README.rst
setup.py
src/stk/__init__.py
src/stk/py.typed
src/stk.egg-info/PKG-INFO
src/stk.egg-info/SOURCES.txt
src/stk.egg-info/dependency_links.txt
src/stk.egg-info/requires.txt
src/stk.egg-info/top_level.txt
src/stk/databases/__init__.py
src/stk/databases/constructed_molecule.py
src/stk/databases/molecule.py
src/stk/databases/value.py
src/stk/databases/mongo_db/__init__.py
src/stk/databases/mongo_db/constructed_molecule.py
src/stk/databases/mongo_db/molecule.py
src/stk/databases/mongo_db/utilities.py
src/stk/databases/mongo_db/value.py
src/stk/ea/__init__.py
src/stk/ea/generation.py
src/stk/ea/crossover/__init__.py
src/stk/ea/crossover/crossers/__init__.py
src/stk/ea/crossover/crossers/compound/__init__.py
src/stk/ea/crossover/crossers/compound/random.py
src/stk/ea/crossover/crossers/molecule/__init__.py
src/stk/ea/crossover/crossers/molecule/crosser.py
src/stk/ea/crossover/crossers/molecule/genetic_recombination.py
src/stk/ea/crossover/records/__init__.py
src/stk/ea/crossover/records/record.py
src/stk/ea/evolutionary_algorithm/__init__.py
src/stk/ea/evolutionary_algorithm/evolutionary_algorithm.py
src/stk/ea/evolutionary_algorithm/implementations/__init__.py
src/stk/ea/evolutionary_algorithm/implementations/implementation.py
src/stk/ea/evolutionary_algorithm/implementations/parallel.py
src/stk/ea/evolutionary_algorithm/implementations/serial.py
src/stk/ea/fitness_calculators/__init__.py
src/stk/ea/fitness_calculators/fitness_calculator.py
src/stk/ea/fitness_calculators/fitness_function.py
src/stk/ea/fitness_calculators/property_vector.py
src/stk/ea/fitness_normalizers/__init__.py
src/stk/ea/fitness_normalizers/add.py
src/stk/ea/fitness_normalizers/divide_by_mean.py
src/stk/ea/fitness_normalizers/fitness_normalizer.py
src/stk/ea/fitness_normalizers/multiply.py
src/stk/ea/fitness_normalizers/null.py
src/stk/ea/fitness_normalizers/power.py
src/stk/ea/fitness_normalizers/replace_fitness.py
src/stk/ea/fitness_normalizers/sequence.py
src/stk/ea/fitness_normalizers/shift_up.py
src/stk/ea/fitness_normalizers/sum.py
src/stk/ea/molecule_records/__init__.py
src/stk/ea/molecule_records/molecule.py
src/stk/ea/mutation/__init__.py
src/stk/ea/mutation/mutators/__init__.py
src/stk/ea/mutation/mutators/compound/__init__.py
src/stk/ea/mutation/mutators/compound/random.py
src/stk/ea/mutation/mutators/molecule/__init__.py
src/stk/ea/mutation/mutators/molecule/mutator.py
src/stk/ea/mutation/mutators/molecule/random_building_block.py
src/stk/ea/mutation/mutators/molecule/random_topology_graph.py
src/stk/ea/mutation/mutators/molecule/similar_building_block.py
src/stk/ea/mutation/records/__init__.py
src/stk/ea/mutation/records/record.py
src/stk/ea/plotters/__init__.py
src/stk/ea/plotters/progress.py
src/stk/ea/plotters/selection.py
src/stk/ea/selection/__init__.py
src/stk/ea/selection/batch.py
src/stk/ea/selection/selectors/__init__.py
src/stk/ea/selection/selectors/above_average.py
src/stk/ea/selection/selectors/best.py
src/stk/ea/selection/selectors/filter_batches.py
src/stk/ea/selection/selectors/filter_molecules.py
src/stk/ea/selection/selectors/remove_batches.py
src/stk/ea/selection/selectors/remove_molecules.py
src/stk/ea/selection/selectors/roulette.py
src/stk/ea/selection/selectors/selector.py
src/stk/ea/selection/selectors/stochastic_universal_sampling.py
src/stk/ea/selection/selectors/tournament.py
src/stk/ea/selection/selectors/worst.py
src/stk/ea/selection/selectors/utilities/__init__.py
src/stk/ea/selection/selectors/utilities/yielded_batches.py
src/stk/molecular/__init__.py
src/stk/molecular/periodic_info.py
src/stk/molecular/atoms/__init__.py
src/stk/molecular/atoms/atom.py
src/stk/molecular/atoms/atom_info.py
src/stk/molecular/atoms/elements.py
src/stk/molecular/bonds/__init__.py
src/stk/molecular/bonds/bond.py
