Index

A

active_atoms (rdmc.reaction.Reaction property) active_bonds (rdmc.reaction.Reaction property) add_angle_constraint() (rdmc.forcefield.OpenBabelFF method) (rdmc.forcefield.RDKitFF method) add_bond() (in module rdtools.bond) add_bonds() (in module rdtools.bond) add_conformer() (in module rdtools.conf) add_distance_constraint() (rdmc.forcefield.OpenBabelFF method) (rdmc.forcefield.RDKitFF method) add_header_to_xyz() (in module rdtools.conversion.xyz) add_null_conformer() (in module rdtools.conf) add_torsion_constraint() (rdmc.forcefield.OpenBabelFF method) (rdmc.forcefield.RDKitFF method)

AdjacentLonePairRadicalPathFinder (class in rdtools.resonance.pathfinder) align_reactant_fragments() (in module rdmc.conformer_generation.align) all_geometries (rdmc.external.logparser.base.CclibLog property) all_remedies (rdtools.fix.remedy.RemedyManager property) AllylRadicalPathFinder (class in rdtools.resonance.pathfinder) analyze_molecule() (in module rdtools.resonance.rmg_backend) animation_viewer() (in module rdtools.view.base) apply_resonance_correction() (rdmc.reaction.Reaction method) aromaticity_filtration() (in module rdtools.resonance.filtration) auto_update_prop() (rdmc.external.logparser.base.BaseLog method) available_force_field (rdmc.forcefield.OpenBabelFF attribute) (rdmc.forcefield.RDKitFF attribute) available_solver (rdmc.forcefield.OpenBabelFF attribute) AvalonGenerator (class in rdtools.featurizer)

B

base_viewer() (in module rdtools.view.base) BaseLog (class in rdmc.external.logparser.base)

bond_analysis() (rdmc.reaction.Reaction method) broken_bonds (rdmc.reaction.Reaction property)

C

cached_property (class in rdmc.external.logparser.utils) calculate_entropy() (rdmc.conformer_generation.metrics.SCGMetric method) calculate_metric() (rdmc.conformer_generation.metrics.SCGMetric method) calculate_partition_function() (rdmc.conformer_generation.metrics.SCGMetric method) Canonicalize() (rdmc.conf.EditableConformer method) cclib_results (rdmc.external.logparser.base.CclibLog property) CclibLog (class in rdmc.external.logparser.base) changed_bonds (rdmc.reaction.Reaction property) charge (rdmc.external.logparser.base.CclibLog property) charge_filtration() (in module rdtools.resonance.filtration) check_isomorphic_molecules() (in module rdmc.external.rmg) check_metric() (rdmc.conformer_generation.metrics.SCGMetric method)

clear_atom_map_numbers() (in module rdtools.atommap) clear_rxn_prop() (in module rdtools.atom) cluster_confs() (in module rdmc.conformer_generation.utils) combine_mols() (in module rdtools.mol) compare_to_adjacent_point() (in module rdmc.mathlib.greedymin) conformer_animation() (in module rdtools.view.conf) conformer_viewer() (in module rdtools.view.conf) ConformerGenerator (class in rdmc.conformer_generation.generators) ConfSolv (class in rdmc.conformer_generation.solvation) converged_geometries (rdmc.external.logparser.base.CclibLog property) convert_log_to_mol() (in module rdmc.conformer_generation.utils) create_conformer() (in module rdtools.conf)

D

decrement_bond_order() (in module rdtools.bond) decrement_radical() (in module rdtools.atom) default_remedies (rdtools.fix.remedy.RemedyManager property) determine_smallest_atom_index_in_torsion() (in module rdtools.torsion)

dict_to_mol() (in module rdmc.conformer_generation.utils) dist (rdmc.conformer_generation.align.NaiveAlign attribute) draw_2d() (rdmc.reaction.Reaction method) draw_3d() (rdmc.reaction.Reaction method) draw_reaction() (in module rdtools.reaction.draw)

E

edit_conf_by_add_bonds() (in module rdtools.conf) EditableConformer (class in rdmc.conf) embed_conformer() (in module rdtools.conf) embed_multiple_confs() (in module rdtools.conf)

embed_multiple_null_confs() (in module rdtools.conf) embed_stable_species() (rdmc.conformer_generation.generators.ConformerGenerator method) (rdmc.conformer_generation.ts_generators.TSConformerGenerator method) Estimator (class in rdmc.conformer_generation.solvation) examine_normal_mode() (in module rdtools.reaction.ts)

