Index

_

__init__() (backend.transpiling_sampler.TranspilingSampler method) (builder.hamiltonian_builder.HamiltonianBuilder method) (contact.contact_map.ContactMap method) (distance.distance_map.DistanceMap method) (exceptions.ChainLengthError method) (exceptions.ConformationEncodingError method) (exceptions.InvalidBackendError method) (exceptions.InvalidInteractionTypeError method) (exceptions.InvalidOperatorError method) (exceptions.UnsupportedAminoAcidSymbolError method) (interaction.hp_interaction.HPInteraction method) (interaction.interaction.Interaction method) (interaction.mj_interaction.MJInteraction method) (protein.bead.bead.Bead method) (protein.bead.main_bead._MainBead method) (protein.bead.placeholder_side_bead._PlaceholderSideBead method) (protein.bead.side_bead._SideBead method) (protein.chain.chain.Chain method) (protein.chain.main_chain._MainChain method) (protein.chain.side_chain._SideChain method) (protein.protein.Protein method) (result.interpreter.result_interpreter.ResultInterpreter method) (result.models.BeadPosition method) (result.models.SparseVQEOutput method) (result.visualizer.result_visualizer.ResultVisualizer method) _abc_impl (backend.transpiling_sampler.TranspilingSampler attribute) (interaction.hp_interaction.HPInteraction attribute) (interaction.interaction.Interaction attribute) (interaction.mj_interaction.MJInteraction attribute) (protein.bead.bead.Bead attribute) (protein.bead.main_bead._MainBead attribute) (protein.bead.placeholder_side_bead._PlaceholderSideBead attribute) (protein.bead.side_bead._SideBead attribute) (protein.chain.chain.Chain attribute) (protein.chain.main_chain._MainChain attribute) (protein.chain.side_chain._SideChain attribute) _add_backtracking_penalty() (builder.hamiltonian_builder.HamiltonianBuilder method)

_build_backbone_contact_term() (builder.hamiltonian_builder.HamiltonianBuilder method) _calc_distances_main_chain() (distance.distance_map.DistanceMap method) _calc_updated_coeffs() (in module utils.qubit_utils) _create_main_main_contact() (contact.contact_map.ContactMap method) _dense_turn_fun_0() (protein.bead.main_bead._MainBead method) _dense_turn_fun_1() (protein.bead.main_bead._MainBead method) _dense_turn_fun_2() (protein.bead.main_bead._MainBead method) _dense_turn_fun_3() (protein.bead.main_bead._MainBead method) _dump_result_dict_to_json() (result.interpreter.result_interpreter.ResultInterpreter method) _dump_vqe_iterations_to_file() (result.interpreter.result_interpreter.ResultInterpreter method) _find_main_main_contacts() (result.interpreter.result_interpreter.ResultInterpreter method) _generate_3d_coordinates() (result.interpreter.result_interpreter.ResultInterpreter method) _generate_lattice_points() (result.visualizer.result_visualizer.ResultVisualizer method) _generate_turn_sequence() (result.interpreter.result_interpreter.ResultInterpreter method) _get_ibm_quantum_sampler() (in module backend.backend_factory) _get_local_statevector_sampler() (in module backend.backend_factory) _get_target_sequence_length_main_chain() (result.interpreter.result_interpreter.ResultInterpreter method) _get_text_color() (result.visualizer.result_visualizer.ResultVisualizer static method) _initialize_beads() (protein.chain.chain.Chain method) (protein.chain.main_chain._MainChain method) (protein.chain.side_chain._SideChain method) _initialize_contact_map() (contact.contact_map.ContactMap method) _initialize_turn_qubits() (protein.bead.bead.Bead method) _interpret_raw_vqe_results() (result.interpreter.result_interpreter.ResultInterpreter method) _is_hydrophobic() (interaction.hp_interaction.HPInteraction method) _load_hp_symbols() (interaction.hp_interaction.HPInteraction method) _log_coordinates_3d() (result.interpreter.result_interpreter.ResultInterpreter method) _log_turn_sequence() (result.interpreter.result_interpreter.ResultInterpreter method) _MainBead (class in protein.bead.main_bead) _MainChain (class in protein.chain.main_chain) _PlaceholderSideBead (class in protein.bead.placeholder_side_bead) _prepare_mj_interaction_matrix() (interaction.mj_interaction.MJInteraction method) _preprocess_bitstring() (result.interpreter.result_interpreter.ResultInterpreter method) _preset_binary_vals() (in module utils.qubit_utils) _preset_single_binary_val() (in module utils.qubit_utils) _SideBead (class in protein.bead.side_bead) _SideChain (class in protein.chain.side_chain)

A

A (enums.SubLattice attribute)

B

B (enums.SubLattice attribute) BACK_PENALTY (enums.Penalties attribute) backend.backend_factory module backend.transpiling_sampler module BackendType (class in enums) Bead (class in protein.bead.bead)

BeadPosition (class in result.models) bitstring (result.models.SparseVQEOutput attribute) build_and_compress_hamiltonian() (in module utils.setup_utils) build_identity_op() (in module utils.qubit_utils) build_pauli_z_operator() (in module utils.qubit_utils) build_turn_qubit() (in module utils.qubit_utils) builder.hamiltonian_builder module

C

Chain (class in protein.chain.chain) ChainLengthError CHIRALITY_PENALTY (enums.Penalties attribute) ConformationEncoding (class in enums) ConformationEncodingError constants module

contact.contact_map module ContactMap (class in contact.contact_map) convert_to_qubits() (in module utils.qubit_utils) coordinates_3d (result.interpreter.result_interpreter.ResultInterpreter property) create_xyz_file() (in module utils.result_interpretation_utils)