src/stk/molecular/bonds/bond_info.py
src/stk/molecular/functional_groups/__init__.py
src/stk/molecular/functional_groups/factories/__init__.py
src/stk/molecular/functional_groups/factories/alcohol_factory.py
src/stk/molecular/functional_groups/factories/aldehyde_factory.py
src/stk/molecular/functional_groups/factories/amide_factory.py
src/stk/molecular/functional_groups/factories/boronic_acid_factory.py
src/stk/molecular/functional_groups/factories/bromo_factory.py
src/stk/molecular/functional_groups/factories/carboxylic_acid_factory.py
src/stk/molecular/functional_groups/factories/dibromo_factory.py
src/stk/molecular/functional_groups/factories/difluoro_factory.py
src/stk/molecular/functional_groups/factories/diol_factory.py
src/stk/molecular/functional_groups/factories/fluoro_factory.py
src/stk/molecular/functional_groups/factories/functional_group_factory.py
src/stk/molecular/functional_groups/factories/iodo_factory.py
src/stk/molecular/functional_groups/factories/primary_amino_factory.py
src/stk/molecular/functional_groups/factories/ring_amine_factory.py
src/stk/molecular/functional_groups/factories/secondary_amino_factory.py
src/stk/molecular/functional_groups/factories/smarts_functional_group_factory.py
src/stk/molecular/functional_groups/factories/terminal_alkene_factory.py
src/stk/molecular/functional_groups/factories/terminal_alkyne_factory.py
src/stk/molecular/functional_groups/factories/thioacid_factory.py
src/stk/molecular/functional_groups/factories/thiol_factory.py
src/stk/molecular/functional_groups/factories/utilities.py
src/stk/molecular/functional_groups/functional_groups/__init__.py
src/stk/molecular/functional_groups/functional_groups/alcohol.py
src/stk/molecular/functional_groups/functional_groups/aldehyde.py
src/stk/molecular/functional_groups/functional_groups/alkene.py
src/stk/molecular/functional_groups/functional_groups/alkyne.py
src/stk/molecular/functional_groups/functional_groups/amide.py
src/stk/molecular/functional_groups/functional_groups/boronic_acid.py
src/stk/molecular/functional_groups/functional_groups/bromo.py
src/stk/molecular/functional_groups/functional_groups/carboxylic_acid.py
src/stk/molecular/functional_groups/functional_groups/dibromo.py
src/stk/molecular/functional_groups/functional_groups/difluoro.py
src/stk/molecular/functional_groups/functional_groups/diol.py
src/stk/molecular/functional_groups/functional_groups/fluoro.py
src/stk/molecular/functional_groups/functional_groups/functional_group.py
src/stk/molecular/functional_groups/functional_groups/generic_functional_group.py
src/stk/molecular/functional_groups/functional_groups/iodo.py
src/stk/molecular/functional_groups/functional_groups/primary_amino.py
src/stk/molecular/functional_groups/functional_groups/ring_amine.py
src/stk/molecular/functional_groups/functional_groups/secondary_amino.py
src/stk/molecular/functional_groups/functional_groups/single_atom.py
src/stk/molecular/functional_groups/functional_groups/thioacid.py
src/stk/molecular/functional_groups/functional_groups/thiol.py
src/stk/molecular/key_makers/__init__.py
src/stk/molecular/key_makers/inchi.py
src/stk/molecular/key_makers/inchi_key.py
src/stk/molecular/key_makers/molecule.py
src/stk/molecular/key_makers/smiles.py
src/stk/molecular/key_makers/utilities.py
src/stk/molecular/molecules/__init__.py
src/stk/molecular/molecules/building_block.py
src/stk/molecular/molecules/constructed_molecule.py
src/stk/molecular/molecules/utilities.py
src/stk/molecular/molecules/molecule/__init__.py
src/stk/molecular/molecules/molecule/molecule.py
src/stk/molecular/molecules/molecule/utilities/__init__.py
src/stk/molecular/molecules/molecule/utilities/updaters/__init__.py
src/stk/molecular/molecules/molecule/utilities/updaters/mae.py
