Index

_

__init__() (AboveAverage method) (Ac method) (Ag method) (Al method) (AllTerminators method) (Am method) (AnyTerminator method) (Ar method) (As method) (At method) (Atom method) (Au method) (B method) (Ba method) (Batch method) (Be method) (Best method) (Bh method) (Bi method) (Bk method) (Bond method) (Br method) (BuildingBlock method) (C method) (COF method) (Ca method) (Cage method) (CageOptimizerSequence method) (Calculator method) (Cd method) (Ce method) (Cell method) (Cf method) (ChargedMolError method) (Cl method) (Cm method) (Cn method) (Co method) (Complex method) (ConstructedMolecule method) (ConstructionError method) (Cr method) (Crosser method) (Cs method) (Cu method) (Db method) (DivideByMean method) (Ds method) (Dy method) (EAHistory method) (EAOperation method) (EAPopulation method) (ETKDG method) (Edge method) (EdgeData method) (EightPlusSixteen method) (EightPlusTwelve method) (ElectronicPropertyCalculator method) (EnergyCalculator method) (EnergyError method) (Er method) (Es method) (Eu method) (F method) (FGType method) (Fe method) (FilterBatches method) (FilterMolecules method) (FitnessCalculator method) (FitnessFunction method) (FitnessNormalizer method) (FitnessPlateau method) (FivePlusTen method) (Fl method) (Fm method) (FormationEnergy method) (FourPlusEight method) (FourPlusFour method) (FourPlusSix method) (FourPlusSix2 method) (Fr method) (FunctionalGroup method) (Ga method) (Gd method) (Ge method) (GeneticRecombination method) (H method) (He method) (Hexagonal method) (Hf method) (Hg method) (Ho method) (Honeycomb method) (Hs method) (I method) (If method) (In method) (Ir method) (Jumble method) (K method) (Kagome method) (Kr method) (La method) (LazyAttr method) (Li method) (Linear method) (LinkerlessHoneycomb method) (Lr method) (Lu method) (Lv method) (MAEExtractor method) (MMFF method) (MMFFEnergy method) (MOPAC method) (MOPACElectronicProperties method) (MOPACEnergy method) (MacroModelConversionError method) (MacroModelEnergy method) (MacroModelForceField method) (MacroModelForceFieldError method) (MacroModelInputError method) (MacroModelLewisStructureError method) (MacroModelMD method) (MacroModelOptimizationError method) (MacroModelPathError method) (Macrocycle method) (Mc method) (Md method) (Mg method) (Mn method) (Mo method) (MolFileError method) (Molecule method) (MoleculeCalculator method) (MoleculePresent method) (MoleculeSubclassError method) (Mt method) (Multiply method) (MutationError method) (Mutator method) (N method) (NRotaxane method) (Na method) (Nb method) (Nd method) (Ne method) (Nh method) (Ni method) (No method) (Np method) (NullFitnessNormalizer method) (NullOptimizer method) (NumGenerations method) (O method) (Og method) (OnePlusOne method) (Optimizer method) (Os method) (P method) (Pa method) (Pb method) (Pd method) (PlacementResult method) (Plotter method) (Pm method) (Po method) (Population method) (PopulationSizeError method) (Power method) (Pr method) (ProgressPlotter method) (PropertyVector method) (Pt method) (Pu method) (Ra method) (RaisingCalculator method) (RaisingCalculatorError method) (Random method) (RandomBuildingBlock method) (RandomTopologyGraph method) (Rb method) (Re method) (Reactor method) (RemoveBatches method) (RemoveMolecules method) (ReplaceFitness method) (Rf method) (Rg method) (Rh method) (Rn method) (Roulette method) (Ru method) (S method) (Sb method) (Sc method) (Se method) (SelectionPlotter method) (Selector method) (Sequence method) (Sg method) (ShiftUp method) (Si method) (SimilarBuildingBlock method) (SixPlusEight method) (SixPlusNine method) (SixPlusTwelve method) (Sm method) (Sn method) (Square method) (Sr method) (StochasticUniversalSampling method) (Sum method) (Ta method) (Tb method) (Tc method) (Te method) (TenPlusTwenty method) (Terminator method) (Th method) (ThreePlusSix method) (Ti method) (Tl method) (Tm method) (TopologyGraph method) (Tournament method) (TryCatch method) (Ts method) (TwelvePlusThirty method) (TwentyPlusThirty method) (TwoPlusFour method) (TwoPlusThree method) (TwoPlusTwo method) (U method) (UFF method) (UFFEnergy method) (V method) (Vertex method) (VertexData method) (W method) (Worst method) (XTB method) (XTBConvergenceError method) (XTBEnergy method) (XTBExtractor method) (XTBInvalidSolventError method) (XTBOptimizerError method) (Xe method) (Y method) (Yb method) (Zn method) (Zr method)