F

FakeModule (class in rdtools.utils) fast_sanitize() (in module rdtools.mol) filter_kwargs() (in module rdmc.utils) filter_structures() (in module rdtools.resonance.filtration) find() (rdtools.resonance.pathfinder.PathFinder class method) find_internal_torsions() (in module rdtools.torsion) find_oxonium_bonds() (in module rdtools.fix.fix) find_reaction_family() (in module rdmc.external.rmg) find_ring_torsions() (in module rdtools.torsion) finished (rdmc.external.logparser.base.BaseLog property) fit() (rdmc.mathlib.curvefit.FourierSeries1D method) fix_atom() (rdmc.forcefield.OpenBabelFF method) (rdmc.forcefield.RDKitFF method) fix_mol() (in module rdtools.fix.fix) fix_mol_by_remedies() (in module rdtools.fix.fix)

fix_mol_by_remedy() (in module rdtools.fix.fix) fix_oxonium_bonds() (in module rdtools.fix.fix) force_no_implicit() (in module rdtools.mol) formed_bonds (rdmc.reaction.Reaction property) ForwardAdjacentLonePairMultipleBondPathFinder (class in rdtools.resonance.pathfinder) ForwardAdjacentLonePairRadicalMultipleBondPathFinder (class in rdtools.resonance.pathfinder) FourierSeries1D (class in rdmc.mathlib.curvefit) freq_viewer() (in module rdtools.view.freq) freqs (rdmc.external.logparser.base.CclibLog property) from_complex() (rdmc.conformer_generation.align.NaiveAlign class method) from_r_and_p_complex() (rdmc.conformer_generation.align.NaiveAlign class method) from_rdkit_mol() (in module rdmc.external.rmg) from_reactant_and_product_smiles() (rdmc.reaction.Reaction class method) from_reactants() (rdmc.conformer_generation.align.NaiveAlign class method) from_reaction_smiles() (rdmc.reaction.Reaction class method)

G

GaussianLog (class in rdmc.external.logparser.gaussian) generate_aromatic_resonance_structure() (in module rdtools.resonance.rmg_backend) generate_aryne_resonance_structures() (in module rdtools.resonance.rmg_backend) generate_charged_resonance_structures() (in module rdtools.resonance.rdkit_backend) generate_clar_structures() (in module rdtools.resonance.rmg_backend) generate_kekule_structure() (in module rdtools.resonance.rmg_backend) generate_optimal_aromatic_resonance_structures() (in module rdtools.resonance.rmg_backend) generate_radical_resonance_structures() (in module rdtools.resonance.rdkit_backend) generate_reaction_complex() (in module rdmc.external.rmg) generate_resonance_structures() (in module rdtools.resonance.base) (in module rdtools.resonance.rdkit_backend) (in module rdtools.resonance.rmg_backend) generate_resonance_structures_with_pathfinder() (in module rdtools.resonance.rmg_backend) generate_seed_mols() (rdmc.conformer_generation.ts_generators.TSConformerGenerator method) get() (rdtools.resonance.base.ResonanceAlgoRegistry class method) (rdtools.resonance.pathfinder.PathFinderRegistry class method) get_adjacency_matrix() (in module rdtools.dist) get_alignment_coords() (rdmc.conformer_generation.align.NaiveAlign method) get_all_changing_bonds() (in module rdtools.bond) get_angle_deg() (in module rdtools.conf) get_atom_map_numbers() (in module rdtools.atommap) get_atom_mass() (in module rdtools.atom) (in module rdtools.element) get_atom_masses() (in module rdtools.mol) get_atomic_num() (in module rdtools.element) get_atomic_nums() (in module rdtools.mol) get_atoms_in_bonds() (in module rdtools.bond) get_best_opt_geom() (rdmc.external.logparser.base.CclibLog method) get_biradical_12_query() (in module rdtools.fix.mult) get_biradical_cdb_query() (in module rdtools.fix.mult) get_bond_distance_matrix() (in module rdtools.dist) get_bond_length() (in module rdtools.conf) get_bond_radius() (in module rdtools.element) get_bonds_as_tuples() (in module rdtools.bond) get_bonds_with_BO_changed() (in module rdtools.bond) get_broken_bonds() (in module rdtools.bond) get_carbene_query() (in module rdtools.fix.mult) get_centroid() (in module rdmc.mathlib.geom) get_charge_distance() (in module rdtools.resonance.filtration) get_charge_span_list() (in module rdtools.resonance.filtration) get_closed_shell_explicit() (in module rdtools.mol) get_closed_shell_implicit() (in module rdtools.mol) get_closed_shell_mol() (in module rdtools.mol) get_colliding_atoms() (in module rdtools.dist) get_conf_failure_mode() (in module rdmc.conformer_generation.utils) get_conformer_energies() (rdmc.forcefield.RDKitFF method) get_conformers_by_change_torsions() (rdmc.conformer_generation.sampler.TorsionalSampler method) get_converged_geom_idx() (rdmc.external.logparser.base.CclibLog method) get_covalent_distance_matrix() (in module rdtools.dist) get_covalent_radius() (in module rdtools.element) get_dehydrogenated_mol() (in module rdtools.mol) get_distance_matrix() (in module rdtools.dist) get_distances_from_a_point() (in module rdmc.mathlib.geom) get_electronegativity() (in module rdtools.atom) (in module rdtools.element) get_element_counts() (in module rdtools.mol) get_element_symbol() (in module rdtools.atom) (in module rdtools.element) get_element_symbols() (in module rdtools.mol) get_energy() (in module rdmc.conformer_generation.sampler) (in module rdmc.mathlib.greedymin) (rdmc.forcefield.RDKitFF method) get_fake_module() (in module rdtools.utils) get_fingerprint() (in module rdtools.featurizer) (rdmc.reaction.Reaction method) get_fingerprint_generator() (in module rdtools.featurizer) get_formal_charge() (in module rdtools.mol) get_formed_and_broken_bonds() (in module rdtools.bond) get_formed_bonds() (in module rdtools.bond) get_fragment_radii() (rdmc.conformer_generation.align.NaiveAlign method)