src/stk/molecular/molecules/molecule/utilities/updaters/mdl_mol.py
src/stk/molecular/molecules/molecule/utilities/updaters/pdb.py
src/stk/molecular/molecules/molecule/utilities/updaters/turbomole.py
src/stk/molecular/molecules/molecule/utilities/updaters/xyz.py
src/stk/molecular/molecules/molecule/utilities/writers/__init__.py
src/stk/molecular/molecules/molecule/utilities/writers/mdl_mol.py
src/stk/molecular/molecules/molecule/utilities/writers/pdb.py
src/stk/molecular/molecules/molecule/utilities/writers/xyz.py
src/stk/molecular/reactions/__init__.py
src/stk/molecular/reactions/factories/__init__.py
src/stk/molecular/reactions/factories/dative_reaction_factory.py
src/stk/molecular/reactions/factories/generic_reaction_factory.py
src/stk/molecular/reactions/factories/reaction_factory.py
src/stk/molecular/reactions/reactions/__init__.py
src/stk/molecular/reactions/reactions/one_one_reaction.py
src/stk/molecular/reactions/reactions/one_two_reaction.py
src/stk/molecular/reactions/reactions/ring_amine_reaction.py
src/stk/molecular/reactions/reactions/two_two_reaction.py
src/stk/molecular/reactions/reactions/dative_reaction/__init__.py
src/stk/molecular/reactions/reactions/dative_reaction/dative_reaction.py
src/stk/molecular/reactions/reactions/dative_reaction/utilities.py
src/stk/molecular/reactions/reactions/reaction/__init__.py
src/stk/molecular/reactions/reactions/reaction/new_atom.py
src/stk/molecular/reactions/reactions/reaction/reaction.py
src/stk/molecular/reactions/reactions/reaction/reaction_result.py
src/stk/molecular/topology_graphs/__init__.py
src/stk/molecular/topology_graphs/cage/__init__.py
src/stk/molecular/topology_graphs/cage/cage.py
src/stk/molecular/topology_graphs/cage/cage_construction_state.py
src/stk/molecular/topology_graphs/cage/vertices.py
src/stk/molecular/topology_graphs/cage/metal_topologies/__init__.py
src/stk/molecular/topology_graphs/cage/metal_topologies/m12l24.py
src/stk/molecular/topology_graphs/cage/metal_topologies/m24l48.py
src/stk/molecular/topology_graphs/cage/metal_topologies/m2l4_lantern.py
src/stk/molecular/topology_graphs/cage/metal_topologies/m3l3_triangle.py
src/stk/molecular/topology_graphs/cage/metal_topologies/m3l6.py
src/stk/molecular/topology_graphs/cage/metal_topologies/m4l4_square.py
src/stk/molecular/topology_graphs/cage/metal_topologies/m4l4_tetrahedron.py
src/stk/molecular/topology_graphs/cage/metal_topologies/m4l6_tetrahedron.py
src/stk/molecular/topology_graphs/cage/metal_topologies/m4l6_tetrahedron_spacer.py
src/stk/molecular/topology_graphs/cage/metal_topologies/m4l8.py
src/stk/molecular/topology_graphs/cage/metal_topologies/m6l12_cube.py
src/stk/molecular/topology_graphs/cage/metal_topologies/m6l2l3_prism.py
src/stk/molecular/topology_graphs/cage/metal_topologies/m8l6_cube.py
src/stk/molecular/topology_graphs/cage/three_plus_four/__init__.py
src/stk/molecular/topology_graphs/cage/three_plus_four/six_plus_eight.py
src/stk/molecular/topology_graphs/cage/three_plus_three/__init__.py
src/stk/molecular/topology_graphs/cage/three_plus_three/four_plus_four.py
src/stk/molecular/topology_graphs/cage/three_plus_three/one_plus_one.py
src/stk/molecular/topology_graphs/cage/three_plus_three/two_plus_two.py
src/stk/molecular/topology_graphs/cage/two_plus_five/__init__.py
src/stk/molecular/topology_graphs/cage/two_plus_five/twelve_plus_thirty.py
src/stk/molecular/topology_graphs/cage/two_plus_four/__init__.py
src/stk/molecular/topology_graphs/cage/two_plus_four/eight_plus_sixteen.py
src/stk/molecular/topology_graphs/cage/two_plus_four/five_plus_ten.py
src/stk/molecular/topology_graphs/cage/two_plus_four/four_plus_eight.py
src/stk/molecular/topology_graphs/cage/two_plus_four/six_plus_twelve.py
src/stk/molecular/topology_graphs/cage/two_plus_four/ten_plus_twenty.py
