Table of Contents - rubabel-0.4.3 Documentation
Classes and Modules
- Enumerable
- Object
- OpenBabel
- OpenBabel::OBAtom
- OpenBabel::OBBond
- OpenBabel::OBConversion
- OpenBabel::OBMol
- OpenBabelUnableToSetupForceFieldError
- Rubabel
- Rubabel::Atom
- Rubabel::Bond
- Rubabel::Molecule
- Rubabel::MoleculeData
- Rubabel::Smarts
Methods
- ::[] — Rubabel
- ::filetype — Rubabel
- ::force_field — Rubabel
- ::foreach — Rubabel
- ::format_from_ext — Rubabel
- ::format_from_mime — Rubabel
- ::formats_to_hash — Rubabel
- ::from_atoms_and_bonds — Rubabel::Molecule
- ::from_file — Rubabel::Molecule
- ::from_id — Rubabel::Molecule
- ::from_key — Rubabel::Molecule
- ::from_string — Rubabel::Molecule
- ::id_formats — Rubabel
- ::in_formats — Rubabel
- ::molecule_from_file — Rubabel
- ::molecule_from_string — Rubabel
- ::new — Rubabel::Atom
- ::new — Rubabel::Bond
- ::new — Rubabel::Molecule
- ::new — Rubabel::MoleculeData
- ::new — Rubabel::Smarts
- ::out_formats — Rubabel
- ::read_first_obmol — Rubabel
- ::retrieve_info_from_url — Rubabel::Molecule
- ::tanimoto — Rubabel::Molecule
- #+ — Rubabel::Bond
- #- — Rubabel::Bond
- #<< — Rubabel::Atom
- #<< — Rubabel::Molecule
- #== — Rubabel::Atom
- #== — Rubabel::Molecule
- #[] — Rubabel::Molecule
- #[] — Rubabel::MoleculeData
- #[]= — Rubabel::MoleculeData
- #add_atom! — Rubabel::Molecule
- #add_bond! — Rubabel::Molecule
- #add_h! — Rubabel::Molecule
- #add_opts! — OpenBabel::OBConversion
- #add_polar_h! — Rubabel::Molecule
- #amide_nitrogen? — Rubabel::Atom
- #anti_clockwise? — Rubabel::Atom
- #aromatic? — Rubabel::Atom
- #aromatic_noxide? — Rubabel::Atom
- #associate_atom! — Rubabel::Molecule
- #atom — Rubabel::Molecule
- #atomic_mass — Rubabel::Atom
- #atomic_num — Rubabel::Atom
- #atoms — Rubabel::Atom
- #atoms — Rubabel::Bond
- #atoms — Rubabel::Molecule
- #avg_mass — Rubabel::Molecule
- #axial? — Rubabel::Atom
- #bond — Rubabel::Molecule
- #bond! — Rubabel::Atom
- #bond_order — Rubabel::Bond
- #bond_order= — Rubabel::Bond
- #bonds — Rubabel::Atom
- #bonds — Rubabel::Molecule
- #carbon? — Rubabel::Atom
- #carbonyl_carbon? — Rubabel::Atom
- #carbonyl_oxygen? — Rubabel::Atom
- #carboxyl_carbon? — Rubabel::Atom
- #carboxyl_oxygen? — Rubabel::Atom
- #center! — Rubabel::Molecule
- #charge — Rubabel::Atom
- #charge — Rubabel::Molecule
- #charge= — Rubabel::Atom
- #charge= — Rubabel::Molecule
- #chiral? — Rubabel::Atom
- #chiral_volume? — Rubabel::Atom
- #chirality_specified? — Rubabel::Atom
- #clockwise? — Rubabel::Atom
- #connect! — Rubabel::Atom
- #connected? — Rubabel::Atom
- #convert_dative_bonds! — Rubabel::Molecule
- #coords — Rubabel::Atom
- #correct_for_ph! — Rubabel::Molecule
- #csmiles — Rubabel::Molecule
- #data — Rubabel::Molecule
- #dec! — Rubabel::Bond
- #dec_implicit_valence! — Rubabel::Atom
- #delete — Rubabel::Molecule
- #delete — Rubabel::MoleculeData
- #delete_and_restore_bonds — Rubabel::Molecule
- #delete_atom — Rubabel::Molecule
- #delete_bond — Rubabel::Molecule
- #delete_hydrogens! — Rubabel::Molecule
- #dim — Rubabel::Molecule
- #do_with_hydrogens — Rubabel::Atom
- #do_with_hydrogens — Rubabel::Molecule
- #do_without_hydrogens — Rubabel::Atom
- #do_without_hydrogens — Rubabel::Molecule
- #double_bond? — Rubabel::Atom
- #each — Rubabel::Atom
- #each — Rubabel::Bond
- #each — Rubabel::Molecule
- #each — Rubabel::MoleculeData
- #each_atom — Rubabel::Atom
- #each_atom — Rubabel::Bond
- #each_atom — Rubabel::Molecule
- #each_bond — Rubabel::Atom
- #each_bond — Rubabel::Molecule
- #each_fragment — Rubabel::Molecule
- #each_match — Rubabel::Molecule
- #el — Rubabel::Atom
- #element — Rubabel::Atom
- #eql? — Rubabel::Atom
- #eql? — Rubabel::Molecule
- #equal? — Rubabel::Atom