A

AboveAverage (class in stk.calculators.ea.selectors) Ac (class in stk.molecular.elements) add_members() (EAPopulation method) (Population method) add_reaction() (Reactor method) add_subpopulation() (EAPopulation method) (Population method) add_to_cache() (CageOptimizerSequence method) (ETKDG method) (EnergyCalculator method) (FitnessCalculator method) (FitnessFunction method) (FormationEnergy method) (If method) (MMFF method) (MMFFEnergy method) (MOPAC method) (MOPACEnergy method) (MacroModelEnergy method) (MacroModelForceField method) (MacroModelMD method) (MoleculeCalculator method) (NullOptimizer method) (Optimizer method) (PropertyVector method) (RaisingCalculator method) (Random method) (Sequence method) (TryCatch method) (UFF method) (UFFEnergy method) (XTB method) (XTBEnergy method) after_assign_func_groups_to_edges() (Vertex method) Ag (class in stk.molecular.elements) Al (class in stk.molecular.elements) AllTerminators (class in stk.calculators.ea.terminators) Am (class in stk.molecular.elements) AnyTerminator (class in stk.calculators.ea.terminators) apply_displacement() (BuildingBlock method) (ConstructedMolecule method) (Molecule method) apply_rotation_about_axis() (BuildingBlock method) (ConstructedMolecule method) (Molecule method) apply_rotation_between_vectors() (BuildingBlock method) (ConstructedMolecule method) (Molecule method) apply_rotation_to_minimize_angle() (BuildingBlock method) (ConstructedMolecule method) (Molecule method) apply_scale() (Edge method) (Vertex method) Ar (class in stk.molecular.elements) archive_output() (in module stk.utilities.utilities) args (ChargedMolError attribute) (ConstructionError attribute) (EnergyError attribute) (MacroModelConversionError attribute) (MacroModelForceFieldError attribute) (MacroModelInputError attribute) (MacroModelLewisStructureError attribute) (MacroModelOptimizationError attribute) (MacroModelPathError attribute) (MolFileError attribute) (MoleculeSubclassError attribute) (MutationError attribute) (PopulationSizeError attribute) (RaisingCalculatorError attribute) (XTBConvergenceError attribute) (XTBInvalidSolventError attribute) (XTBOptimizerError attribute) As (class in stk.molecular.elements) assign_building_blocks_to_vertices() (Cage method) (COF method) (Complex method) (EightPlusSixteen method) (EightPlusTwelve method) (FivePlusTen method) (FourPlusEight method) (FourPlusFour method) (FourPlusSix method) (FourPlusSix2 method) (Hexagonal method) (Honeycomb method) (Kagome method) (Linear method) (LinkerlessHoneycomb method) (Macrocycle method) (NRotaxane method) (OnePlusOne method) (SixPlusEight method) (SixPlusNine method) (SixPlusTwelve method) (Square method) (TenPlusTwenty method) (ThreePlusSix method) (TopologyGraph method) (TwelvePlusThirty method) (TwentyPlusThirty method) (TwoPlusFour method) (TwoPlusThree method) (TwoPlusTwo method) assign_func_group() (Edge method) assign_func_groups_to_edges() (Vertex method) assignments() (PlacementResult property) At (class in stk.molecular.elements) Atom (class in stk.molecular.elements) atom1 (Bond attribute), [1] atom2 (Bond attribute), [1] atomic_number (Ac attribute) (Ag attribute) (Al attribute) (Am attribute) (Ar attribute) (As attribute) (At attribute) (Atom attribute) (Au attribute) (B attribute) (Ba attribute) (Be attribute) (Bh attribute) (Bi attribute) (Bk attribute) (Br attribute) (C attribute) (Ca attribute) (Cd attribute) (Ce attribute) (Cf attribute) (Cl attribute) (Cm attribute) (Cn attribute) (Co attribute) (Cr attribute) (Cs attribute) (Cu attribute) (Db attribute) (Ds attribute) (Dy attribute) (Er attribute) (Es attribute) (Eu attribute) (F attribute) (Fe attribute) (Fl attribute) (Fm attribute) (Fr attribute) (Ga attribute) (Gd attribute) (Ge attribute) (H attribute) (He attribute) (Hf attribute) (Hg attribute) (Ho attribute) (Hs attribute) (I attribute) (In attribute) (Ir attribute) (K attribute) (Kr attribute) (La attribute) (Li attribute) (Lr attribute) (Lu attribute) (Lv attribute) (Mc attribute) (Md attribute) (Mg attribute) (Mn attribute) (Mo attribute) (Mt attribute) (N attribute) (Na attribute) (Nb attribute) (Nd attribute) (Ne attribute) (Nh attribute) (Ni attribute) (No attribute) (Np attribute) (O attribute) (Og attribute) (Os attribute) (P attribute) (Pa attribute) (Pb attribute) (Pd attribute) (Pm attribute) (Po attribute) (Pr attribute) (Pt attribute) (Pu attribute) (Ra attribute) (Rb attribute) (Re attribute) (Rf attribute) (Rg attribute) (Rh attribute) (Rn attribute) (Ru attribute) (S attribute) (Sb attribute) (Sc attribute) (Se attribute) (Sg attribute) (Si attribute) (Sm attribute) (Sn attribute) (Sr attribute) (Ta attribute) (Tb attribute) (Tc attribute) (Te attribute) (Th attribute) (Ti attribute) (Tl attribute) (Tm attribute) (Ts attribute) (U attribute) (V attribute) (W attribute) (Xe attribute) (Y attribute) (Yb attribute) (Zn attribute) (Zr attribute)

atoms (BuildingBlock attribute) (ConstructedMolecule attribute) (FunctionalGroup attribute) (Molecule attribute) Au (class in stk.molecular.elements)

B

B (class in stk.molecular.elements) Ba (class in stk.molecular.elements) Batch (class in stk.calculators.ea.selectors) Be (class in stk.molecular.elements) Best (class in stk.calculators.ea.selectors) Bh (class in stk.molecular.elements) Bi (class in stk.molecular.elements) Bk (class in stk.molecular.elements) Bond (class in stk.molecular.bonds)

bonders (FunctionalGroup attribute) bonds (BuildingBlock attribute) (ConstructedMolecule attribute) (Molecule attribute) Br (class in stk.molecular.elements) building_block() (PlacementResult property) building_block_counter (ConstructedMolecule attribute) building_block_vertices (ConstructedMolecule attribute) BuildingBlock (class in stk.molecular.molecules.building_block)