D

DENSE (enums.ConformationEncoding attribute) DIR_0 (enums.TurnDirection attribute) DIR_1 (enums.TurnDirection attribute) DIR_2 (enums.TurnDirection attribute)

DIR_3 (enums.TurnDirection attribute) distance.distance_map module DistanceMap (class in distance.distance_map) dump_results_to_files() (result.interpreter.result_interpreter.ResultInterpreter method)

E

energy_value (result.models.SparseVQEOutput attribute) enums module

exceptions module

F

find_unused_qubits() (in module utils.qubit_utils)

fix_qubits() (in module utils.qubit_utils)

G

generate_3d_gif() (result.visualizer.result_visualizer.ResultVisualizer method) get_energy() (interaction.hp_interaction.HPInteraction method) (interaction.interaction.Interaction method) (interaction.mj_interaction.MJInteraction method) get_first_neighbor_hamiltonian() (builder.hamiltonian_builder.HamiltonianBuilder method)

get_logger() (in module logger.logger) get_sampler() (in module backend.backend_factory) get_second_neighbor_hamiltonian() (builder.hamiltonian_builder.HamiltonianBuilder method) get_symbol_at() (protein.chain.chain.Chain method) get_turn_operators() (builder.hamiltonian_builder.HamiltonianBuilder method)

H

HamiltonianBuilder (class in builder.hamiltonian_builder)

HP (enums.InteractionType attribute) HPInteraction (class in interaction.hp_interaction)

I

IBM_QUANTUM (enums.BackendType attribute) index (result.models.BeadPosition attribute) Interaction (class in interaction.interaction) interaction.hp_interaction module interaction.interaction module

interaction.mj_interaction module InteractionType (class in enums) InvalidBackendError InvalidInteractionTypeError InvalidOperatorError

L

LOCAL_STATEVECTOR (enums.BackendType attribute)

logger.logger module

M

main module main() (in module main) main_main_contacts_detected (result.interpreter.result_interpreter.ResultInterpreter property) MJ (enums.InteractionType attribute) MJInteraction (class in interaction.mj_interaction) module backend.backend_factory backend.transpiling_sampler builder.hamiltonian_builder constants contact.contact_map distance.distance_map enums exceptions interaction.hp_interaction interaction.interaction interaction.mj_interaction logger.logger main protein.bead.bead protein.bead.main_bead protein.bead.placeholder_side_bead protein.bead.side_bead protein.chain.chain protein.chain.main_chain protein.chain.side_chain protein.protein result.interpreter.result_interpreter result.models result.visualizer.result_visualizer utils.qubit_utils utils.result_interpretation_utils utils.setup_utils

O

OVERLAP_PENALTY (enums.Penalties attribute)

P

pad_to_n_qubits() (in module utils.qubit_utils) Penalties (class in enums) probability (result.models.SparseVQEOutput attribute) Protein (class in protein.protein) protein.bead.bead module protein.bead.main_bead module protein.bead.placeholder_side_bead module

protein.bead.side_bead module protein.chain.chain module protein.chain.main_chain module protein.chain.side_chain module protein.protein module

R

read_xyz_file() (in module utils.result_interpretation_utils) remove_unused_qubits() (in module utils.qubit_utils) result.interpreter.result_interpreter module result.models module

result.visualizer.result_visualizer module ResultInterpreter (class in result.interpreter.result_interpreter) ResultVisualizer (class in result.visualizer.result_visualizer) run() (backend.transpiling_sampler.TranspilingSampler method) run_vqe_optimization() (in module utils.setup_utils)

S

sanitize_for_json() (in module utils.result_interpretation_utils) setup_folding_system() (in module utils.setup_utils) setup_result_analysis() (in module utils.setup_utils) setup_vqe_optimization() (in module utils.setup_utils) SPARSE (enums.ConformationEncoding attribute)

SparseVQEOutput (class in result.models) state (result.models.SparseVQEOutput attribute) SubLattice (class in enums) sum_hamiltonians() (builder.hamiltonian_builder.HamiltonianBuilder method) symbol (result.models.BeadPosition attribute)

T

TranspilingSampler (class in backend.transpiling_sampler) turn_0() (protein.bead.bead.Bead method) (protein.bead.main_bead._MainBead method) (protein.bead.placeholder_side_bead._PlaceholderSideBead method) (protein.bead.side_bead._SideBead method) turn_1() (protein.bead.bead.Bead method) (protein.bead.main_bead._MainBead method) (protein.bead.placeholder_side_bead._PlaceholderSideBead method) (protein.bead.side_bead._SideBead method) turn_2() (protein.bead.bead.Bead method) (protein.bead.main_bead._MainBead method) (protein.bead.placeholder_side_bead._PlaceholderSideBead method) (protein.bead.side_bead._SideBead method)

turn_3() (protein.bead.bead.Bead method) (protein.bead.main_bead._MainBead method) (protein.bead.placeholder_side_bead._PlaceholderSideBead method) (protein.bead.side_bead._SideBead method) turn_funcs() (protein.bead.bead.Bead method) turn_sequence (result.interpreter.result_interpreter.ResultInterpreter property) TurnDirection (class in enums)

U

UnsupportedAminoAcidSymbolError utils.qubit_utils module

utils.result_interpretation_utils module utils.setup_utils module

V

visualize_2d() (result.visualizer.result_visualizer.ResultVisualizer method)

visualize_3d() (result.visualizer.result_visualizer.ResultVisualizer method)

X

x (result.models.BeadPosition attribute)

Y

y (result.models.BeadPosition attribute)

Z

z (result.models.BeadPosition attribute)