1
+set_attribute -1
+set_origin -1
+get_attribute -1
+get_data_type -1
+get_value -1
+get_origin -1
+**************************************************
+OpenBabel::OBOrbital
+**************************************************
+set_data -1
+get_energy -1
+get_occupation -1
+get_symbol -1
+**************************************************
+OpenBabel::OBDOSData
+**************************************************
+set_data -1
+get_fermi_energy -1
+get_energies -1
+get_densities -1
+get_integration -1
+set_attribute -1
+set_origin -1
+get_attribute -1
+get_data_type -1
+get_value -1
+get_origin -1
+**************************************************
+OpenBabel::OBVibrationData
+**************************************************
+set_data -1
+get_lx -1
+get_frequencies -1
+get_intensities -1
+get_raman_activities -1
+get_number_of_frequencies -1
+set_attribute -1
+set_origin -1
+get_attribute -1
+get_data_type -1
+get_value -1
+get_origin -1
+**************************************************
+OpenBabel::OBSerialNums
+**************************************************
+get_data -1
+set_data -1
+set_attribute -1
+set_origin -1
+get_attribute -1
+get_data_type -1
+get_value -1
+get_origin -1
+**************************************************
+OpenBabel::OBChiralData
+**************************************************
+clear -1
+get_atom_4refs -1
+get_atom_ref -1
+set_atom_4refs -1
+add_atom_ref -1
+get_size -1
+set_attribute -1
+set_origin -1
+get_attribute -1
+get_data_type -1
+get_value -1
+get_origin -1
+**************************************************
+OpenBabel::OBAngle
+**************************************************
+clear -1
+get_angle -1
+set_angle -1
+set_atoms -1
+**************************************************
+OpenBabel::OBCommentData
+**************************************************
+set_data -1
+get_data -1
+set_attribute -1
+set_origin -1
+get_attribute -1
+get_data_type -1
+get_value -1
+get_origin -1
+**************************************************
+OpenBabel::OBBase
+**************************************************
+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
+**************************************************
+OpenBabel::OBGenericData
+**************************************************
+set_attribute -1
+set_origin -1
+get_attribute -1
+get_data_type -1
+get_value -1
+get_origin -1
+**************************************************
+OpenBabel::Matrix3x3
+**************************************************
+get_array -1
+call -1
+inverse -1
+transpose -1
+random_rotation -1
+determinant -1
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+get_row -1
+setup_rot_mat -1
+plane_reflection -1
+rot_about_axis_by_angle -1
+fill_orth -1
+find_eigenvectors_if_symmetric -1
+jacobi -1
+**************************************************
+OpenBabel::Vector3
+**************************************************
+set -1
+set_x -1
+set_y -1
+set_z -1
+get_x -1
+get_y -1
+get_z -1
+get -1
+idx -1
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+add -1
+random_unit_vector -1
+normalize -1
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+length_2 -1
+length -1
+x -1
+y -1
+z -1
+is_approx -1
+dist_sq -1
+create_ortho_vector -1
+**************************************************
+OpenBabel::OBSqrtTbl
+**************************************************
+sqrt -1
+init -1
+**************************************************
+OpenBabel::OBStopwatch
+**************************************************
+start -1
+lap -1
+elapsed -1
+**************************************************
+OpenBabel::OBRandom
+**************************************************
+seed -1
+time_seed -1
+next_int -1
+next_float -1
+**************************************************
+OpenBabel::DoubleType
+**************************************************
+hi= -1
+hi -1
+lo= -1
+lo -1
+**************************************************
+OpenBabel::OBResidueData
+**************************************************
+set_res_name -1
+lookup_bo -1
+lookup_type -1
+assign_bonds -1
+init -1
+get_size -1
+set_read_directory -1
+set_environment_variable -1
+parse_line -1
+**************************************************
+OpenBabel::OBTypeTable
+**************************************************
+set_from_type -1
+set_to_type -1
+translate -1
+get_from_type -1
+get_to_type -1
+init -1
+get_size -1
+set_read_directory -1
+set_environment_variable -1
+parse_line -1
+**************************************************
+OpenBabel::OBIsotopeTable
+**************************************************
+get_exact_mass -1
+init -1
+get_size -1
+set_read_directory -1
+set_environment_variable -1
+parse_line -1
+**************************************************
+OpenBabel::OBElementTable
+**************************************************
+get_number_of_elements -1
+get_atomic_num -1
+get_symbol -1
+get_vdw_rad -1
+get_covalent_rad -1
+get_mass -1
+corrected_bond_rad -1
+corrected_vdw_rad -1
+get_max_bonds -1
+get_electro_neg -1
+get_allred_rochow_electro_neg -1
+get_ionization -1
+get_electron_affinity -1
+get_rgb -1
+get_name -1
+init -1
+get_size -1
+set_read_directory -1
+set_environment_variable -1
+parse_line -1
+**************************************************
+OpenBabel::OBElement
+**************************************************
+get_atomic_num -1
+get_symbol -1
+get_covalent_rad -1
+get_vdw_rad -1
+get_mass -1
+get_max_bonds -1
+get_electro_neg -1
+get_allred_rochow_electro_neg -1
+get_ionization -1
+get_electron_affinity -1
+get_name -1
+get_red -1
+get_green -1
+get_blue -1
+**************************************************
+OpenBabel::OBGlobalDataBase
+**************************************************
+init -1
+get_size -1
+set_read_directory -1
+set_environment_variable -1
+parse_line -1
+**************************************************
+OpenBabel::VectorpOBGenericData
+**************************************************
+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
+**************************************************
+OpenBabel::VectorpOBRing
+**************************************************
+to_a -1
+slice -1
+each -1
+select -1
+reject_bang -1
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+__delete_2__ -1
+push -1
+<< -1
+reject -1
+at -1
+[] -1
+[]= -1
+shift -1
+unshift -1
+**************************************************
+OpenBabel::VectorOBRing
+**************************************************
+to_a -1
+slice -1
+each -1
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+reject_bang -1
+delete_if -1
+delete_at -1
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+member? 1
+each_with_index -1
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+each_entry -1
+each_slice 1
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+each_with_object 1
+zip -1
+take 1
+take_while 0
+drop 1
+drop_while 0
+cycle -1
+chunk -1
+slice_before -1
+**************************************************
+OpenBabel::VectorOBResidue
+**************************************************
+to_a -1
+slice -1
+each -1
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+first -1
+all? 0
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+none? 0
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+member? 1
+each_with_index -1
+reverse_each -1
+each_entry -1
+each_slice 1
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+each_with_object 1
+zip -1
+take 1
+take_while 0
+drop 1
+drop_while 0
+cycle -1
+chunk -1
+slice_before -1
+**************************************************
+OpenBabel::VectorOBBond
+**************************************************
+to_a -1
+slice -1
+each -1
+select -1
+reject_bang -1
+delete_if -1
+delete_at -1
+__delete_2__ -1
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+inject -1
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+all? 0
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+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::VectorOBMol
+**************************************************
+to_a -1
+slice -1
+each -1
+select -1
+reject_bang -1
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+**************************************************
+OpenBabel::VectorVector3
+**************************************************
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+**************************************************
+OpenBabel::VectorString
+**************************************************
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+**************************************************
+OpenBabel::VectorDouble
+**************************************************
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+**************************************************
+OpenBabel::VectorVInt
+**************************************************
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