RDtools APIs

RDTools package.

This package provides tool functions that can directly applied onto RDKit objects.

• rdtools.conversion
  • rdtools.conversion.smiles
    • get_smiles_parser_params()
    • mol_from_smiles()
    • mol_to_smiles()
    • process_mol_from_smiles()
  • rdtools.conversion.xyz
    • add_header_to_xyz()
    • mol_from_xyz()
    • mol_to_xyz()
    • parse_xyz_by_openbabel()
    • parse_xyz_by_xyz2mol()
    • parse_xyz_by_xyz2mol_rdkit_native()
    • xyz_to_coords()
  • rdtools.conversion.rmg
    • mol_from_rmg_mol()
    • mol_to_rmg_mol()
• rdtools.view
  • rdtools.view.base
    • animation_viewer()
    • base_viewer()
    • grid_viewer()
  • rdtools.view.mol
    • mol_animation()
    • mol_viewer()
    • ts_viewer()
  • rdtools.view.conf
    • conformer_animation()
    • conformer_viewer()
  • rdtools.view.freq
    • freq_viewer()
  • rdtools.view.reaction
    • reaction_viewer()
  • rdtools.view.interact
    • interactive_conformer_viewer()
• rdtools.fix
  • rdtools.fix.fix
    • find_oxonium_bonds()
    • fix_mol()
    • fix_mol_by_remedies()
    • fix_mol_by_remedy()
    • fix_oxonium_bonds()
  • rdtools.fix.mult
    • get_biradical_12_query()
    • get_biradical_cdb_query()
    • get_carbene_query()
    • get_radical_site_query()
    • saturate_biradical_12()
    • saturate_biradical_cdb()
    • saturate_carbene()
    • saturate_mol()
  • rdtools.fix.remedy
    • RemedyManager
      • RemedyManager.all_remedies
      • RemedyManager.default_remedies
      • RemedyManager.get_remedies()
    • get_oxonium_remedies()
    • get_recommend_remedies()
    • get_ring_remedies()
    • get_zwitterion_remedies()
• rdtools.resonance
  • rdtools.resonance.base
    • ResonanceAlgoRegistry
      • ResonanceAlgoRegistry.get()
      • ResonanceAlgoRegistry.register()
    • generate_resonance_structures()
  • rdtools.resonance.filtration
    • aromaticity_filtration()
    • charge_filtration()
    • filter_structures()
    • get_charge_distance()
    • get_charge_span_list()
    • get_octet_deviation()
    • get_octet_deviation_list()
    • has_unique_sites()
    • multiplicity_filtration()
    • octet_filtration()
    • stabilize_charges_by_electronegativity()
    • stabilize_charges_by_proximity()
  • rdtools.resonance.pathfinder
    • AdjacentLonePairRadicalPathFinder
      • AdjacentLonePairRadicalPathFinder.reverse
      • AdjacentLonePairRadicalPathFinder.reverse_abbr
      • AdjacentLonePairRadicalPathFinder.template
      • AdjacentLonePairRadicalPathFinder.transform()
      • AdjacentLonePairRadicalPathFinder.verify()
    • AllylRadicalPathFinder
      • AllylRadicalPathFinder.reverse
      • AllylRadicalPathFinder.reverse_abbr
      • AllylRadicalPathFinder.template
      • AllylRadicalPathFinder.transform()
      • AllylRadicalPathFinder.verify()
    • ForwardAdjacentLonePairMultipleBondPathFinder
      • ForwardAdjacentLonePairMultipleBondPathFinder.template
      • ForwardAdjacentLonePairMultipleBondPathFinder.reverse
      • ForwardAdjacentLonePairMultipleBondPathFinder.reverse_abbr
      • ForwardAdjacentLonePairMultipleBondPathFinder.reverse
      • ForwardAdjacentLonePairMultipleBondPathFinder.reverse_abbr
      • ForwardAdjacentLonePairMultipleBondPathFinder.template
      • ForwardAdjacentLonePairMultipleBondPathFinder.transform()
      • ForwardAdjacentLonePairMultipleBondPathFinder.verify()