get_frames_from_freq() (in module rdmc.conformer_generation.utils) get_heavy_atoms() (in module rdtools.mol) get_heavy_hydrogen_query() (in module rdtools.mol) get_irc_midpoint() (rdmc.external.logparser.base.CclibLog method) get_lone_pair() (in module rdtools.atom) get_lowest_e_geometry() (rdmc.external.logparser.base.CclibLog method) get_mass_center() (in module rdmc.mathlib.geom) get_match_and_recover_recipe() (in module rdtools.compare) get_max_distance_from_center() (in module rdmc.mathlib.geom) get_missing_bonds() (in module rdtools.dist) get_mol() (rdmc.external.logparser.base.CclibLog method) (rdmc.external.logparser.qchem.QChemLog method) get_mol_weight() (in module rdtools.mol) get_n_outer_electrons() (in module rdtools.atom) (in module rdtools.element) get_num_occupied_orbitals() (in module rdtools.atom) get_obmol_coords() (in module rdtools.obabel) get_octet_deviation() (in module rdtools.resonance.filtration) get_octet_deviation_list() (in module rdtools.resonance.filtration) get_optimized_mol() (rdmc.forcefield.OpenBabelFF method) (rdmc.forcefield.RDKitFF method) get_oxonium_remedies() (in module rdtools.fix.remedy) get_radical_site_query() (in module rdtools.fix.mult) get_reacting_atoms_in_fragments() (rdmc.conformer_generation.align.NaiveAlign method) get_recommend_remedies() (in module rdtools.fix.remedy) get_remedies() (rdtools.fix.remedy.RemedyManager method) get_resonance_structure_match() (in module rdtools.compare) get_reverse_reaction() (rdmc.reaction.Reaction method) get_ring_remedies() (in module rdtools.fix.remedy) get_roo_radical_atoms() (in module rdmc.forcefield) get_rxn_fingerprint() (in module rdtools.featurizer) get_scannames() (rdmc.external.logparser.base.CclibLog method) get_scanparams() (rdmc.external.logparser.base.CclibLog method) get_scf_energies() (rdmc.external.logparser.base.CclibLog method) (rdmc.external.logparser.qchem.QChemLog method) get_separable_angle_list() (in module rdmc.conformer_generation.sampler) get_shortest_path() (in module rdtools.dist) get_smiles_parser_params() (in module rdtools.conversion.smiles) get_spin_multiplicity() (in module rdtools.mol) get_step_to_adjacent_points() (in module rdmc.mathlib.greedymin) get_torsion_deg() (in module rdtools.conf) get_torsion_tops() (in module rdtools.torsion) get_torsional_modes() (in module rdtools.torsion) get_total_bond_order() (in module rdtools.atom) get_unique_mols() (in module rdtools.compare) get_vdw_distance_matrix() (in module rdtools.dist) get_vdw_radius() (in module rdtools.element) get_weighted_center() (in module rdmc.mathlib.geom) get_writable_copy() (in module rdtools.mol) get_xyzs() (rdmc.external.logparser.base.CclibLog method) get_zwitterion_remedies() (in module rdtools.fix.remedy) GetAllTorsionsDeg() (rdmc.conf.EditableConformer method) GetAngleDeg() (rdmc.conf.EditableConformer method) GetAngleRad() (rdmc.conf.EditableConformer method) GetAvalonGenerator() (in module rdtools.featurizer) GetBondLength() (rdmc.conf.EditableConformer method) GetCentroid() (rdmc.conf.EditableConformer method) GetCountFingerprintAsNumPy() (rdtools.featurizer.AvalonGenerator static method) GetDistanceMatrix() (rdmc.conf.EditableConformer method) GetFingerprintAsNumPy() (rdtools.featurizer.AvalonGenerator static method) (rdtools.featurizer.MACCSGenerator static method) GetMACCSGenerator() (in module rdtools.featurizer) GetOwningMol() (rdmc.conf.EditableConformer method) GetPrincipalAxesAndMoments() (rdmc.conf.EditableConformer method) GetTorsionalModes() (rdmc.conf.EditableConformer method) GetTorsionDeg() (rdmc.conf.EditableConformer method) grid_viewer() (in module rdtools.view.base) guess_rxn_from_irc() (rdmc.external.logparser.base.CclibLog method) guess_rxn_from_normal_mode() (in module rdtools.reaction.ts) (rdmc.external.logparser.base.CclibLog method)