C

C (class in stk.molecular.elements) Ca (class in stk.molecular.elements) Cage (class in stk.molecular.topology_graphs.cage.base) CageOptimizerSequence (class in stk.calculators.optimization.optimizers) Calculator (class in stk.calculators.base_calculators) Cd (class in stk.molecular.elements) Ce (class in stk.molecular.elements) Cell (class in stk.utilities.utilities) cell (VertexData attribute) Cf (class in stk.molecular.elements) charge (Atom attribute) (MOPAC attribute) ChargedMolError Cl (class in stk.molecular.elements) clone() (Ac method) (Ag method) (Al method) (Am method) (Ar method) (As method) (At method) (Atom method) (Au method) (B method) (Ba method) (Be method) (Bh method) (Bi method) (Bk method) (Bond method) (Br method) (BuildingBlock method) (C method) (Ca method) (Cd method) (Ce method) (Cf method) (Cl method) (Cm method) (Cn method) (Co method) (ConstructedMolecule method) (Cr method) (Cs method) (Cu method) (Db method) (Ds method) (Dy method) (EAPopulation method) (Edge method) (EdgeData method) (Er method) (Es method) (Eu method) (F method) (Fe method) (Fl method) (Fm method) (Fr method) (FunctionalGroup method) (Ga method) (Gd method) (Ge method) (H method) (He method) (Hf method) (Hg method) (Ho method) (Hs method) (I method) (In method) (Ir method) (K method) (Kr method) (La method) (Li method) (Lr method) (Lu method) (Lv method) (Mc method) (Md method) (Mg method) (Mn method) (Mo method) (Molecule method) (Mt method) (N method) (Na method) (Nb method) (Nd method) (Ne method) (Nh method) (Ni method) (No method) (Np method) (O method) (Og method) (Os method) (P method) (Pa method) (Pb method) (Pd method) (Pm method) (Po method) (Population method) (Pr method) (Pt method) (Pu method) (Ra method) (Rb method) (Re method) (Rf method) (Rg method) (Rh method) (Rn method) (Ru method) (S method) (Sb method) (Sc method) (Se method) (Sg method) (Si method) (Sm method) (Sn method) (Sr method) (Ta method) (Tb method) (Tc method) (Te method) (Th method) (Ti method) (Tl method) (Tm method) (Ts method) (U method) (V method) (Vertex method) (VertexData method) (W method) (Xe method) (Y method) (Yb method) (Zn method) (Zr method)

close_process_pool() (EAPopulation method) (Population method) Cm (class in stk.molecular.elements) Cn (class in stk.molecular.elements) Co (class in stk.molecular.elements) COF (class in stk.molecular.topology_graphs.cof) Complex (class in stk.molecular.topology_graphs.host_guest) construct() (Cage method) (COF method) (Complex method) (EightPlusSixteen method) (EightPlusTwelve method) (FivePlusTen method) (FourPlusEight method) (FourPlusFour method) (FourPlusSix method) (FourPlusSix2 method) (Hexagonal method) (Honeycomb method) (Kagome method) (Linear method) (LinkerlessHoneycomb method) (Macrocycle method) (NRotaxane method) (OnePlusOne method) (SixPlusEight method) (SixPlusNine method) (SixPlusTwelve method) (Square method) (TenPlusTwenty method) (ThreePlusSix method) (TopologyGraph method) (TwelvePlusThirty method) (TwentyPlusThirty method) (TwoPlusFour method) (TwoPlusThree method) (TwoPlusTwo method) ConstructedMolecule (class in stk.molecular.molecules.constructed_molecule) construction_bonds (ConstructedMolecule attribute) ConstructionError content (MAEExtractor attribute) count() (PlacementResult method) Cr (class in stk.molecular.elements) cross() (Crosser method) (GeneticRecombination method) (If method) (Jumble method) (RaisingCalculator method) (Random method) (TryCatch method) Crosser (class in stk.calculators.ea.crossers) Cs (class in stk.molecular.elements) Cu (class in stk.molecular.elements) custom_position (EdgeData attribute)

D

database_dump (EAHistory attribute) Db (class in stk.molecular.elements) db() (EAHistory method) db_pop (EAHistory attribute) dedupe() (in module stk.utilities.utilities) deleters (FunctionalGroup attribute) dice_similarity() (in module stk.utilities.utilities) dipole_moment() (ElectronicPropertyCalculator method) (MOPACElectronicProperties method) direct_members (EAPopulation attribute) (Population attribute)

DivideByMean (class in stk.calculators.ea.fitness_normalizers) Ds (class in stk.molecular.elements) dump() (BuildingBlock method) (ConstructedMolecule method) (EAHistory method) (EAPopulation method) (Molecule method) (Population method) dump_attrs (EAHistory attribute) Dy (class in stk.molecular.elements)

E

ea_run() (in module stk.ea) EAHistory (class in stk.ea) EAOperation (class in stk.calculators.base_calculators) EAPopulation (class in stk.populations) Edge (class in stk.molecular.topology_graphs.topology_graph) edge_data (Cage attribute) (COF attribute) (EightPlusSixteen attribute), [1] (EightPlusTwelve attribute), [1] (FivePlusTen attribute), [1] (FourPlusEight attribute), [1] (FourPlusFour attribute), [1] (FourPlusSix attribute), [1] (FourPlusSix2 attribute), [1] (Hexagonal attribute), [1] (Honeycomb attribute), [1] (Kagome attribute), [1] (LinkerlessHoneycomb attribute), [1] (OnePlusOne attribute), [1] (SixPlusEight attribute), [1] (SixPlusNine attribute), [1] (SixPlusTwelve attribute), [1] (Square attribute), [1] (TenPlusTwenty attribute), [1] (ThreePlusSix attribute), [1] (TwelvePlusThirty attribute), [1] (TwentyPlusThirty attribute), [1] (TwoPlusFour attribute), [1] (TwoPlusThree attribute), [1] (TwoPlusTwo attribute), [1] EdgeData (class in stk.molecular.topology_graphs.topology_graph) edges (Cage attribute) (COF attribute) (Complex attribute) (EightPlusSixteen attribute) (EightPlusTwelve attribute) (FivePlusTen attribute) (FourPlusEight attribute) (FourPlusFour attribute) (FourPlusSix attribute) (FourPlusSix2 attribute) (Hexagonal attribute) (Honeycomb attribute) (Kagome attribute) (Linear attribute) (LinkerlessHoneycomb attribute) (Macrocycle attribute) (NRotaxane attribute) (OnePlusOne attribute) (SixPlusEight attribute) (SixPlusNine attribute) (SixPlusTwelve attribute) (Square attribute) (TenPlusTwenty attribute) (ThreePlusSix attribute) (TopologyGraph attribute) (TwelvePlusThirty attribute) (TwentyPlusThirty attribute) (TwoPlusFour attribute) (TwoPlusThree attribute) (TwoPlusTwo attribute) (VertexData attribute)