    • ForwardAdjacentLonePairRadicalMultipleBondPathFinder
      • ForwardAdjacentLonePairRadicalMultipleBondPathFinder.template
      • ForwardAdjacentLonePairRadicalMultipleBondPathFinder.reverse
      • ForwardAdjacentLonePairRadicalMultipleBondPathFinder.reverse_abbr
      • ForwardAdjacentLonePairRadicalMultipleBondPathFinder.reverse
      • ForwardAdjacentLonePairRadicalMultipleBondPathFinder.reverse_abbr
      • ForwardAdjacentLonePairRadicalMultipleBondPathFinder.template
      • ForwardAdjacentLonePairRadicalMultipleBondPathFinder.transform()
      • ForwardAdjacentLonePairRadicalMultipleBondPathFinder.verify()
    • LonePairMultipleBondPathFinder
      • LonePairMultipleBondPathFinder.template
      • LonePairMultipleBondPathFinder.reverse
      • LonePairMultipleBondPathFinder.reverse_abbr
      • LonePairMultipleBondPathFinder.reverse
      • LonePairMultipleBondPathFinder.reverse_abbr
      • LonePairMultipleBondPathFinder.template
      • LonePairMultipleBondPathFinder.transform()
      • LonePairMultipleBondPathFinder.verify()
    • PathFinder
      • PathFinder.template
      • PathFinder.reverse
      • PathFinder.reverse_abbr
      • PathFinder.find()
      • PathFinder.reverse
      • PathFinder.reverse_abbr
      • PathFinder.template
      • PathFinder.transform()
      • PathFinder.verify()
    • PathFinderRegistry
      • PathFinderRegistry.get()
      • PathFinderRegistry.register()
    • ReverseAdjacentLonePairMultipleBondPathFinder
      • ReverseAdjacentLonePairMultipleBondPathFinder.template
      • ReverseAdjacentLonePairMultipleBondPathFinder.reverse
      • ReverseAdjacentLonePairMultipleBondPathFinder.reverse_abbr
      • ReverseAdjacentLonePairMultipleBondPathFinder.reverse
      • ReverseAdjacentLonePairMultipleBondPathFinder.reverse_abbr
      • ReverseAdjacentLonePairMultipleBondPathFinder.template
      • ReverseAdjacentLonePairMultipleBondPathFinder.transform()
      • ReverseAdjacentLonePairMultipleBondPathFinder.verify()
    • ReverseAdjacentLonePairRadicalMultipleBondPathFinder
      • ReverseAdjacentLonePairRadicalMultipleBondPathFinder.template
      • ReverseAdjacentLonePairRadicalMultipleBondPathFinder.reverse
      • ReverseAdjacentLonePairRadicalMultipleBondPathFinder.reverse_abbr
      • ReverseAdjacentLonePairRadicalMultipleBondPathFinder.reverse
      • ReverseAdjacentLonePairRadicalMultipleBondPathFinder.reverse_abbr
      • ReverseAdjacentLonePairRadicalMultipleBondPathFinder.template
      • ReverseAdjacentLonePairRadicalMultipleBondPathFinder.transform()
      • ReverseAdjacentLonePairRadicalMultipleBondPathFinder.verify()
    • transform_pre_and_post_process()
  • rdtools.resonance.rdkit_backend
    • generate_charged_resonance_structures()
    • generate_radical_resonance_structures()
    • generate_resonance_structures()
  • rdtools.resonance.rmg_backend
    • analyze_molecule()
    • generate_aromatic_resonance_structure()
    • generate_aryne_resonance_structures()
    • generate_clar_structures()
    • generate_kekule_structure()
    • generate_optimal_aromatic_resonance_structures()
    • generate_resonance_structures()
    • generate_resonance_structures_with_pathfinder()
    • populate_resonance_algorithms()
• rdtools.reaction
  • rdtools.reaction.draw
    • draw_reaction()
  • rdtools.reaction.stereo
    • is_DA_rxn_endo()
  • rdtools.reaction.ts
    • examine_normal_mode()
