from stk import (
    cage,
    cof,
    host_guest,
    macrocycle,
    metal_complex,
    polymer,
    rotaxane,
    small,
)
from stk._internal.atom import Atom
from stk._internal.atom_info import AtomInfo
from stk._internal.bond import Bond
from stk._internal.bond_info import BondInfo
from stk._internal.building_block import BuildingBlock
from stk._internal.constructed_molecule import ConstructedMolecule
from stk._internal.construction_result.construction_result import (
    ConstructionResult,
)
from stk._internal.construction_state.construction_state import (
    ConstructionState,
)
from stk._internal.construction_state.graph_state import GraphState
from stk._internal.construction_state.molecule_state.molecule_state import (
    MoleculeState,
)
from stk._internal.databases.constructed_molecule import (
    ConstructedMoleculeDatabase,
)
from stk._internal.databases.molecule import MoleculeDatabase
from stk._internal.databases.mongo_db.constructed_molecule import (
    ConstructedMoleculeMongoDb,
)
from stk._internal.databases.mongo_db.molecule import MoleculeMongoDb
from stk._internal.databases.mongo_db.value import ValueMongoDb
from stk._internal.databases.value import ValueDatabase
from stk._internal.ea.crossover.genetic_recombination import (
    GeneticRecombination,
)
from stk._internal.ea.crossover.molecule_crosser import MoleculeCrosser
from stk._internal.ea.crossover.random import RandomCrosser
from stk._internal.ea.crossover.record import CrossoverRecord
from stk._internal.ea.evolutionary_algorithm.evolutionary_algorithm import (
    EvolutionaryAlgorithm,
)
from stk._internal.ea.fitness_calculators.fitness_calculator import (
    FitnessCalculator,
)
from stk._internal.ea.fitness_calculators.fitness_function import (
    FitnessFunction,
)
from stk._internal.ea.fitness_calculators.property_vector import PropertyVector
from stk._internal.ea.fitness_normalizers.add import Add
from stk._internal.ea.fitness_normalizers.divide_by_mean import DivideByMean
from stk._internal.ea.fitness_normalizers.fitness_normalizer import (
    FitnessNormalizer,
)
from stk._internal.ea.fitness_normalizers.multiply import Multiply
from stk._internal.ea.fitness_normalizers.null import NullFitnessNormalizer
from stk._internal.ea.fitness_normalizers.power import Power
from stk._internal.ea.fitness_normalizers.replace_fitness import ReplaceFitness
from stk._internal.ea.fitness_normalizers.sequence import NormalizerSequence
from stk._internal.ea.fitness_normalizers.shift_up import ShiftUp
from stk._internal.ea.fitness_normalizers.sum import Sum
from stk._internal.ea.generation import FitnessValues, Generation
from stk._internal.ea.molecule_record import MoleculeRecord
from stk._internal.ea.mutation.mutator import MoleculeMutator
from stk._internal.ea.mutation.random import RandomMutator
from stk._internal.ea.mutation.random_building_block import RandomBuildingBlock
from stk._internal.ea.mutation.random_topology_graph import RandomTopologyGraph
from stk._internal.ea.mutation.record import MutationRecord
from stk._internal.ea.mutation.similar_building_block import (
    SimilarBuildingBlock,
)
from stk._internal.ea.plotters.progress import ProgressPlotter
from stk._internal.ea.plotters.selection import SelectionPlotter
from stk._internal.ea.selection.batch import Batch, BatchKey
from stk._internal.ea.selection.selectors.above_average import AboveAverage
from stk._internal.ea.selection.selectors.best import Best
from stk._internal.ea.selection.selectors.filter_batches import FilterBatches
from stk._internal.ea.selection.selectors.filter_molecules import (
    FilterMolecules,
)
from stk._internal.ea.selection.selectors.remove_batches import RemoveBatches
from stk._internal.ea.selection.selectors.remove_molecules import (