EightPlusSixteen (class in stk.molecular.topology_graphs.cage.two_plus_four) EightPlusTwelve (class in stk.molecular.topology_graphs.cage.two_plus_three) electron_affinity() (ElectronicPropertyCalculator method) (MOPACElectronicProperties method) ElectronicPropertyCalculator (class in stk.calculators.electronic_property.electronic_property_calculators) energies (MAEExtractor attribute) energy() (MOPACEnergy method) EnergyCalculator (class in stk.calculators.energy.energy_calculators) EnergyError eps (MOPAC attribute) Er (class in stk.molecular.elements) Es (class in stk.molecular.elements) ETKDG (class in stk.calculators.optimization.optimizers) Eu (class in stk.molecular.elements) extract_conformers() (MAEExtractor method) extract_energy() (MAEExtractor method)

F

F (class in stk.molecular.elements) Fe (class in stk.molecular.elements) fermi_level (XTBExtractor attribute) fermi_levels (XTBEnergy attribute) fg_type (FunctionalGroup attribute) fgs (Cell attribute) FGType (class in stk.molecular.functional_groups) fileout (MOPAC attribute) FilterBatches (class in stk.calculators.ea.selectors) FilterMolecules (class in stk.calculators.ea.selectors) finalize() (Reactor method) fitness_calculator (EAHistory attribute) FitnessCalculator (class in stk.calculators.ea.fitness_calculators) FitnessFunction (class in stk.calculators.ea.fitness_calculators) FitnessNormalizer (class in stk.calculators.ea.fitness_normalizers) FitnessPlateau (class in stk.calculators.ea.terminators) FivePlusTen (class in stk.molecular.topology_graphs.cage.two_plus_four) Fl (class in stk.molecular.elements)

flatten() (in module stk.utilities.utilities) Fm (class in stk.molecular.elements) FormationEnergy (class in stk.calculators.energy.energy_calculators) FourPlusEight (class in stk.molecular.topology_graphs.cage.two_plus_four) FourPlusFour (class in stk.molecular.topology_graphs.cage.three_plus_three) FourPlusSix (class in stk.molecular.topology_graphs.cage.two_plus_three) FourPlusSix2 (class in stk.molecular.topology_graphs.cage.two_plus_three) Fr (class in stk.molecular.elements) frequencies (XTBEnergy attribute) (XTBExtractor attribute) full_dipole_moment (XTBExtractor attribute) full_dipole_moments (XTBEnergy attribute) full_quadrupole_moment (XTBExtractor attribute) full_quadrupole_moments (XTBEnergy attribute) func_groups (BuildingBlock attribute) (ConstructedMolecule attribute) functional_group_types (BuildingBlock attribute) FunctionalGroup (class in stk.molecular.functional_groups)

G

Ga (class in stk.molecular.elements) Gd (class in stk.molecular.elements) Ge (class in stk.molecular.elements) generate_mop() (MOPAC method) GeneticRecombination (class in stk.calculators.ea.crossers) get_atom_distance() (BuildingBlock method) (ConstructedMolecule method) (Molecule method) get_atom_ids() (FunctionalGroup method) get_atom_positions() (BuildingBlock method) (ConstructedMolecule method) (Molecule method) get_bonder_centroids() (BuildingBlock method) get_bonder_direction_vectors() (BuildingBlock method) get_bonder_distances() (BuildingBlock method) get_bonder_ids() (BuildingBlock method) (FunctionalGroup method) get_bonder_plane() (BuildingBlock method) get_bonder_plane_normal() (BuildingBlock method) get_building_blocks() (ConstructedMolecule method) get_cached_mol() (BuildingBlock class method) (ConstructedMolecule class method) (Molecule class method) get_cached_value() (CageOptimizerSequence method) (ETKDG method) (EnergyCalculator method) (FitnessCalculator method) (FitnessFunction method) (FormationEnergy method) (If method) (MMFF method) (MMFFEnergy method) (MOPAC method) (MOPACEnergy method) (MacroModelEnergy method) (MacroModelForceField method) (MacroModelMD method) (MoleculeCalculator method) (NullOptimizer method) (Optimizer method) (PropertyVector method) (RaisingCalculator method) (Random method) (Sequence method) (TryCatch method) (UFF method) (UFFEnergy method) (XTB method) (XTBEnergy method) get_cell() (Vertex method) get_center_of_mass() (BuildingBlock method) (ConstructedMolecule method) (Molecule method)

get_centroid() (BuildingBlock method) (ConstructedMolecule method) (Molecule method) get_centroid_centroid_direction_vector() (BuildingBlock method) get_deleter_ids() (FunctionalGroup method) get_direction() (BuildingBlock method) (ConstructedMolecule method) (Molecule method) get_edge() (EdgeData method) get_edge_ids() (Vertex method) get_energy() (EnergyCalculator method) (FormationEnergy method) (If method) (MMFFEnergy method) (MOPACEnergy method) (MacroModelEnergy method) (RaisingCalculator method) (Random method) (TryCatch method) (UFFEnergy method) (XTBEnergy method) get_fitness() (Batch method) (FitnessCalculator method) (FitnessFunction method) (If method) (PropertyVector method) (RaisingCalculator method) (Random method) (TryCatch method) get_fitness_values() (EAPopulation method) get_func_groups() (Edge method) get_functional_groups() (FGType method) get_identity_key() (Batch method) (BuildingBlock method) (ConstructedMolecule method) (Molecule method) get_maximum_diameter() (BuildingBlock method) (ConstructedMolecule method) (Molecule method) get_num_edges() (Vertex method) get_periodicity() (Edge method) get_plane_normal() (BuildingBlock method) (ConstructedMolecule method) (Molecule method) get_position() (Edge method) (Vertex method) get_position_matrix() (BuildingBlock method) (ConstructedMolecule method) (Molecule method) get_size() (Batch method) get_vertex() (VertexData method) get_vertex_ids() (Edge method)

H

H (class in stk.molecular.elements) hamiltonian (MOPAC attribute) has_cached_mol() (BuildingBlock class method) (ConstructedMolecule class method) (Molecule class method) He (class in stk.molecular.elements) Hexagonal (class in stk.molecular.topology_graphs.cof) Hf (class in stk.molecular.elements)

