Index

_

__add__() (mythos.energy.base.BaseEnergyFunction method) (mythos.energy.base.ComposedEnergyFunction method) (mythos.simulators.io.SimulatorTrajectory method) __call__() (mythos.energy.base.BaseEnergyFunction method) (mythos.energy.base.ComposedEnergyFunction method) (mythos.energy.base.EnergyFunction method) (mythos.losses.observable_wrappers.LossFn method) (mythos.losses.observable_wrappers.ObservableLossFn method) (mythos.losses.observable_wrappers.RootMeanSquaredError method) (mythos.losses.observable_wrappers.SquaredError method) (mythos.observables.area_per_lipid.AreaPerLipid method) (mythos.observables.base.BaseObservable method) (mythos.observables.diameter.Diameter method) (mythos.observables.melting_temp.MeltingTemp method) (mythos.observables.membrane_thickness.MembraneThickness method) (mythos.observables.persistence_length.PersistenceLength method) (mythos.observables.pitch.PitchAngle method) (mythos.observables.propeller.PropellerTwist method) (mythos.observables.rise.Rise method) (mythos.observables.rmse.RMSE method) (mythos.observables.stretch_torsion.ExtensionZ method) (mythos.observables.stretch_torsion.TwistXY method) __commit_id__ (in module mythos._version) __contains__() (mythos.energy.martini.base.MartiniEnergyConfiguration method) __getitem__() (mythos.energy.martini.base.MartiniEnergyConfiguration method) __merge__baseconfig() (mythos.energy.configuration.BaseConfiguration method) __merge__dict() (mythos.energy.configuration.BaseConfiguration method) __mul__() (mythos.energy.base.BaseEnergyFunction method) __or__() (mythos.energy.configuration.BaseConfiguration method) (mythos.energy.martini.base.MartiniEnergyConfiguration method) __post_init__() (mythos.energy.base.BaseEnergyFunction method) (mythos.energy.base.ComposedEnergyFunction method) (mythos.energy.configuration.BaseConfiguration method) (mythos.energy.dna2.Debye method) (mythos.energy.dna2.debye.Debye method) (mythos.energy.martini.base.MartiniEnergyConfiguration method) (mythos.energy.martini.base.MartiniTopology method) (mythos.energy.martini.m2.Angle method) (mythos.energy.martini.m2.angle.Angle method) (mythos.energy.martini.m2.angle.AngleConfiguration method) (mythos.energy.martini.m2.AngleConfiguration method) (mythos.energy.martini.m2.Bond method) (mythos.energy.martini.m2.bond.Bond method) (mythos.energy.martini.m2.bond.BondConfiguration method) (mythos.energy.martini.m2.BondConfiguration method) (mythos.energy.martini.m2.LJ method) (mythos.energy.martini.m2.lj.LJ method) (mythos.energy.martini.m2.lj.LJConfiguration method) (mythos.energy.martini.m2.LJConfiguration method) (mythos.input.sequence_constraints.SequenceConstraints method) (mythos.input.topology.Topology method) (mythos.input.trajectory.NucleotideState method) (mythos.input.trajectory.Trajectory method) (mythos.observables.diameter.Diameter method) (mythos.observables.persistence_length.PersistenceLength method) (mythos.observables.pitch.PitchAngle method) (mythos.observables.propeller.PropellerTwist method) (mythos.observables.rise.Rise method) (mythos.observables.rmse.RMSE method) (mythos.observables.stretch_torsion.ExtensionZ method) (mythos.observables.stretch_torsion.TwistXY method) (mythos.optimization.objective.DiffTReObjective method) (mythos.optimization.objective.Objective method) (mythos.optimization.optimization.RayOptimizer method) (mythos.simulators.gromacs.gromacs.GromacsSimulator method) (mythos.simulators.gromacs.GromacsSimulator method) (mythos.simulators.jax_md.jaxmd.JaxMDSimulator method) (mythos.simulators.jax_md.JaxMDSimulator method) (mythos.simulators.jax_md.NeighborList method) (mythos.simulators.jax_md.utils.NeighborList method) (mythos.simulators.lammps.lammps_oxdna.LAMMPSoxDNASimulator method) (mythos.simulators.oxdna.oxdna.oxDNASimulator method) (mythos.simulators.oxdna.oxdna.oxDNAUmbrellaSampler method) (mythos.simulators.oxdna.oxDNASimulator method) (mythos.simulators.oxdna.oxDNAUmbrellaSampler method)

__project__ (in module mythos) __radd__() (mythos.energy.base.ComposedEnergyFunction