H

has_atom_map_numbers() (in module rdtools.atommap) has_colliding_atoms() (in module rdtools.dist) has_empty_orbitals() (in module rdtools.atom) has_matched_mol() (in module rdtools.compare)

has_same_products() (rdmc.reaction.Reaction method) has_same_reactants() (rdmc.reaction.Reaction method) has_unique_sites() (in module rdtools.resonance.filtration) HasCollidingAtoms() (rdmc.conf.EditableConformer method) HasOwningMol() (rdmc.conf.EditableConformer method)

I

increment_bond_order() (in module rdtools.bond) increment_radical() (in module rdtools.atom) init_reactant_product() (rdmc.reaction.Reaction method) initial_geometry (rdmc.external.logparser.base.CclibLog property) initialize_align() (rdmc.conformer_generation.align.NaiveAlign method) interact_freq() (rdmc.external.logparser.base.CclibLog method) interact_irc() (rdmc.external.logparser.base.CclibLog method) interact_opt() (rdmc.external.logparser.base.CclibLog method) interact_scan() (rdmc.external.logparser.base.CclibLog method) interactive_conformer_viewer() (in module rdtools.view.interact) involved_atoms (rdmc.reaction.Reaction property) involved_bonds (rdmc.reaction.Reaction property) is_charge_balanced (rdmc.reaction.Reaction property) is_DA_rxn_endo() (in module rdtools.reaction.stereo)

is_element_balanced (rdmc.reaction.Reaction property) is_equivalent() (rdmc.reaction.Reaction method) is_equivalent_reaction() (in module rdmc.reaction) is_mult_equal (rdmc.reaction.Reaction property) is_num_atoms_balanced (rdmc.reaction.Reaction property) is_optimizable() (rdmc.forcefield.OpenBabelFF method) (rdmc.forcefield.RDKitFF method) is_resonance_corrected (rdmc.reaction.Reaction property) is_same_complex() (in module rdtools.compare) is_same_connectivity_conf() (in module rdtools.compare) is_same_connectivity_mol() (in module rdtools.compare) is_same_products() (rdmc.reaction.Reaction method) is_same_reactants() (rdmc.reaction.Reaction method) is_ts (rdmc.external.logparser.base.BaseLog property) is_valid_habs_ts() (in module rdtools.reaction.ts)

J

job_type (rdmc.external.logparser.base.BaseLog property)

L

load_rmg_database() (in module rdmc.external.rmg)

load_rxn_family_database() (in module rdmc.external.rmg) LonePairMultipleBondPathFinder (class in rdtools.resonance.pathfinder)