    • guess_rxn_from_normal_mode()
    • is_valid_habs_ts()

• rdtools.atom
  • clear_rxn_prop()
  • decrement_radical()
  • get_atom_mass()
  • get_electronegativity()
  • get_element_symbol()
  • get_lone_pair()
  • get_n_outer_electrons()
  • get_num_occupied_orbitals()
  • get_total_bond_order()
  • has_empty_orbitals()
  • increment_radical()
• rdtools.atommap
  • clear_atom_map_numbers()
  • get_atom_map_numbers()
  • has_atom_map_numbers()
  • map_h_atoms_in_reaction()
  • move_atommaps_to_notes()
  • move_notes_to_atommaps()
  • needs_renumber()
  • renumber_atoms()
  • renumber_atoms_by_atom_map_numbers()
  • renumber_atoms_by_map_dict()
  • renumber_atoms_by_substruct_match_result()
  • reset_atom_map_numbers()
  • reverse_map()
  • update_product_atom_map_after_reaction()
• rdtools.bond
  • add_bond()
  • add_bonds()
  • decrement_bond_order()
  • get_all_changing_bonds()
  • get_atoms_in_bonds()
  • get_bonds_as_tuples()
  • get_bonds_with_BO_changed()
  • get_broken_bonds()
  • get_formed_and_broken_bonds()
  • get_formed_bonds()
  • increment_bond_order()
• rdtools.compare
  • get_match_and_recover_recipe()
  • get_resonance_structure_match()
  • get_unique_mols()
  • has_matched_mol()
  • is_same_complex()
  • is_same_connectivity_conf()
  • is_same_connectivity_mol()
• rdtools.conf
  • add_conformer()
  • add_null_conformer()
  • create_conformer()
  • edit_conf_by_add_bonds()
  • embed_conformer()
  • embed_multiple_confs()
  • embed_multiple_null_confs()
  • get_angle_deg()
  • get_bond_length()
  • get_torsion_deg()
  • reflect()
  • set_angle_deg()
  • set_bond_length()
  • set_conformer_coordinates()
  • set_torsion_deg()
• rdtools.dist
  • get_adjacency_matrix()
  • get_bond_distance_matrix()
  • get_colliding_atoms()
  • get_covalent_distance_matrix()
  • get_distance_matrix()
  • get_missing_bonds()
  • get_shortest_path()
  • get_vdw_distance_matrix()
  • has_colliding_atoms()
• rdtools.element
  • get_atom_mass()
  • get_atomic_num()
  • get_bond_radius()
  • get_covalent_radius()
  • get_electronegativity()
  • get_element_symbol()
  • get_n_outer_electrons()
  • get_vdw_radius()
• rdtools.featurizer
  • AvalonGenerator
    • AvalonGenerator.GetCountFingerprintAsNumPy()
    • AvalonGenerator.GetFingerprintAsNumPy()
  • GetAvalonGenerator()
  • GetMACCSGenerator()
  • MACCSGenerator
    • MACCSGenerator.GetFingerprintAsNumPy()
  • get_fingerprint()
  • get_fingerprint_generator()
  • get_rxn_fingerprint()
  • rdkit_vector_to_array()
• rdtools.mol
  • combine_mols()
  • fast_sanitize()
  • force_no_implicit()
  • get_atom_masses()
  • get_atomic_nums()
  • get_closed_shell_explicit()
  • get_closed_shell_implicit()
  • get_closed_shell_mol()
  • get_dehydrogenated_mol()
  • get_element_counts()
  • get_element_symbols()
  • get_formal_charge()
  • get_heavy_atoms()
  • get_heavy_hydrogen_query()
  • get_mol_weight()
  • get_spin_multiplicity()
  • get_writable_copy()
  • reflect()
  • set_mol_positions()
• rdtools.obabel
  • get_obmol_coords()
  • openbabel_mol_to_rdkit_mol()
  • parse_xyz_by_openbabel()
  • rdkit_mol_to_openbabel_mol()
  • rdkit_mol_to_openbabel_mol_manual()
  • set_obmol_coords()
• rdtools.torsion
  • determine_smallest_atom_index_in_torsion()
  • find_internal_torsions()
  • find_ring_torsions()
  • get_torsion_tops()
  • get_torsional_modes()
• rdtools.utils
  • FakeModule
  • get_fake_module()