method) __repr__() (mythos.input.trajectory.Trajectory method) __version__ (in module mythos) (in module mythos._version) __version_tuple__ (in module mythos._version) _create_and_run_remote() (mythos.optimization.optimization.RayOptimizer method) _determine_oxdna_format() (in module mythos.input.topology) _from_file_oxdna_classic() (in module mythos.input.topology) _from_file_oxdna_new() (in module mythos.input.topology) _get_bonded_neighbors() (in module mythos.input.topology) _get_file_handle() (mythos.ui.loggers.disk.PerMetricFileLogger method) _get_order_parameter_names() (in module mythos.simulators.oxdna.utils) _get_ray_options() (mythos.optimization.optimization.RayOptimizer method) _get_unbonded_neighbors() (in module mythos.input.topology) _guess_binary_location() (in module mythos.simulators.oxdna) (in module mythos.simulators.oxdna.oxdna) _handle_molecule_section_data() (mythos.input.gromacs_input.GromacsParamsParser method) _handle_nonbond_params() (mythos.input.gromacs_input.GromacsParamsParser method) _handle_section_data() (mythos.input.gromacs_input.GromacsParamsParser method) _handle_section_header() (mythos.input.gromacs_input.GromacsParamsParser method) _lammps_oxdna_replace_inputs() (in module mythos.simulators.lammps.lammps_oxdna) _merge_metadata() (in module mythos.simulators.io) _param_in_fn() (mythos.energy.base.ComposedEnergyFunction method) (mythos.energy.base.QualifiedComposedEnergyFunction method) _parse_boolean() (in module mythos.input.gromacs_input) (in module mythos.input.oxdna_input) _parse_dict() (in module mythos.input.oxdna_input) _parse_numeric() (in module mythos.input.gromacs_input) (in module mythos.input.oxdna_input) _parse_value() (in module mythos.input.gromacs_input) (in module mythos.input.oxdna_input) _parse_value_in() (in module mythos.simulators.oxdna.utils) _parse_value_out() (in module mythos.simulators.oxdna.utils) _parser_init() (mythos.input.gromacs_input.GromacsParamsParser method) _process_line() (mythos.input.gromacs_input.GromacsParamsParser method) _read_file() (in module mythos.input.trajectory) _read_file_process_wrapper() (in module mythos.input.trajectory) _read_lammps_output() (in module mythos.simulators.lammps.lammps_oxdna) _read_parallel() (in module mythos.input.trajectory) _read_trajectory() (mythos.simulators.gromacs.gromacs.GromacsSimulator method) (mythos.simulators.gromacs.GromacsSimulator method) (mythos.simulators.oxdna.oxdna.oxDNASimulator method) (mythos.simulators.oxdna.oxDNASimulator method) _rename_param_for_fn() (mythos.energy.base.ComposedEnergyFunction method) (mythos.energy.base.QualifiedComposedEnergyFunction method) _rename_param_from_fn() (mythos.energy.base.ComposedEnergyFunction method) (mythos.energy.base.QualifiedComposedEnergyFunction method) _replace_parameters() (mythos.simulators.lammps.lammps_oxdna.LAMMPSoxDNASimulator method) _replace_parts_in_line() (in module mythos.simulators.lammps.lammps_oxdna) _reweight_from_histogram() (in module mythos.simulators.oxdna.oxdna) _run_gromacs() (mythos.simulators.gromacs.gromacs.GromacsSimulator method) (mythos.simulators.gromacs.GromacsSimulator method) _run_objective() (mythos.optimization.optimization.RayOptimizer method) _run_simulation_step() (mythos.simulators.gromacs.gromacs.GromacsSimulator method) (mythos.simulators.gromacs.GromacsSimulator method) _run_simulator() (mythos.optimization.optimization.RayOptimizer method) _solve_f1_b() (in module mythos.energy.dna1.base_smoothing_functions) _solve_f1_xc_star() (in module mythos.energy.dna1.base_smoothing_functions) _solve_f2_b() (in module mythos.energy.dna1.base_smoothing_functions) _solve_f2_xc_star() (in module mythos.energy.dna1.base_smoothing_functions) _solve_f3_b() (in module mythos.energy.dna1.base_smoothing_functions) _solve_f3_xc() (in module mythos.energy.dna1.base_smoothing_functions) _solve_f4_b() (in module mythos.energy.dna1.base_smoothing_functions) _solve_f4_xc() (in module mythos.energy.dna1.base_smoothing_functions) _solve_f5_b() (in