M

MACCSGenerator (class in rdtools.featurizer) make_optimizable() (rdmc.forcefield.RDKitFF method) make_ts() (rdmc.reaction.Reaction method) map_h_atoms() (rdmc.reaction.Reaction method) map_h_atoms_in_reaction() (in module rdtools.atommap) max_num_term (rdmc.mathlib.curvefit.FourierSeries1D attribute) module rdmc rdmc.conf rdmc.conformer_generation rdmc.conformer_generation.align rdmc.conformer_generation.embedders rdmc.conformer_generation.generators rdmc.conformer_generation.metrics rdmc.conformer_generation.optimizers rdmc.conformer_generation.pruners rdmc.conformer_generation.sampler rdmc.conformer_generation.solvation rdmc.conformer_generation.ts_generators rdmc.conformer_generation.ts_guessers rdmc.conformer_generation.ts_optimizers rdmc.conformer_generation.ts_verifiers rdmc.conformer_generation.utils rdmc.conformer_generation.verifiers rdmc.external rdmc.external.inpwriter rdmc.external.inpwriter.gaussian rdmc.external.inpwriter.orca rdmc.external.inpwriter.qchem rdmc.external.inpwriter.utils rdmc.external.logparser rdmc.external.logparser.base rdmc.external.logparser.gaussian rdmc.external.logparser.orca rdmc.external.logparser.qchem rdmc.external.logparser.utils rdmc.external.rmg rdmc.forcefield rdmc.mathlib rdmc.mathlib.curvefit rdmc.mathlib.geom rdmc.mathlib.greedymin rdmc.mol rdmc.reaction rdmc.utils rdtools rdtools.atom rdtools.atommap rdtools.bond rdtools.compare rdtools.conf rdtools.conversion.rmg rdtools.conversion.smiles rdtools.conversion.xyz rdtools.dist rdtools.element rdtools.featurizer rdtools.fix.fix rdtools.fix.mult rdtools.fix.remedy rdtools.mol rdtools.obabel rdtools.reaction.draw rdtools.reaction.stereo rdtools.reaction.ts rdtools.resonance.base rdtools.resonance.filtration rdtools.resonance.pathfinder rdtools.resonance.rdkit_backend rdtools.resonance.rmg_backend rdtools.torsion rdtools.utils rdtools.view.base rdtools.view.conf rdtools.view.freq rdtools.view.interact rdtools.view.mol rdtools.view.reaction

mol (rdmc.forcefield.OpenBabelFF property) (rdmc.forcefield.RDKitFF property) mol_animation() (in module rdtools.view.mol) mol_from_rmg_mol() (in module rdtools.conversion.rmg) mol_from_smiles() (in module rdtools.conversion.smiles) mol_from_xyz() (in module rdtools.conversion.xyz) mol_to_dict() (in module rdmc.conformer_generation.utils) mol_to_rmg_mol() (in module rdtools.conversion.rmg) mol_to_smiles() (in module rdtools.conversion.smiles) mol_to_xyz() (in module rdtools.conversion.xyz) mol_viewer() (in module rdtools.view.mol) move_atommaps_to_notes() (in module rdtools.atommap) move_notes_to_atommaps() (in module rdtools.atommap) multiplicity (rdmc.external.logparser.base.CclibLog property) (rdmc.external.logparser.orca.ORCALog property) multiplicity_filtration() (in module rdtools.resonance.filtration)

N

NaiveAlign (class in rdmc.conformer_generation.align) needs_renumber() (in module rdtools.atommap) neg_freqs (rdmc.external.logparser.base.CclibLog property) num_all_geoms (rdmc.external.logparser.base.CclibLog property) num_atoms (rdmc.reaction.Reaction property) num_broken_bonds (rdmc.reaction.Reaction property)

num_changed_bonds (rdmc.reaction.Reaction property) num_converged_geoms (rdmc.external.logparser.base.CclibLog property) num_formed_bonds (rdmc.reaction.Reaction property) num_heavy_atoms (rdmc.reaction.Reaction property) num_neg_freqs (rdmc.external.logparser.base.CclibLog property) num_products (rdmc.reaction.Reaction property) num_reactants (rdmc.reaction.Reaction property)

O

octet_filtration() (in module rdtools.resonance.filtration) openbabel_mol_to_rdkit_mol() (in module rdtools.obabel) OpenBabelFF (class in rdmc.forcefield) opt_convergence (rdmc.external.logparser.base.CclibLog property) opt_criteria (rdmc.external.logparser.base.BaseLog attribute) (rdmc.external.logparser.gaussian.GaussianLog attribute) (rdmc.external.logparser.orca.ORCALog attribute)

opt_critieria (rdmc.external.logparser.qchem.QChemLog attribute) optimize() (rdmc.forcefield.OpenBabelFF method) (rdmc.forcefield.RDKitFF method) optimize_confs() (rdmc.forcefield.RDKitFF method) optimize_mol() (in module rdmc.forcefield) optstatus (rdmc.external.logparser.base.CclibLog property) ORCALog (class in rdmc.external.logparser.orca)