Hg (class in stk.molecular.elements) Ho (class in stk.molecular.elements) homo_lumo_gap (XTBExtractor attribute) homo_lumo_gaps (XTBEnergy attribute) homo_lumo_occ (XTBExtractor attribute) homo_lumo_orbitals (XTBEnergy attribute) Honeycomb (class in stk.molecular.topology_graphs.cof) Hs (class in stk.molecular.elements)

I

I (class in stk.molecular.elements) id (Atom attribute) (Cell attribute) (Edge attribute) (EdgeData attribute) (Vertex attribute) (VertexData attribute) If (class in stk.calculators.compound) In (class in stk.molecular.elements) incomplete (XTB attribute) index() (PlacementResult method) init_all() (EAPopulation class method) (Population class method) init_at_center() (VertexData class method) init_diverse() (EAPopulation class method) (Population class method) init_from_dict() (BuildingBlock class method) (ConstructedMolecule class method) (Molecule class method) init_from_file() (BuildingBlock class method) init_from_list() (EAPopulation class method) (Population class method) init_from_molecule() (BuildingBlock class method) init_from_random_file() (BuildingBlock class method) init_from_rdkit_mol() (BuildingBlock class method) init_random() (EAPopulation class method) (Population class method) ionization_potential() (ElectronicPropertyCalculator method) (MOPACElectronicProperties method) Ir (class in stk.molecular.elements) is_caching() (CageOptimizerSequence method) (ETKDG method) (EnergyCalculator method) (FitnessCalculator method) (FitnessFunction method) (FormationEnergy method) (If method) (MMFF method) (MMFFEnergy method) (MOPAC method) (MOPACEnergy method) (MacroModelEnergy method) (MacroModelForceField method) (MacroModelMD method) (MoleculeCalculator method) (NullOptimizer method) (Optimizer method) (PropertyVector method) (RaisingCalculator method) (Random method) (Sequence method) (TryCatch method) (UFF method) (UFFEnergy method) (XTB method) (XTBEnergy method)

is_in_cache() (CageOptimizerSequence method) (ETKDG method) (EnergyCalculator method) (FitnessCalculator method) (FitnessFunction method) (FormationEnergy method) (If method) (MMFF method) (MMFFEnergy method) (MOPAC method) (MOPACEnergy method) (MacroModelEnergy method) (MacroModelForceField method) (MacroModelMD method) (MoleculeCalculator method) (NullOptimizer method) (Optimizer method) (PropertyVector method) (RaisingCalculator method) (Random method) (Sequence method) (TryCatch method) (UFF method) (UFFEnergy method) (XTB method) (XTBEnergy method) is_periodic() (Bond method) (Edge method) is_valid_xtb_solvent() (in module stk.utilities.utilities)

J

Jumble (class in stk.calculators.ea.crossers)

K

K (class in stk.molecular.elements) kabsch() (in module stk.utilities.utilities) Kagome (class in stk.molecular.topology_graphs.cof)

kill_macromodel() (in module stk.utilities.utilities) kill_mopac() (MOPAC method) Kr (class in stk.molecular.elements)

L

La (class in stk.molecular.elements) lattice_constants (EdgeData attribute) LazyAttr (class in stk.utilities.utilities) Li (class in stk.molecular.elements) Linear (class in stk.molecular.topology_graphs.polymer) LinkerlessHoneycomb (class in stk.molecular.topology_graphs.cof) load() (BuildingBlock class method) (ConstructedMolecule class method) (EAPopulation class method) (Molecule class method) (Population class method)

log_file_content() (EAHistory static method) log_pop() (EAHistory method) lowest_energy_conformers() (MAEExtractor method) Lr (class in stk.molecular.elements) Lu (class in stk.molecular.elements) Lv (class in stk.molecular.elements)

M

Macrocycle (class in stk.molecular.topology_graphs.macrocycle) MacroModelConversionError MacroModelEnergy (class in stk.calculators.energy.macromodel) MacroModelForceField (class in stk.calculators.optimization.macromodel) MacroModelForceFieldError MacroModelInputError MacroModelLewisStructureError MacroModelMD (class in stk.calculators.optimization.macromodel) MacroModelOptimizationError MacroModelPathError mae_path (MAEExtractor attribute) MAEExtractor (class in stk.utilities.utilities) maegz_path (MAEExtractor attribute) maegz_to_mae() (MAEExtractor method) mass (Ac attribute) (Ag attribute) (Al attribute) (Am attribute) (Ar attribute) (As attribute) (At attribute) (Atom attribute) (Au attribute) (B attribute) (Ba attribute) (Be attribute) (Bh attribute) (Bi attribute) (Bk attribute) (Br attribute) (C attribute) (Ca attribute) (Cd attribute) (Ce attribute) (Cf attribute) (Cl attribute) (Cm attribute) (Cn attribute) (Co attribute) (Cr attribute) (Cs attribute) (Cu attribute) (Db attribute) (Ds attribute) (Dy attribute) (Er attribute) (Es attribute) (Eu attribute) (F attribute) (Fe attribute) (Fl attribute) (Fm attribute) (Fr attribute) (Ga attribute) (Gd attribute) (Ge attribute) (H attribute) (He attribute) (Hf attribute) (Hg attribute) (Ho attribute) (Hs attribute) (I attribute) (In attribute) (Ir attribute) (K attribute) (Kr attribute) (La attribute) (Li attribute) (Lr attribute) (Lu attribute) (Lv attribute) (Mc attribute) (Md attribute) (Mg attribute) (Mn attribute) (Mo attribute) (Mt attribute) (N attribute) (Na attribute) (Nb attribute) (Nd attribute) (Ne attribute) (Nh attribute) (Ni attribute) (No attribute) (Np attribute) (O attribute) (Og attribute) (Os attribute) (P attribute) (Pa attribute) (Pb attribute) (Pd attribute) (Pm attribute) (Po attribute) (Pr attribute) (Pt attribute) (Pu attribute) (Ra attribute) (Rb attribute) (Re attribute) (Rf attribute) (Rg attribute) (Rh attribute) (Rn attribute) (Ru attribute) (S attribute) (Sb attribute) (Sc attribute) (Se attribute) (Sg attribute) (Si attribute) (Sm attribute) (Sn attribute) (Sr attribute) (Ta attribute) (Tb attribute) (Tc attribute) (Te attribute) (Th attribute) (Ti attribute) (Tl attribute) (Tm attribute) (Ts attribute) (U attribute) (V attribute) (W attribute) (Xe attribute) (Y attribute) (Yb attribute) (Zn attribute) (Zr attribute)