module mythos.energy.dna1.base_smoothing_functions) _solve_f5_xc() (in module mythos.energy.dna1.base_smoothing_functions) _transform_lammps_quat() (in module mythos.simulators.lammps.lammps_oxdna) _transform_lammps_state() (in module mythos.simulators.lammps.lammps_oxdna) _transform_param() (in module mythos.simulators.lammps.lammps_oxdna) _update_topology_params() (mythos.simulators.gromacs.gromacs.GromacsSimulator method) (mythos.simulators.gromacs.GromacsSimulator method) _wait_remotes() (mythos.optimization.optimization.RayOptimizer method) _write_state() (in module mythos.input.trajectory)

A

a_coax_1 (mythos.energy.dna1.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.dna1.CoaxialStackingConfiguration attribute) (mythos.energy.dna2.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.dna2.CoaxialStackingConfiguration attribute) a_coax_1_f6 (mythos.energy.dna2.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.dna2.CoaxialStackingConfiguration attribute) a_coax_3p (mythos.energy.dna1.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.dna1.CoaxialStackingConfiguration attribute) a_coax_4 (mythos.energy.dna1.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.dna1.CoaxialStackingConfiguration attribute) (mythos.energy.dna2.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.dna2.CoaxialStackingConfiguration attribute) a_coax_4p (mythos.energy.dna1.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.dna1.CoaxialStackingConfiguration attribute) a_coax_5 (mythos.energy.dna1.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.dna1.CoaxialStackingConfiguration attribute) (mythos.energy.dna2.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.dna2.CoaxialStackingConfiguration attribute) a_coax_6 (mythos.energy.dna1.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.dna1.CoaxialStackingConfiguration attribute) (mythos.energy.dna2.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.dna2.CoaxialStackingConfiguration attribute) a_cross_1 (mythos.energy.dna1.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.dna1.CrossStackingConfiguration attribute) (mythos.energy.dna2.CrossStackingConfiguration attribute) (mythos.energy.rna2.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.rna2.CrossStackingConfiguration attribute) a_cross_2 (mythos.energy.dna1.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.dna1.CrossStackingConfiguration attribute) (mythos.energy.dna2.CrossStackingConfiguration attribute) (mythos.energy.rna2.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.rna2.CrossStackingConfiguration attribute) a_cross_3 (mythos.energy.dna1.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.dna1.CrossStackingConfiguration attribute) (mythos.energy.dna2.CrossStackingConfiguration attribute) (mythos.energy.rna2.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.rna2.CrossStackingConfiguration attribute) a_cross_4 (mythos.energy.dna1.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.dna1.CrossStackingConfiguration attribute) (mythos.energy.dna2.CrossStackingConfiguration attribute) a_cross_7 (mythos.energy.dna1.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.dna1.CrossStackingConfiguration attribute) (mythos.energy.dna2.CrossStackingConfiguration attribute) (mythos.energy.rna2.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.rna2.CrossStackingConfiguration attribute) a_cross_8 (mythos.energy.dna1.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.dna1.CrossStackingConfiguration attribute) (mythos.energy.dna2.CrossStackingConfiguration attribute) (mythos.energy.rna2.