P

parse_xyz_by_openbabel() (in module rdtools.conversion.xyz) (in module rdtools.obabel) parse_xyz_by_xyz2mol() (in module rdtools.conversion.xyz) parse_xyz_by_xyz2mol_rdkit_native() (in module rdtools.conversion.xyz) PathFinder (class in rdtools.resonance.pathfinder) PathFinderRegistry (class in rdtools.resonance.pathfinder) plot_heat_map() (in module rdmc.conformer_generation.sampler) plot_irc_energies() (rdmc.external.logparser.base.CclibLog method) plot_opt_convergence() (rdmc.external.logparser.base.CclibLog method)

plot_scan_energies() (rdmc.external.logparser.base.CclibLog method) populate_resonance_algorithms() (in module rdtools.resonance.rmg_backend) predict() (rdmc.mathlib.curvefit.FourierSeries1D method) predict_energies() (rdmc.conformer_generation.solvation.ConfSolv method) (rdmc.conformer_generation.solvation.Estimator method) prepare_mols() (in module rdmc.conformer_generation.align) preprocess_energies() (in module rdmc.conformer_generation.sampler) process_mol_from_smiles() (in module rdtools.conversion.smiles) product_element_count (rdmc.reaction.Reaction property)

Q

QChemLog (class in rdmc.external.logparser.qchem)

R

rdkit_mol_to_openbabel_mol() (in module rdtools.obabel) rdkit_mol_to_openbabel_mol_manual() (in module rdtools.obabel) rdkit_vector_to_array() (in module rdtools.featurizer) RDKitFF (class in rdmc.forcefield) rdmc module rdmc.conf module rdmc.conformer_generation module rdmc.conformer_generation.align module rdmc.conformer_generation.embedders module rdmc.conformer_generation.generators module rdmc.conformer_generation.metrics module rdmc.conformer_generation.optimizers module rdmc.conformer_generation.pruners module rdmc.conformer_generation.sampler module rdmc.conformer_generation.solvation module rdmc.conformer_generation.ts_generators module rdmc.conformer_generation.ts_guessers module rdmc.conformer_generation.ts_optimizers module rdmc.conformer_generation.ts_verifiers module rdmc.conformer_generation.utils module rdmc.conformer_generation.verifiers module rdmc.external module rdmc.external.inpwriter module rdmc.external.inpwriter.gaussian module rdmc.external.inpwriter.orca module rdmc.external.inpwriter.qchem module rdmc.external.inpwriter.utils module rdmc.external.logparser module rdmc.external.logparser.base module rdmc.external.logparser.gaussian module rdmc.external.logparser.orca module rdmc.external.logparser.qchem module rdmc.external.logparser.utils module rdmc.external.rmg module rdmc.forcefield module rdmc.mathlib module rdmc.mathlib.curvefit module rdmc.mathlib.geom module rdmc.mathlib.greedymin module rdmc.mol module rdmc.reaction module rdmc.utils module rdtools module rdtools.atom module rdtools.atommap module rdtools.bond module rdtools.compare module rdtools.conf module rdtools.conversion.rmg module