matrix_centroid() (in module stk.utilities.utilities) Mc (class in stk.molecular.elements) Md (class in stk.molecular.elements) method (MOPAC attribute) Mg (class in stk.molecular.elements) min_energy (MAEExtractor attribute) minimum_gradient (MOPAC attribute) MMFF (class in stk.calculators.optimization.optimizers) MMFFEnergy (class in stk.calculators.energy.energy_calculators) Mn (class in stk.molecular.elements) Mo (class in stk.molecular.elements) mol_from_mae_file() (in module stk.utilities.utilities) mol_from_mol_file() (in module stk.utilities.utilities) Molecule (class in stk.molecular.molecules.molecule) MoleculeCalculator (class in stk.calculators.base_calculators) MoleculePresent (class in stk.calculators.ea.terminators) MoleculeSubclassError MolFileError mop_header() (MOPAC method) MOPAC (class in stk.calculators.optimization.mopac) mopac_path (MOPAC attribute) MOPACElectronicProperties (class in stk.calculators.electronic_property.mopac) MOPACEnergy (class in stk.calculators.energy.mopac) move_generated_macromodel_files() (in module stk.utilities.utilities) Mt (class in stk.molecular.elements) Multiply (class in stk.calculators.ea.fitness_normalizers) mutate() (If method) (Mutator method) (RaisingCalculator method) (Random method) (RandomBuildingBlock method) (RandomTopologyGraph method) (SimilarBuildingBlock method) (TryCatch method) MutationError Mutator (class in stk.calculators.ea.mutators)

N

N (class in stk.molecular.elements) Na (class in stk.molecular.elements) name (FGType attribute) Nb (class in stk.molecular.elements) Nd (class in stk.molecular.elements) Ne (class in stk.molecular.elements) Nh (class in stk.molecular.elements) Ni (class in stk.molecular.elements) No (class in stk.molecular.elements) normalize() (DivideByMean method) (FitnessNormalizer method) (If method) (Multiply method) (NullFitnessNormalizer method) (Power method) (RaisingCalculator method) (Random method) (ReplaceFitness method) (Sequence method) (ShiftUp method) (Sum method) (TryCatch method) normalize_vector() (in module stk.utilities.utilities) Np (class in stk.molecular.elements) NRotaxane (class in stk.molecular.topology_graphs.rotaxane) NullFitnessNormalizer (class in stk.calculators.ea.fitness_normalizers) NullOptimizer (class in stk.calculators.optimization.optimizers) num_window_types (EightPlusSixteen attribute) (EightPlusTwelve attribute) (FivePlusTen attribute) (FourPlusEight attribute) (FourPlusFour attribute) (FourPlusSix attribute) (FourPlusSix2 attribute) (OnePlusOne attribute) (SixPlusEight attribute) (SixPlusNine attribute) (SixPlusTwelve attribute) (TenPlusTwenty attribute) (ThreePlusSix attribute) (TwelvePlusThirty attribute) (TwentyPlusThirty attribute) (TwoPlusFour attribute) (TwoPlusThree attribute) (TwoPlusTwo attribute)

num_windows (EightPlusSixteen attribute) (EightPlusTwelve attribute) (FivePlusTen attribute) (FourPlusEight attribute) (FourPlusFour attribute) (FourPlusSix attribute) (FourPlusSix2 attribute) (OnePlusOne attribute) (SixPlusEight attribute) (SixPlusNine attribute) (SixPlusTwelve attribute) (TenPlusTwenty attribute) (ThreePlusSix attribute) (TwelvePlusThirty attribute) (TwentyPlusThirty attribute) (TwoPlusFour attribute) (TwoPlusThree attribute) (TwoPlusTwo attribute) NumGenerations (class in stk.calculators.ea.terminators)

O

O (class in stk.molecular.elements) Og (class in stk.molecular.elements) OnePlusOne (class in stk.molecular.topology_graphs.cage.three_plus_three) open_process_pool() (EAPopulation method) (Population method) optimize() (CageOptimizerSequence method) (EAPopulation method) (ETKDG method) (If method) (MMFF method) (MOPAC method) (MacroModelForceField method) (MacroModelMD method) (NullOptimizer method) (Optimizer method) (Population method) (RaisingCalculator method) (Random method) (Sequence method) (TryCatch method) (UFF method) (XTB method)

Optimizer (class in stk.calculators.optimization.optimizers) order (Bond attribute), [1] orthogonal_vector() (in module stk.utilities.utilities) Os (class in stk.molecular.elements) output_file (XTBExtractor attribute) output_lines (XTBExtractor attribute)

P

P (class in stk.molecular.elements) Pa (class in stk.molecular.elements) path (MAEExtractor attribute) Pb (class in stk.molecular.elements) Pd (class in stk.molecular.elements) periodicity (Bond attribute), [1] (EdgeData attribute) place_building_block() (Vertex method) PlacementResult (class in stk.molecular.topology_graphs.topology_graph) plot() (Plotter method) (ProgressPlotter method) (SelectionPlotter method) Plotter (class in stk.calculators.ea.plotters) Pm (class in stk.molecular.elements)

Po (class in stk.molecular.elements) pop_log_content() (EAHistory method) Population (class in stk.populations) PopulationSizeError position (EdgeData attribute) (VertexData attribute) Power (class in stk.calculators.ea.fitness_normalizers) Pr (class in stk.molecular.elements) progress (EAHistory attribute) progress_dump (EAHistory attribute) ProgressPlotter (class in stk.calculators.ea.plotters) PropertyVector (class in stk.calculators.ea.fitness_calculators) Pt (class in stk.molecular.elements) Pu (class in stk.molecular.elements)