- #equal? — Rubabel::Molecule
- #exact_mass — Rubabel::Atom
- #exact_mass — Rubabel::Molecule
- #explicit_hydrogen_count — Rubabel::Atom
- #formal_charge — Rubabel::Atom
- #formal_charge= — Rubabel::Atom
- #formula — Rubabel::Molecule
- #get_bond — Rubabel::Atom
- #graph_diameter — Rubabel::Molecule
- #h_added? — Rubabel::Molecule
- #hbond_acceptor? — Rubabel::Atom
- #hbond_donor? — Rubabel::Atom
- #hbond_donor_h? — Rubabel::Atom
- #hetero_valence — Rubabel::Atom
- #heteroatom? — Rubabel::Atom
- #highlight_substructure! — Rubabel::Molecule
- #hyb — Rubabel::Atom
- #hydrogen? — Rubabel::Atom
- #hydrogen_count — Rubabel::Atom
- #hydrogens_added? — Rubabel::Molecule
- #id — Rubabel::Atom
- #id= — Rubabel::Atom
- #idx — Rubabel::Atom
- #implicit_hydrogen_count — Rubabel::Atom
- #implicit_valence — Rubabel::Atom
- #implicit_valence= — Rubabel::Atom
- #in_ring? — Rubabel::Atom
- #in_ring_size? — Rubabel::Atom
- #inc! — Rubabel::Bond
- #inc_implicit_valence! — Rubabel::Atom
- #include? — Rubabel::Bond
- #index_by — Enumerable
- #initialize_copy — Rubabel::Molecule
- #inspect — Rubabel::Atom
- #inspect — Rubabel::Bond
- #inspect — Rubabel::Molecule
- #inspect — Rubabel::Smarts
- #inspect_internals — Rubabel::Atom
- #isotope — Rubabel::Atom
- #kekulize! — Rubabel::Molecule
- #key? — Rubabel::MoleculeData
- #keys — Rubabel::MoleculeData
- #length — Rubabel::MoleculeData
- #local_optimize! — Rubabel::Molecule
- #make3d! — Rubabel::Molecule
- #make_3d! — Rubabel::Molecule
- #mass — Rubabel::Molecule
- #matches — Rubabel::Molecule
- #matches? — Rubabel::Molecule
- #mol — Rubabel::Atom
- #mol_wt — Rubabel::Molecule
- #negative_stereo? — Rubabel::Atom
- #neutral! — Rubabel::Molecule
- #new_bond — Rubabel::Molecule
- #nitro_oxygen? — Rubabel::Atom
- #nitrogen? — Rubabel::Atom
- #non_polar_hydrogen? — Rubabel::Atom
- #not_c_or_h? — Rubabel::Atom
- #num_atoms — Rubabel::Molecule
- #num_bonds — Rubabel::Molecule
- #num_h — Rubabel::Atom
- #num_hvy_atoms — Rubabel::Molecule
- #num_residues — Rubabel::Molecule
- #num_rotors — Rubabel::Molecule
- #ob_fingerprint — Rubabel::Molecule
- #ob_sssr — Rubabel::Molecule
- #one_four? — Rubabel::Atom
- #one_three? — Rubabel::Atom
- #order — Rubabel::Bond
- #order= — Rubabel::Bond
- #oxygen? — Rubabel::Atom
- #pair_data — Rubabel::MoleculeData
- #partial_charge — Rubabel::Atom
- #phosphate_oxygen? — Rubabel::Atom
- #phosphorus? — Rubabel::Atom
- #pm — Object
- #png_transformer — Rubabel::Molecule
- #polar_hydrogen? — Rubabel::Atom
- #positive_stereo? — Rubabel::Atom
- #putsev — Object
- #putsv — Object
- #remove_a_hydride! — Rubabel::Atom
- #remove_a_hydrogen! — Rubabel::Atom
- #remove_a_proton! — Rubabel::Atom
- #remove_h! — Rubabel::Molecule
- #remove_hydrogens! — Rubabel::Molecule
- #set_atoms! — Rubabel::Bond
- #set_begin! — Rubabel::Bond
- #set_end! — Rubabel::Bond
- #single_bond? — Rubabel::Atom
- #size — Rubabel::MoleculeData
- #smarts_indices — Rubabel::Molecule
- #smiles — Rubabel::Molecule
- #spin — Rubabel::Atom
- #spin — Rubabel::Molecule
- #spin= — Rubabel::Atom
- #split — Rubabel::Molecule
- #strip_salts! — Rubabel::Molecule
- #sulfate_oxygen? — Rubabel::Atom
- #sulfur? — Rubabel::Atom
- #swap! — Rubabel::Molecule
- #tanimoto — Rubabel::Molecule
- #title — Rubabel::Molecule
- #title= — Rubabel::Molecule
- #to_a — Rubabel::MoleculeData
- #to_s — Rubabel::Molecule
- #to_s — Rubabel::Smarts
- #type — Rubabel::Atom
- #uniq_by — Enumerable
- #upcast — OpenBabel::OBAtom
- #upcast — OpenBabel::OBBond
- #upcast — OpenBabel::OBMol
- #valence — Rubabel::Atom
- #values — Rubabel::MoleculeData
- #vector — Rubabel::Atom
- #write — Rubabel::Molecule
- #write_file — Rubabel::Molecule
- #write_string — Rubabel::Molecule