rdtools.conversion.smiles module rdtools.conversion.xyz module rdtools.dist module rdtools.element module rdtools.featurizer module rdtools.fix.fix module rdtools.fix.mult module rdtools.fix.remedy module rdtools.mol module rdtools.obabel module rdtools.reaction.draw module rdtools.reaction.stereo module rdtools.reaction.ts module rdtools.resonance.base module rdtools.resonance.filtration module rdtools.resonance.pathfinder module rdtools.resonance.rdkit_backend module rdtools.resonance.rmg_backend module rdtools.torsion module rdtools.utils module rdtools.view.base module rdtools.view.conf module rdtools.view.freq module rdtools.view.interact module rdtools.view.mol module rdtools.view.reaction module reactant_element_count (rdmc.reaction.Reaction property) Reaction (class in rdmc.reaction) reaction_viewer() (in module rdtools.view.reaction) recover_mol() (rdmc.forcefield.RDKitFF method) reflect() (in module rdtools.conf) (in module rdtools.mol) register() (rdtools.resonance.base.ResonanceAlgoRegistry class method) (rdtools.resonance.pathfinder.PathFinderRegistry class method) RemedyManager (class in rdtools.fix.remedy) renumber_atoms() (in module rdtools.atommap) renumber_atoms_by_atom_map_numbers() (in module rdtools.atommap) renumber_atoms_by_map_dict() (in module rdtools.atommap) renumber_atoms_by_substruct_match_result() (in module rdtools.atommap) require_bond_analysis() (rdmc.reaction.Reaction method) require_job_type() (rdmc.external.logparser.base.BaseLog method) require_ts() (rdmc.external.logparser.base.BaseLog method) reset_atom_map_numbers() (in module rdtools.atommap) reset_pmol() (in module rdmc.conformer_generation.align) ResonanceAlgoRegistry (class in rdtools.resonance.base) reverse (rdtools.resonance.pathfinder.AdjacentLonePairRadicalPathFinder attribute) (rdtools.resonance.pathfinder.AllylRadicalPathFinder attribute) (rdtools.resonance.pathfinder.ForwardAdjacentLonePairMultipleBondPathFinder attribute), [1] (rdtools.resonance.pathfinder.ForwardAdjacentLonePairRadicalMultipleBondPathFinder attribute), [1] (rdtools.resonance.pathfinder.LonePairMultipleBondPathFinder attribute), [1] (rdtools.resonance.pathfinder.PathFinder attribute), [1] (rdtools.resonance.pathfinder.ReverseAdjacentLonePairMultipleBondPathFinder attribute), [1] (rdtools.resonance.pathfinder.ReverseAdjacentLonePairRadicalMultipleBondPathFinder attribute), [1] reverse_abbr (rdtools.resonance.pathfinder.AdjacentLonePairRadicalPathFinder attribute) (rdtools.resonance.pathfinder.AllylRadicalPathFinder attribute) (rdtools.resonance.pathfinder.ForwardAdjacentLonePairMultipleBondPathFinder attribute), [1] (rdtools.resonance.pathfinder.ForwardAdjacentLonePairRadicalMultipleBondPathFinder attribute), [1] (rdtools.resonance.pathfinder.LonePairMultipleBondPathFinder attribute), [1] (rdtools.resonance.pathfinder.PathFinder attribute), [1] (rdtools.resonance.pathfinder.ReverseAdjacentLonePairMultipleBondPathFinder attribute), [1] (rdtools.resonance.pathfinder.ReverseAdjacentLonePairRadicalMultipleBondPathFinder attribute), [1] reverse_map() (in module rdtools.atommap) ReverseAdjacentLonePairMultipleBondPathFinder (class in rdtools.resonance.pathfinder) ReverseAdjacentLonePairRadicalMultipleBondPathFinder (class in rdtools.resonance.pathfinder) rotate() (in module rdmc.mathlib.geom) rotate_fragment_separately() (rdmc.conformer_generation.align.NaiveAlign method)

S

saturate_biradical_12() (in module rdtools.fix.mult) saturate_biradical_cdb() (in module rdtools.fix.mult) saturate_carbene() (in module rdtools.fix.mult) saturate_mol() (in module rdtools.fix.mult) SCGMetric (class in rdmc.conformer_generation.metrics) scheme_to_dict() (in module rdmc.external.logparser.utils) schemes (rdmc.external.logparser.base.BaseLog property) score_bimolecule() (rdmc.conformer_generation.align.NaiveAlign method) search_for_a_minimum() (in module rdmc.mathlib.greedymin) search_minimum() (in module rdmc.mathlib.greedymin) set_angle_deg() (in module rdtools.conf) set_bond_length() (in module rdtools.conf) set_config() (rdmc.conformer_generation.generators.StochasticConformerGenerator method) set_conformer_coordinates() (in module rdtools.conf) set_filter() (rdmc.conformer_generation.generators.ConformerGenerator method) (rdmc.conformer_generation.ts_generators.TSConformerGenerator method) set_mol_positions() (in module rdtools.mol)

set_obmol_coords() (in module rdtools.obabel) set_solver() (rdmc.forcefield.OpenBabelFF method) set_torsion_deg() (in module rdtools.conf) SetAllTorsionsDeg() (rdmc.conf.EditableConformer method) SetAngleDeg() (rdmc.conf.EditableConformer method) SetAngleRad() (rdmc.conf.EditableConformer method) SetBondLength() (rdmc.conf.EditableConformer method) SetOwningMol() (rdmc.conf.EditableConformer method) SetPositions() (rdmc.conf.EditableConformer method) SetTorsionalModes() (rdmc.conf.EditableConformer method) SetTorsionDeg() (rdmc.conf.EditableConformer method) setup() (rdmc.forcefield.OpenBabelFF method) (rdmc.forcefield.RDKitFF method) stabilize_charges_by_electronegativity() (in module rdtools.resonance.filtration) stabilize_charges_by_proximity() (in module rdtools.resonance.filtration) StochasticConformerGenerator (class in rdmc.conformer_generation.generators) subprocess_runner() (in module rdmc.conformer_generation.utils) success (rdmc.external.logparser.base.BaseLog property)