Q

qdip_quadrupole_moment (XTBExtractor attribute) qdip_quadrupole_moments (XTBEnergy attribute) qonly_dipole_moment (XTBExtractor attribute)

qonly_dipole_moments (XTBEnergy attribute) qonly_quadrupole_moment (XTBExtractor attribute) qonly_quadrupole_moments (XTBEnergy attribute) quaternion() (in module stk.utilities.utilities)

R

Ra (class in stk.molecular.elements) RaisingCalculator (class in stk.calculators.compound) RaisingCalculatorError Random (class in stk.calculators.compound) RandomBuildingBlock (class in stk.calculators.ea.mutators) RandomTopologyGraph (class in stk.calculators.ea.mutators) Rb (class in stk.molecular.elements) Re (class in stk.molecular.elements) Reactor (class in stk.molecular.reactor) remake() (in module stk.utilities.utilities) remove_duplicates() (EAPopulation method) (Population method) remove_members() (EAPopulation method) (Population method)

RemoveBatches (class in stk.calculators.ea.selectors) RemoveMolecules (class in stk.calculators.ea.selectors) ReplaceFitness (class in stk.calculators.ea.fitness_normalizers) Rf (class in stk.molecular.elements) Rg (class in stk.molecular.elements) Rh (class in stk.molecular.elements) Rn (class in stk.molecular.elements) rotation_matrix() (in module stk.utilities.utilities) rotation_matrix_arbitrary_axis() (in module stk.utilities.utilities) Roulette (class in stk.calculators.ea.selectors) Ru (class in stk.molecular.elements) run_mopac() (MOPAC method)

S

S (class in stk.molecular.elements) Sb (class in stk.molecular.elements) Sc (class in stk.molecular.elements) Se (class in stk.molecular.elements) select() (AboveAverage method) (Best method) (FilterBatches method) (FilterMolecules method) (If method) (Random method) (RemoveBatches method) (RemoveMolecules method) (Roulette method) (Selector method) (Sequence method) (StochasticUniversalSampling method) (Tournament method) (Worst method) SelectionPlotter (class in stk.calculators.ea.plotters) Selector (class in stk.calculators.ea.selectors) Sequence (class in stk.calculators.compound) set_cache_use() (CageOptimizerSequence method) (Crosser method) (EAOperation method) (ETKDG method) (EnergyCalculator method) (FitnessCalculator method) (FitnessFunction method) (FormationEnergy method) (GeneticRecombination method) (If method) (Jumble method) (MMFF method) (MMFFEnergy method) (MOPAC method) (MOPACEnergy method) (MacroModelEnergy method) (MacroModelForceField method) (MacroModelMD method) (MoleculeCalculator method) (Mutator method) (NullOptimizer method) (Optimizer method) (PropertyVector method) (RaisingCalculator method) (Random method) (RandomBuildingBlock method) (RandomTopologyGraph method) (Sequence method) (SimilarBuildingBlock method) (TryCatch method) (UFF method) (UFFEnergy method) (XTB method) (XTBEnergy method) set_centroid() (BuildingBlock method) (ConstructedMolecule method) (Molecule method) set_contructed_molecule() (Vertex method) set_fitness_values_from_calculators() (EAPopulation method) set_fitness_values_from_dict() (EAPopulation method) set_mol_ids() (EAPopulation method) (Population method) set_position_matrix() (BuildingBlock method) (ConstructedMolecule method) (Molecule method)

Sg (class in stk.molecular.elements) ShiftUp (class in stk.calculators.ea.fitness_normalizers) Si (class in stk.molecular.elements) SimilarBuildingBlock (class in stk.calculators.ea.mutators) SixPlusEight (class in stk.molecular.topology_graphs.cage.three_plus_four) SixPlusNine (class in stk.molecular.topology_graphs.cage.two_plus_three) SixPlusTwelve (class in stk.molecular.topology_graphs.cage.two_plus_four) Sm (class in stk.molecular.elements) Sn (class in stk.molecular.elements) Square (class in stk.molecular.topology_graphs.cof) Sr (class in stk.molecular.elements) stk (module) stk.calculators (module) stk.calculators.base_calculators (module) stk.calculators.compound (module) stk.calculators.ea (module) stk.calculators.ea.crossers (module) stk.calculators.ea.fitness_calculators (module) stk.calculators.ea.fitness_normalizers (module) stk.calculators.ea.mutators (module) stk.calculators.ea.plotters (module) stk.calculators.ea.selectors (module) stk.calculators.ea.terminators (module) stk.calculators.electronic_property (module) stk.calculators.electronic_property.electronic_property_calculators (module) stk.calculators.electronic_property.mopac (module) stk.calculators.energy (module) stk.calculators.energy.energy_calculators (module) stk.calculators.energy.macromodel (module) stk.calculators.energy.mopac (module) stk.calculators.optimization (module) stk.calculators.optimization.macromodel (module) stk.calculators.optimization.mopac (module) stk.calculators.optimization.optimizers (module) stk.ea (module) stk.molecular (module) stk.molecular.bonds (module) stk.molecular.elements (module) stk.molecular.functional_groups (module) stk.molecular.molecules (module) stk.molecular.molecules.building_block (module) stk.molecular.molecules.constructed_molecule (module) stk.molecular.molecules.molecule (module) stk.molecular.reactor (module) stk.molecular.topology_graphs (module) stk.molecular.topology_graphs.cage (module) stk.molecular.topology_graphs.cage.base (module) stk.molecular.topology_graphs.cage.three_plus_four (module) stk.molecular.topology_graphs.cage.three_plus_three (module) stk.molecular.topology_graphs.cage.two_plus_five (module) stk.molecular.topology_graphs.cage.two_plus_four (module) stk.molecular.topology_graphs.cage.two_plus_three (module) stk.molecular.topology_graphs.cof (module) stk.molecular.topology_graphs.host_guest (module) stk.molecular.topology_graphs.macrocycle (module) stk.molecular.topology_graphs.polymer (module) stk.molecular.topology_graphs.rotaxane (module) stk.molecular.topology_graphs.topology_graph (module) stk.populations (module) stk.utilities (module) stk.utilities.utilities (module) StochasticUniversalSampling (class in stk.calculators.ea.selectors) subpopulations (EAPopulation attribute) (Population attribute) Sum (class in stk.calculators.ea.fitness_normalizers)