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.rna2.CrossStackingConfiguration attribute) a_hb (mythos.energy.dna1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.dna1.HydrogenBondingConfiguration attribute) (mythos.energy.dna2.HydrogenBondingConfiguration attribute) a_hb_1 (mythos.energy.dna1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.dna1.HydrogenBondingConfiguration attribute) (mythos.energy.dna2.HydrogenBondingConfiguration attribute) a_hb_2 (mythos.energy.dna1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.dna1.HydrogenBondingConfiguration attribute) (mythos.energy.dna2.HydrogenBondingConfiguration attribute) a_hb_3 (mythos.energy.dna1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.dna1.HydrogenBondingConfiguration attribute) (mythos.energy.dna2.HydrogenBondingConfiguration attribute) a_hb_4 (mythos.energy.dna1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.dna1.HydrogenBondingConfiguration attribute) (mythos.energy.dna2.HydrogenBondingConfiguration attribute) a_hb_7 (mythos.energy.dna1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.dna1.HydrogenBondingConfiguration attribute) (mythos.energy.dna2.HydrogenBondingConfiguration attribute) a_hb_8 (mythos.energy.dna1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.dna1.HydrogenBondingConfiguration attribute) (mythos.energy.dna2.HydrogenBondingConfiguration attribute) a_stack (mythos.energy.dna1.stacking.StackingConfiguration attribute) (mythos.energy.dna1.StackingConfiguration attribute) (mythos.energy.dna2.StackingConfiguration attribute) (mythos.energy.rna2.stacking.StackingConfiguration attribute) (mythos.energy.rna2.StackingConfiguration attribute)

a_stack_1 (mythos.energy.dna1.stacking.StackingConfiguration attribute) (mythos.energy.dna1.StackingConfiguration attribute) (mythos.energy.dna2.StackingConfiguration attribute) (mythos.energy.rna2.stacking.StackingConfiguration attribute) (mythos.energy.rna2.StackingConfiguration attribute) a_stack_10 (mythos.energy.rna2.stacking.StackingConfiguration attribute) (mythos.energy.rna2.StackingConfiguration attribute) a_stack_2 (mythos.energy.dna1.stacking.StackingConfiguration attribute) (mythos.energy.dna1.StackingConfiguration attribute) (mythos.energy.dna2.StackingConfiguration attribute) (mythos.energy.rna2.stacking.StackingConfiguration attribute) (mythos.energy.rna2.StackingConfiguration attribute) a_stack_4 (mythos.energy.dna1.stacking.StackingConfiguration attribute) (mythos.energy.dna1.StackingConfiguration attribute) (mythos.energy.dna2.StackingConfiguration attribute) a_stack_5 (mythos.energy.dna1.stacking.StackingConfiguration attribute) (mythos.energy.dna1.StackingConfiguration attribute) (mythos.energy.dna2.StackingConfiguration attribute) (mythos.energy.rna2.stacking.StackingConfiguration attribute) (mythos.energy.rna2.StackingConfiguration attribute) a_stack_6 (mythos.energy.dna1.stacking.StackingConfiguration attribute) (mythos.energy.dna1.StackingConfiguration attribute) (mythos.energy.dna2.StackingConfiguration attribute) (mythos.energy.rna2.stacking.StackingConfiguration attribute) (mythos.energy.rna2.StackingConfiguration attribute) a_stack_9 (mythos.energy.rna2.stacking.StackingConfiguration attribute) (mythos.energy.rna2.StackingConfiguration attribute) add_composable_energy_fn() (mythos.energy.base.ComposedEnergyFunction method) add_energy_fn() (mythos.energy.base.ComposedEnergyFunction method) aggregate_grad_fn (mythos.optimization.optimization.RayOptimizer attribute) AimLogger (class in mythos.ui.loggers.aim) allocate() (mythos.simulators.jax_md.NeighborList method) (mythos.simulators.jax_md.NoNeighborList method) (mythos.simulators.jax_md.utils.NeighborHelper method) (mythos.simulators.jax_md.utils.NeighborList method) (mythos.simulators.jax_md.utils.NoNeighborList method) Angle (class in mythos.energy.martini.m2) (class in mythos.energy.martini.m2.angle) ANGLE_K_PREFIX (in module mythos.energy.martini.m2.angle) angle_names (mythos.energy.martini.base.MartiniEnergyFunction property) ANGLE_THETA0_PREFIX (in module mythos.energy.martini.m2.angle) AngleConfiguration (class in mythos.energy.martini.m2) (class in mythos.energy.martini.m2.angle) angles (mythos.energy.martini.base.MartiniEnergyFunction attribute) (mythos.energy.martini.base.MartiniTopology attribute), [1] ANGSTROMS_PER_NM (in module mythos.utils.units) ANGSTROMS_PER_OXDNA_LENGTH (in module mythos.utils.units) ANGSTROMS_TO_NM (in module mythos.simulators.gromacs.utils) angular_velocity (mythos.input.trajectory.NucleotideState property) AreaPerLipid (class in mythos.observables.area_per_lipid) Arr_Bonded_Neighbors (in module mythos.utils.types) Arr_Bonded_Neighbors_2 (in module mythos.utils.types) Arr_Box (in module mythos.utils.types) Arr_Bp (in module mythos.utils.types) Arr_Bp_Pseq (in module mythos.utils.types) Arr_N (in module mythos.utils.types) Arr_Nucleotide (in module mythos.utils.types) Arr_Nucleotide_15 (in module mythos.utils.types) Arr_Nucleotide_2 (in module mythos.utils.types) Arr_Nucleotide_2_Int (in module mythos.utils.types) Arr_Nucleotide_3 (in module mythos.utils.types) Arr_Nucleotide_4 (in module mythos.utils.types) Arr_Nucleotide_Int (in module mythos.utils.types) ARR_OR_SCALAR (in module mythos.utils.types) Arr_States (in module mythos.utils.types) Arr_States_3 (in module mythos.utils.types) Arr_Unbonded_Neighbors (in module mythos.utils.types) Arr_Unbonded_Neighbors_2 (in module mythos.utils.types) Arr_Unpaired (in module mythos.utils.types) Arr_Unpaired_Pseq (in module mythos.utils.types) array (mythos.input.trajectory.NucleotideState attribute) atom_names (mythos.energy.martini.base.MartiniEnergyFunction attribute) (mythos.energy.martini.base.MartiniTopology attribute), [1] atom_types (mythos.energy.martini.base.MartiniEnergyFunction attribute) (mythos.energy.martini.base.MartiniTopology attribute), [1]

B

b_back_base (mythos.energy.dna1.bonded_excluded_volume.BondedExcludedVolumeConfiguration attribute) (mythos.energy.dna1.BondedExcludedVolumeConfiguration attribute) (mythos.energy.dna1.unbonded_excluded_volume.UnbondedExcludedVolumeConfiguration attribute) (mythos.energy.dna1.UnbondedExcludedVolumeConfiguration attribute) (mythos.energy.dna2.BondedExcludedVolumeConfiguration attribute) (mythos.energy.dna2.UnbondedExcludedVolumeConfiguration attribute) b_backbone (mythos.energy.dna1.unbonded_excluded_volume.UnbondedExcludedVolumeConfiguration attribute) (mythos.energy.dna1.UnbondedExcludedVolumeConfiguration attribute) (mythos.energy.dna2.UnbondedExcludedVolumeConfiguration attribute) b_base (mythos.energy.dna1.bonded_excluded_volume.BondedExcludedVolumeConfiguration attribute) (mythos.energy.dna1.BondedExcludedVolumeConfiguration attribute) (mythos.energy.dna1.unbonded_excluded_volume.UnbondedExcludedVolumeConfiguration attribute) (mythos.energy.dna1.UnbondedExcludedVolumeConfiguration attribute) (mythos.energy.dna2.BondedExcludedVolumeConfiguration attribute) (mythos.energy.dna2.UnbondedExcludedVolumeConfiguration attribute) b_base_back (mythos.energy.dna1.bonded_excluded_volume.BondedExcludedVolumeConfiguration attribute) (mythos.energy.dna1.BondedExcludedVolumeConfiguration attribute) (mythos.energy.dna1.unbonded_excluded_volume.UnbondedExcludedVolumeConfiguration attribute) (mythos.energy.dna1.UnbondedExcludedVolumeConfiguration attribute) (mythos.energy.dna2.BondedExcludedVolumeConfiguration attribute) (mythos.energy.dna2.UnbondedExcludedVolumeConfiguration attribute) b_coax_1 (mythos.energy.dna1.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.dna1.CoaxialStackingConfiguration attribute) (mythos.energy.dna2.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.dna2.CoaxialStackingConfiguration attribute) b_coax_1_f6 (mythos.energy.dna2.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.dna2.CoaxialStackingConfiguration attribute) b_coax_4 (mythos.energy.dna1.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.dna1.CoaxialStackingConfiguration attribute) (mythos.energy.dna2.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.dna2.CoaxialStackingConfiguration attribute) b_coax_5 (mythos.energy.dna1.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.dna1.CoaxialStackingConfiguration attribute) (mythos.energy.dna2.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.dna2.CoaxialStackingConfiguration attribute) b_coax_6 (mythos.energy.dna1.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.dna1.CoaxialStackingConfiguration attribute) (mythos.energy.dna2.