    RemoveMolecules,
)
from stk._internal.ea.selection.selectors.roulette import Roulette
from stk._internal.ea.selection.selectors.selector import Selector
from stk._internal.ea.selection.selectors.stochastic_universal_sampling import (  # noqa
    StochasticUniversalSampling,
)
from stk._internal.ea.selection.selectors.tournament import Tournament
from stk._internal.ea.selection.selectors.worst import Worst
from stk._internal.elements import (
    Ac,
    Ag,
    Al,
    Am,
    Ar,
    As,
    At,
    Au,
    B,
    Ba,
    Be,
    Bh,
    Bi,
    Bk,
    Br,
    C,
    Ca,
    Cd,
    Ce,
    Cf,
    Cl,
    Cm,
    Cn,
    Co,
    Cr,
    Cs,
    Cu,
    Db,
    Ds,
    Dy,
    Er,
    Es,
    Eu,
    F,
    Fe,
    Fl,
    Fm,
    Fr,
    Ga,
    Gd,
    Ge,
    H,
    He,
    Hf,
    Hg,
    Ho,
    Hs,
    I,
    In,
    Ir,
    K,
    Kr,
    La,
    Li,
    Lr,
    Lu,
    Lv,
    Mc,
    Md,
    Mg,
    Mn,
    Mo,
    Mt,
    N,
    Na,
    Nb,
    Nd,
    Ne,
    Nh,
    Ni,
    No,
    Np,
    O,
    Og,
    Os,
    P,
    Pa,
    Pb,
    Pd,
    Pm,
    Po,
    Pr,
    Pt,
    Pu,
    Ra,
    Rb,
    Re,
    Rf,
    Rg,
    Rh,
    Rn,
    Ru,
    S,
    Sb,
    Sc,
    Se,
    Sg,
    Si,
    Sm,
    Sn,
    Sr,
    Ta,
    Tb,
    Tc,
    Te,
    Th,
    Ti,
    Tl,
    Tm,
    Ts,
    U,
    V,
    W,
    Xe,
    Y,
    Yb,
    Zn,
    Zr,
)
from stk._internal.functional_group_factories.alcohol_factory import (
    AlcoholFactory,
)
from stk._internal.functional_group_factories.aldehyde_factory import (
    AldehydeFactory,
)
from stk._internal.functional_group_factories.amide_factory import (
    AmideFactory,
)
from stk._internal.functional_group_factories.boronic_acid_factory import (
    BoronicAcidFactory,
)
from stk._internal.functional_group_factories.bromo_factory import (
    BromoFactory,
)
from stk._internal.functional_group_factories.carboxylic_acid_factory import (
    CarboxylicAcidFactory,
)
from stk._internal.functional_group_factories.dibromo_factory import (
    DibromoFactory,
)
from stk._internal.functional_group_factories.difluoro_factory import (
    DifluoroFactory,
)
from stk._internal.functional_group_factories.diol_factory import (
    DiolFactory,
)
from stk._internal.functional_group_factories.fluoro_factory import (
    FluoroFactory,
)
from stk._internal.functional_group_factories.functional_group_factory import (
    FunctionalGroupFactory,
)
from stk._internal.functional_group_factories.iodo_factory import (
    IodoFactory,
)
from stk._internal.functional_group_factories.primary_amino_factory import (
    PrimaryAminoFactory,
)
from stk._internal.functional_group_factories.ring_amine_factory import (
    RingAmineFactory,
)
from stk._internal.functional_group_factories.secondary_amino_factory import (
    SecondaryAminoFactory,
)
from stk._internal.functional_group_factories.smarts import (
    SmartsFunctionalGroupFactory,
)
from stk._internal.functional_group_factories.terminal_alkene_factory import (
    TerminalAlkeneFactory,
)
from stk._internal.functional_group_factories.terminal_alkyne_factory import (
    TerminalAlkyneFactory,
)
from stk._internal.functional_group_factories.thioacid_factory import (
    ThioacidFactory,
)
from stk._internal.functional_group_factories.thiol_factory import (
    ThiolFactory,
)
from stk._internal.functional_groups.alcohol import Alcohol
from stk._internal.functional_groups.aldehyde import Aldehyde
from stk._internal.functional_groups.alkene import Alkene
from stk._internal.functional_groups.alkyne import Alkyne
from stk._internal.functional_groups.amide import Amide
from stk._internal.functional_groups.boronic_acid import BoronicAcid
from stk._internal.functional_groups.bromo import Bromo
from stk._internal.functional_groups.carboxylic_acid import CarboxylicAcid