T

Ta (class in stk.molecular.elements) tar_output() (in module stk.utilities.utilities) Tb (class in stk.molecular.elements) Tc (class in stk.molecular.elements) Te (class in stk.molecular.elements) TenPlusTwenty (class in stk.molecular.topology_graphs.cage.two_plus_four) terminate() (AllTerminators method) (AnyTerminator method) (FitnessPlateau method) (MoleculePresent method) (NumGenerations method) (Terminator method) Terminator (class in stk.calculators.ea.terminators) Th (class in stk.molecular.elements) ThreePlusSix (class in stk.molecular.topology_graphs.cage.two_plus_four) Ti (class in stk.molecular.elements) time_it() (in module stk.utilities.utilities) timeout (MOPAC attribute) Tl (class in stk.molecular.elements) Tm (class in stk.molecular.elements) to_dict() (BuildingBlock method) (ConstructedMolecule method) (Molecule method)

to_list() (EAPopulation method) (Population method) to_rdkit_mol() (BuildingBlock method) (ConstructedMolecule method) (Molecule method) topology_graph (ConstructedMolecule attribute) TopologyGraph (class in stk.molecular.topology_graphs.topology_graph) total_energies (XTBEnergy attribute) total_energy (XTBExtractor attribute) total_free_energies (XTBEnergy attribute) total_free_energy (XTBExtractor attribute) Tournament (class in stk.calculators.ea.selectors) translation_component() (in module stk.utilities.utilities) TryCatch (class in stk.calculators.compound) Ts (class in stk.molecular.elements) TwelvePlusThirty (class in stk.molecular.topology_graphs.cage.two_plus_five) TwentyPlusThirty (class in stk.molecular.topology_graphs.cage.two_plus_three) TwoPlusFour (class in stk.molecular.topology_graphs.cage.two_plus_four) TwoPlusThree (class in stk.molecular.topology_graphs.cage.two_plus_three) TwoPlusTwo (class in stk.molecular.topology_graphs.cage.three_plus_three)

U

U (class in stk.molecular.elements) UFF (class in stk.calculators.optimization.optimizers) UFFEnergy (class in stk.calculators.energy.energy_calculators) update_cache() (BuildingBlock method) (ConstructedMolecule method) (Molecule method)

update_from_file() (BuildingBlock method) (ConstructedMolecule method) (Molecule method) update_from_rdkit_mol() (BuildingBlock method) (ConstructedMolecule method) (Molecule method)

V

V (class in stk.molecular.elements) vector_angle() (in module stk.utilities.utilities) Vertex (class in stk.molecular.topology_graphs.topology_graph) vertex() (PlacementResult property) vertex_data (Cage attribute) (COF attribute) (EightPlusSixteen attribute), [1] (EightPlusTwelve attribute), [1] (FivePlusTen attribute), [1] (FourPlusEight attribute), [1] (FourPlusFour attribute), [1] (FourPlusSix attribute), [1] (FourPlusSix2 attribute), [1] (Hexagonal attribute), [1] (Honeycomb attribute), [1] (Kagome attribute), [1] (LinkerlessHoneycomb attribute), [1] (OnePlusOne attribute), [1] (SixPlusEight attribute), [1] (SixPlusNine attribute), [1] (SixPlusTwelve attribute), [1] (Square attribute), [1] (TenPlusTwenty attribute), [1] (ThreePlusSix attribute), [1] (TwelvePlusThirty attribute), [1] (TwentyPlusThirty attribute), [1] (TwoPlusFour attribute), [1] (TwoPlusThree attribute), [1] (TwoPlusTwo attribute), [1] VertexData (class in stk.molecular.topology_graphs.topology_graph)

vertices (Cage attribute) (COF attribute) (Complex attribute) (EdgeData attribute) (EightPlusSixteen attribute) (EightPlusTwelve attribute) (FivePlusTen attribute) (FourPlusEight attribute) (FourPlusFour attribute) (FourPlusSix attribute) (FourPlusSix2 attribute) (Hexagonal attribute) (Honeycomb attribute) (Kagome attribute) (Linear attribute) (LinkerlessHoneycomb attribute) (Macrocycle attribute) (NRotaxane attribute) (OnePlusOne attribute) (SixPlusEight attribute) (SixPlusNine attribute) (SixPlusTwelve attribute) (Square attribute) (TenPlusTwenty attribute) (ThreePlusSix attribute) (TopologyGraph attribute) (TwelvePlusThirty attribute) (TwentyPlusThirty attribute) (TwoPlusFour attribute) (TwoPlusThree attribute) (TwoPlusTwo attribute)

W

W (class in stk.molecular.elements) with_traceback() (ChargedMolError method) (ConstructionError method) (EnergyError method) (MacroModelConversionError method) (MacroModelForceFieldError method) (MacroModelInputError method) (MacroModelLewisStructureError method) (MacroModelOptimizationError method) (MacroModelPathError method) (MolFileError method) (MoleculeSubclassError method) (MutationError method) (PopulationSizeError method) (RaisingCalculatorError method) (XTBConvergenceError method) (XTBInvalidSolventError method) (XTBOptimizerError method)

Worst (class in stk.calculators.ea.selectors) write() (BuildingBlock method) (ConstructedMolecule method) (EAPopulation method) (Molecule method) (Population method)

X

Xe (class in stk.molecular.elements) XTB (class in stk.calculators.optimization.optimizers) XTBConvergenceError

XTBEnergy (class in stk.calculators.energy.energy_calculators) XTBExtractor (class in stk.utilities.utilities) XTBInvalidSolventError XTBOptimizerError

Y

Y (class in stk.molecular.elements)

Yb (class in stk.molecular.elements)

Z

Zn (class in stk.molecular.elements)

Zr (class in stk.molecular.elements)