src/stk/molecular/topology_graphs/cage/two_plus_four/three_plus_six.py
src/stk/molecular/topology_graphs/cage/two_plus_four/two_plus_four.py
src/stk/molecular/topology_graphs/cage/two_plus_three/__init__.py
src/stk/molecular/topology_graphs/cage/two_plus_three/eight_plus_twelve.py
src/stk/molecular/topology_graphs/cage/two_plus_three/four_plus_six.py
src/stk/molecular/topology_graphs/cage/two_plus_three/four_plus_six_2.py
src/stk/molecular/topology_graphs/cage/two_plus_three/six_plus_nine.py
src/stk/molecular/topology_graphs/cage/two_plus_three/twenty_plus_thirty.py
src/stk/molecular/topology_graphs/cage/two_plus_three/two_plus_three.py
src/stk/molecular/topology_graphs/cof/__init__.py
src/stk/molecular/topology_graphs/cof/cof.py
src/stk/molecular/topology_graphs/cof/edge.py
src/stk/molecular/topology_graphs/cof/hexagonal.py
src/stk/molecular/topology_graphs/cof/honeycomb.py
src/stk/molecular/topology_graphs/cof/kagome.py
src/stk/molecular/topology_graphs/cof/linkerless_honeycomb.py
src/stk/molecular/topology_graphs/cof/periodic_hexagonal.py
src/stk/molecular/topology_graphs/cof/periodic_honeycomb.py
src/stk/molecular/topology_graphs/cof/periodic_kagome.py
src/stk/molecular/topology_graphs/cof/periodic_linkerless_honeycomb.py
src/stk/molecular/topology_graphs/cof/periodic_square.py
src/stk/molecular/topology_graphs/cof/square.py
src/stk/molecular/topology_graphs/cof/vertices.py
src/stk/molecular/topology_graphs/host_guest/__init__.py
src/stk/molecular/topology_graphs/host_guest/complex.py
src/stk/molecular/topology_graphs/host_guest/vertices.py
src/stk/molecular/topology_graphs/macrocycle/__init__.py
src/stk/molecular/topology_graphs/macrocycle/macrocycle.py
src/stk/molecular/topology_graphs/macrocycle/vertices.py
src/stk/molecular/topology_graphs/metal_complex/__init__.py
src/stk/molecular/topology_graphs/metal_complex/metal_complex.py
src/stk/molecular/topology_graphs/metal_complex/vertices.py
src/stk/molecular/topology_graphs/metal_complex/octahedral/__init__.py
src/stk/molecular/topology_graphs/metal_complex/octahedral/octahedral.py
src/stk/molecular/topology_graphs/metal_complex/octahedral/octahedral_delta.py
src/stk/molecular/topology_graphs/metal_complex/octahedral/octahedral_lambda.py
src/stk/molecular/topology_graphs/metal_complex/paddlewheel/__init__.py
src/stk/molecular/topology_graphs/metal_complex/paddlewheel/paddlewheel.py
src/stk/molecular/topology_graphs/metal_complex/porphyrin/__init__.py
src/stk/molecular/topology_graphs/metal_complex/porphyrin/porphyrin.py
src/stk/molecular/topology_graphs/metal_complex/square_planar/__init__.py
src/stk/molecular/topology_graphs/metal_complex/square_planar/bidentate_square_planar.py
src/stk/molecular/topology_graphs/metal_complex/square_planar/cis_protected_square_planar.py
src/stk/molecular/topology_graphs/metal_complex/square_planar/square_planar.py
src/stk/molecular/topology_graphs/polymer/__init__.py
src/stk/molecular/topology_graphs/polymer/linear/__init__.py
src/stk/molecular/topology_graphs/polymer/linear/linear.py
src/stk/molecular/topology_graphs/polymer/linear/vertices.py
src/stk/molecular/topology_graphs/rotaxane/__init__.py
src/stk/molecular/topology_graphs/rotaxane/nrotaxane.py
src/stk/molecular/topology_graphs/rotaxane/vertices.py
src/stk/molecular/topology_graphs/topology_graph/__init__.py
src/stk/molecular/topology_graphs/topology_graph/edge.py
src/stk/molecular/topology_graphs/topology_graph/edge_group.py
src/stk/molecular/topology_graphs/topology_graph/vertex.py
src/stk/molecular/topology_graphs/topology_graph/construction_result/__init__.py
src/stk/molecular/topology_graphs/topology_graph/construction_result/construction_result.py
src/stk/molecular/topology_graphs/topology_graph/construction_result/periodic.py