from stk._internal.functional_groups.dibromo import Dibromo
from stk._internal.functional_groups.difluoro import Difluoro
from stk._internal.functional_groups.diol import Diol
from stk._internal.functional_groups.fluoro import Fluoro
from stk._internal.functional_groups.functional_group import FunctionalGroup
from stk._internal.functional_groups.generic_functional_group import (
    GenericFunctionalGroup,
)
from stk._internal.functional_groups.iodo import Iodo
from stk._internal.functional_groups.primary_amino import PrimaryAmino
from stk._internal.functional_groups.ring_amine import RingAmine
from stk._internal.functional_groups.secondary_amino import SecondaryAmino
from stk._internal.functional_groups.single_atom import SingleAtom
from stk._internal.functional_groups.thioacid import Thioacid
from stk._internal.functional_groups.thiol import Thiol
from stk._internal.json_serde.constructed_molecule import (
    ConstructedMoleculeDejsonizer,
    ConstructedMoleculeJsonizer,
)
from stk._internal.json_serde.molecule import (
    MoleculeDejsonizer,
    MoleculeJsonizer,
)
from stk._internal.key_makers.inchi import Inchi
from stk._internal.key_makers.inchi_key import InchiKey
from stk._internal.key_makers.molecule import MoleculeKeyMaker
from stk._internal.key_makers.smiles import Smiles
from stk._internal.molecule import Molecule
from stk._internal.optimizers.collapser import Collapser
from stk._internal.optimizers.mchammer import MCHammer
from stk._internal.optimizers.null import NullOptimizer
from stk._internal.optimizers.optimizer import Optimizer
from stk._internal.optimizers.periodic_collapser import PeriodicCollapser
from stk._internal.optimizers.spinner import Spinner
from stk._internal.periodic_info import PeriodicInfo
from stk._internal.reaction_factories.dative_reaction_factory import (
    DativeReactionFactory,
)
from stk._internal.reaction_factories.generic_reaction_factory import (
    GenericReactionFactory,
)
from stk._internal.reaction_factories.reaction_factory import ReactionFactory
from stk._internal.reactions.dative_reaction.dative_reaction import (
    DativeReaction,
)
from stk._internal.reactions.one_one_reaction import OneOneReaction
from stk._internal.reactions.one_two_reaction import OneTwoReaction
from stk._internal.reactions.reaction.reaction import Reaction
from stk._internal.reactions.reaction.reaction_result import ReactionResult
from stk._internal.reactions.ring_amine_reaction import RingAmineReaction
from stk._internal.reactions.two_two_reaction import TwoTwoReaction
from stk._internal.topology_graphs.edge import Edge
from stk._internal.topology_graphs.edge_group import EdgeGroup
from stk._internal.topology_graphs.topology_graph.topology_graph import (
    TopologyGraph,
)
from stk._internal.topology_graphs.vertex import Vertex
from stk._internal.utilities.utilities import (
    get_acute_vector,
    normalize_vector,
    rotation_matrix_arbitrary_axis,
    vector_angle,
)
from stk._internal.writers.mdl_mol import MolWriter
from stk._internal.writers.pdb import PdbWriter
from stk._internal.writers.turbomole import TurbomoleWriter
from stk._internal.writers.xyz import XyzWriter
from stk._version import __version__

BatchKey = BatchKey
"""A unique key for a :class:`.Batch`."""

__all__ = [
    "Atom",
    "AtomInfo",
    "Bond",
    "BondInfo",
    "MoleculeRecord",
    "EvolutionaryAlgorithm",
    "MoleculeMutator",
    "RandomMutator",
    "MoleculeState",
    "Edge",
    "Vertex",
    "cof",
    "host_guest",
    "metal_complex",
    "get_acute_vector",
    "normalize_vector",
    "rotation_matrix_arbitrary_axis",
    "vector_angle",
    "CrossoverRecord",
    "ReplaceFitness",
    "RemoveMolecules",
    "MutationRecord",
    "NormalizerSequence",