T

template (rdtools.resonance.pathfinder.AdjacentLonePairRadicalPathFinder attribute) (rdtools.resonance.pathfinder.AllylRadicalPathFinder attribute) (rdtools.resonance.pathfinder.ForwardAdjacentLonePairMultipleBondPathFinder attribute), [1] (rdtools.resonance.pathfinder.ForwardAdjacentLonePairRadicalMultipleBondPathFinder attribute), [1] (rdtools.resonance.pathfinder.LonePairMultipleBondPathFinder attribute), [1] (rdtools.resonance.pathfinder.PathFinder attribute), [1] (rdtools.resonance.pathfinder.ReverseAdjacentLonePairMultipleBondPathFinder attribute), [1] (rdtools.resonance.pathfinder.ReverseAdjacentLonePairRadicalMultipleBondPathFinder attribute), [1] termination_time (rdmc.external.logparser.base.BaseLog property) time_regex (rdmc.external.logparser.base.BaseLog attribute) (rdmc.external.logparser.gaussian.GaussianLog attribute) (rdmc.external.logparser.orca.ORCALog attribute) (rdmc.external.logparser.qchem.QChemLog attribute) to_rdkit_reaction() (rdmc.reaction.Reaction method) to_smiles() (rdmc.reaction.Reaction method) ToConformer() (rdmc.conf.EditableConformer method) ToMol() (rdmc.conf.EditableConformer method)

torsional_scan_1d() (rdmc.forcefield.RDKitFF method) TorsionalSampler (class in rdmc.conformer_generation.sampler) transform() (rdtools.resonance.pathfinder.AdjacentLonePairRadicalPathFinder static method) (rdtools.resonance.pathfinder.AllylRadicalPathFinder static method) (rdtools.resonance.pathfinder.ForwardAdjacentLonePairMultipleBondPathFinder static method) (rdtools.resonance.pathfinder.ForwardAdjacentLonePairRadicalMultipleBondPathFinder static method) (rdtools.resonance.pathfinder.LonePairMultipleBondPathFinder static method) (rdtools.resonance.pathfinder.PathFinder static method) (rdtools.resonance.pathfinder.ReverseAdjacentLonePairMultipleBondPathFinder static method) (rdtools.resonance.pathfinder.ReverseAdjacentLonePairRadicalMultipleBondPathFinder static method) transform_pre_and_post_process() (in module rdtools.resonance.pathfinder) translate() (in module rdmc.mathlib.geom) translate_centroid() (in module rdmc.mathlib.geom) ts (rdmc.reaction.Reaction property) ts_viewer() (in module rdtools.view.mol) TSConformerGenerator (class in rdmc.conformer_generation.ts_generators) type (rdmc.forcefield.OpenBabelFF property) (rdmc.forcefield.RDKitFF property)

U

update_atom_idx() (rdmc.forcefield.OpenBabelFF method) (rdmc.forcefield.RDKitFF method)

update_product_atom_map_after_reaction() (in module rdtools.atommap)

V

verify() (rdtools.resonance.pathfinder.AdjacentLonePairRadicalPathFinder static method) (rdtools.resonance.pathfinder.AllylRadicalPathFinder static method) (rdtools.resonance.pathfinder.ForwardAdjacentLonePairMultipleBondPathFinder static method) (rdtools.resonance.pathfinder.ForwardAdjacentLonePairRadicalMultipleBondPathFinder static method) (rdtools.resonance.pathfinder.LonePairMultipleBondPathFinder static method) (rdtools.resonance.pathfinder.PathFinder static method) (rdtools.resonance.pathfinder.ReverseAdjacentLonePairMultipleBondPathFinder static method) (rdtools.resonance.pathfinder.ReverseAdjacentLonePairRadicalMultipleBondPathFinder static method)

view_freq() (rdmc.external.logparser.base.CclibLog method) view_mol() (rdmc.external.logparser.base.CclibLog method) view_traj() (rdmc.external.logparser.base.CclibLog method)

W

write_gaussian_config() (in module rdmc.external.inpwriter.gaussian) write_gaussian_freq() (in module rdmc.external.inpwriter.gaussian) write_gaussian_gsm() (in module rdmc.external.inpwriter.gaussian) write_gaussian_inp() (in module rdmc.external.inpwriter.gaussian) write_gaussian_irc() (in module rdmc.external.inpwriter.gaussian) write_gaussian_opt() (in module rdmc.external.inpwriter.gaussian)

write_orca_freq() (in module rdmc.external.inpwriter.orca) write_orca_gsm() (in module rdmc.external.inpwriter.orca) write_orca_irc() (in module rdmc.external.inpwriter.orca) write_orca_opt() (in module rdmc.external.inpwriter.orca) write_qchem_freq() (in module rdmc.external.inpwriter.qchem) write_qchem_irc() (in module rdmc.external.inpwriter.qchem) write_qchem_opt() (in module rdmc.external.inpwriter.qchem)

X

xyz_to_coords() (in module rdtools.conversion.xyz)