src/stk/molecular/topology_graphs/topology_graph/construction_state/__init__.py
src/stk/molecular/topology_graphs/topology_graph/construction_state/construction_state.py
src/stk/molecular/topology_graphs/topology_graph/construction_state/graph_state.py
src/stk/molecular/topology_graphs/topology_graph/construction_state/molecule_state/__init__.py
src/stk/molecular/topology_graphs/topology_graph/construction_state/molecule_state/deletions_summary.py
src/stk/molecular/topology_graphs/topology_graph/construction_state/molecule_state/molecule_state.py
src/stk/molecular/topology_graphs/topology_graph/construction_state/molecule_state/placements_summary/__init__.py
src/stk/molecular/topology_graphs/topology_graph/construction_state/molecule_state/placements_summary/atom_batch.py
src/stk/molecular/topology_graphs/topology_graph/construction_state/molecule_state/placements_summary/bond_batch.py
src/stk/molecular/topology_graphs/topology_graph/construction_state/molecule_state/placements_summary/placements_summary.py
src/stk/molecular/topology_graphs/topology_graph/construction_state/molecule_state/reactions_summary/__init__.py
src/stk/molecular/topology_graphs/topology_graph/construction_state/molecule_state/reactions_summary/atom_batch.py
src/stk/molecular/topology_graphs/topology_graph/construction_state/molecule_state/reactions_summary/bond_batch.py
src/stk/molecular/topology_graphs/topology_graph/construction_state/molecule_state/reactions_summary/reactions_summary.py
src/stk/molecular/topology_graphs/topology_graph/optimizers/__init__.py
src/stk/molecular/topology_graphs/topology_graph/optimizers/collapser.py
src/stk/molecular/topology_graphs/topology_graph/optimizers/mchammer.py
src/stk/molecular/topology_graphs/topology_graph/optimizers/null.py
src/stk/molecular/topology_graphs/topology_graph/optimizers/optimizer.py
src/stk/molecular/topology_graphs/topology_graph/optimizers/periodic_collapser.py
src/stk/molecular/topology_graphs/topology_graph/optimizers/spinner.py
src/stk/molecular/topology_graphs/topology_graph/optimizers/utilities.py
src/stk/molecular/topology_graphs/topology_graph/topology_graph/__init__.py
src/stk/molecular/topology_graphs/topology_graph/topology_graph/topology_graph.py
src/stk/molecular/topology_graphs/topology_graph/topology_graph/implementations/__init__.py
src/stk/molecular/topology_graphs/topology_graph/topology_graph/implementations/parallel.py
src/stk/molecular/topology_graphs/topology_graph/topology_graph/implementations/serial.py
src/stk/molecular/topology_graphs/topology_graph/topology_graph/implementations/utilities.py
src/stk/molecular/topology_graphs/utilities/__init__.py
src/stk/molecular/topology_graphs/utilities/edge_sorter.py
src/stk/molecular/topology_graphs/utilities/functional_group_sorter.py
src/stk/molecular/topology_graphs/utilities/sorter.py
src/stk/molecular/writers/__init__.py
src/stk/molecular/writers/mdl_mol.py
src/stk/molecular/writers/pdb.py
src/stk/molecular/writers/turbomole.py
src/stk/molecular/writers/xyz.py
src/stk/serialization/__init__.py
src/stk/serialization/json/__init__.py
src/stk/serialization/json/deserializers/__init__.py
src/stk/serialization/json/deserializers/constructed_molecule.py
src/stk/serialization/json/deserializers/molecule.py
src/stk/serialization/json/deserializers/utilities.py
src/stk/serialization/json/serializers/__init__.py
src/stk/serialization/json/serializers/constructed_molecule/__init__.py
src/stk/serialization/json/serializers/constructed_molecule/constructed_molecule.py
src/stk/serialization/json/serializers/molecule/__init__.py
src/stk/serialization/json/serializers/molecule/molecule.py
src/stk/serialization/json/serializers/molecule/utilities.py
src/stk/utilities/__init__.py
src/stk/utilities/utilities.py