    "SimilarBuildingBlock",
    "RandomBuildingBlock",
    "RandomTopologyGraph",
    "GeneticRecombination",
    "Generation",
    "PropertyVector",
    "AboveAverage",
    "Best",
    "Worst",
    "FilterBatches",
    "StochasticUniversalSampling",
    "Tournament",
    "RemoveBatches",
    "FilterMolecules",
    "Roulette",
    "Batch",
    "BatchKey",
    "Add",
    "NullFitnessNormalizer",
    "NullOptimizer",
    "Power",
    "DivideByMean",
    "Sum",
    "Multiply",
    "ShiftUp",
    "MoleculeJsonizer",
    "MoleculeDejsonizer",
    "ConstructedMoleculeDejsonizer",
    "ConstructedMoleculeJsonizer",
    "Spinner",
    "MoleculeDejsonizer",
    "MoleculeJsonizer",
    "BuildingBlock",
    "ConstructedMolecule",
    "TopologyGraph",
    "MoleculeCrosser",
    "Optimizer",
    "RandomCrosser",
    "FitnessCalculator",
    "FitnessFunction",
    "FitnessNormalizer",
    "AlcoholFactory",
    "AldehydeFactory",
    "AmideFactory",
    "BoronicAcidFactory",
    "BromoFactory",
    "CarboxylicAcidFactory",
    "DibromoFactory",
    "DifluoroFactory",
    "DiolFactory",
    "FunctionalGroupFactory",
    "FluoroFactory",
    "IodoFactory",
    "PrimaryAminoFactory",
    "RingAmineFactory",
    "SecondaryAminoFactory",
    "SmartsFunctionalGroupFactory",
    "TerminalAlkeneFactory",
    "TerminalAlkyneFactory",
    "ThioacidFactory",
    "ThiolFactory",
    "Alcohol",
    "Aldehyde",
    "Alkene",
    "Alkyne",
    "Amide",
    "BoronicAcid",
    "Bromo",
    "CarboxylicAcid",
    "Dibromo",
    "Difluoro",
    "Diol",
    "Fluoro",
    "FunctionalGroup",
    "GenericFunctionalGroup",
    "Iodo",
    "PrimaryAmino",
    "RingAmine",
    "RingAmineReaction",
    "SecondaryAmino",
    "SingleAtom",
    "Thioacid",
    "Thiol",
    "cage",
    "polymer",
    "small",
    "Collapser",
    "MCHammer",
    "ReactionFactory",
    "Reaction",
    "Selector",
    "ProgressPlotter",
    "SelectionPlotter",
    "XyzWriter",
    "PdbWriter",
    "MolWriter",
    "TurbomoleWriter",
    "DativeReactionFactory",
    "GenericReactionFactory",
    "ValueDatabase",
    "ConstructedMoleculeMongoDb",
    "ConstructedMoleculeDatabase",
    "MoleculeMongoDb",
    "ValueMongoDb",
    "MoleculeDatabase",
    "Inchi",
    "InchiKey",
    "Smiles",
    "MoleculeKeyMaker",
    "Molecule",
    "ConstructionState",
    "ConstructionResult",
    "ReactionResult",
    "GraphState",
    "OneOneReaction",
    "OneTwoReaction",
    "TwoTwoReaction",
    "DativeReaction",
    "PeriodicInfo",
    "rotaxane",
    "macrocycle",
    "EdgeGroup",
    "PeriodicCollapser",
    "FitnessValues",
    "__version__",
    "Ac",
    "Ag",
    "Al",
    "Am",
    "Ar",
    "As",
    "At",
    "Au",
    "B",
    "Ba",
    "Be",
    "Bh",
    "Bi",
    "Bk",
    "Br",
    "C",
    "Ca",
    "Cd",
    "Ce",
    "Cf",
    "Cl",
    "Cm",
    "Cn",
    "Co",
    "Cr",
    "Cs",
    "Cu",
    "Db",
    "Ds",
    "Dy",
    "Er",
    "Es",
    "Eu",
    "F",
    "Fe",
    "Fl",
    "Fm",
    "Fr",
    "Ga",
    "Gd",
    "Ge",
    "H",
    "He",
    "Hf",
    "Hg",
    "Ho",
    "Hs",
    "I",
    "In",
    "Ir",
    "K",
    "Kr",
    "La",
    "Li",
    "Lr",
    "Lu",
    "Lv",
    "Mc",
    "Md",
    "Mg",
    "Mn",
    "Mo",
    "Mt",
    "N",
    "Na",
    "Nb",
    "Nd",
    "Ne",
    "Nh",
    "Ni",
    "No",
    "Np",
    "O",
    "Og",
    "Os",
    "P",
    "Pa",
    "Pb",
    "Pd",
    "Pm",
    "Po",
    "Pr",
    "Pt",
    "Pu",
    "Ra",
    "Rb",
    "Re",
    "Rf",
    "Rg",
    "Rh",
    "Rn",
    "Ru",
    "S",
    "Sb",
    "Sc",
    "Se",
    "Sg",
    "Si",
    "Sm",
    "Sn",
    "Sr",
    "Ta",
    "Tb",
    "Tc",
    "Te",
    "Th",
    "Ti",
    "Tl",
    "Tm",
    "Ts",
    "U",
    "V",
    "W",
    "Xe",
    "Y",
    "Yb",
    "Zn",
    "Zr",
]