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.dna2.CoaxialStackingConfiguration attribute) b_cos_phi3_coax (mythos.energy.dna1.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.dna1.CoaxialStackingConfiguration attribute) b_cos_phi4_coax (mythos.energy.dna1.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.dna1.CoaxialStackingConfiguration attribute) b_cross_1 (mythos.energy.dna1.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.dna1.CrossStackingConfiguration attribute) (mythos.energy.dna2.CrossStackingConfiguration attribute) (mythos.energy.rna2.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.rna2.CrossStackingConfiguration attribute) b_cross_2 (mythos.energy.dna1.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.dna1.CrossStackingConfiguration attribute) (mythos.energy.dna2.CrossStackingConfiguration attribute) (mythos.energy.rna2.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.rna2.CrossStackingConfiguration attribute) b_cross_3 (mythos.energy.dna1.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.dna1.CrossStackingConfiguration attribute) (mythos.energy.dna2.CrossStackingConfiguration attribute) (mythos.energy.rna2.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.rna2.CrossStackingConfiguration attribute) b_cross_4 (mythos.energy.dna1.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.dna1.CrossStackingConfiguration attribute) (mythos.energy.dna2.CrossStackingConfiguration attribute) b_cross_7 (mythos.energy.dna1.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.dna1.CrossStackingConfiguration attribute) (mythos.energy.dna2.CrossStackingConfiguration attribute) (mythos.energy.rna2.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.rna2.CrossStackingConfiguration attribute) b_cross_8 (mythos.energy.dna1.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.dna1.CrossStackingConfiguration attribute) (mythos.energy.dna2.CrossStackingConfiguration attribute) (mythos.energy.rna2.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.rna2.CrossStackingConfiguration attribute) b_hb_1 (mythos.energy.dna1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.dna1.HydrogenBondingConfiguration attribute) (mythos.energy.dna2.HydrogenBondingConfiguration attribute) b_hb_2 (mythos.energy.dna1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.dna1.HydrogenBondingConfiguration attribute) (mythos.energy.dna2.HydrogenBondingConfiguration attribute) b_hb_3 (mythos.energy.dna1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.dna1.HydrogenBondingConfiguration attribute) (mythos.energy.dna2.HydrogenBondingConfiguration attribute) b_hb_4 (mythos.energy.dna1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.dna1.HydrogenBondingConfiguration attribute) (mythos.energy.dna2.HydrogenBondingConfiguration attribute) b_hb_7 (mythos.energy.dna1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.dna1.HydrogenBondingConfiguration attribute) (mythos.energy.dna2.HydrogenBondingConfiguration attribute) b_hb_8 (mythos.energy.dna1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.dna1.HydrogenBondingConfiguration attribute) (mythos.energy.dna2.HydrogenBondingConfiguration attribute) b_high_coax (mythos.energy.dna1.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.dna1.CoaxialStackingConfiguration attribute) (mythos.energy.dna2.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.dna2.CoaxialStackingConfiguration attribute) b_high_cross (mythos.energy.dna1.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.dna1.CrossStackingConfiguration attribute) (mythos.energy.dna2.CrossStackingConfiguration attribute) (mythos.energy.rna2.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.rna2.CrossStackingConfiguration attribute) b_high_hb (mythos.energy.dna1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.dna1.HydrogenBondingConfiguration attribute) (mythos.energy.dna2.HydrogenBondingConfiguration attribute) b_high_stack (mythos.energy.dna1.stacking.StackingConfiguration attribute) (mythos.energy.dna1.StackingConfiguration attribute) (mythos.energy.dna2.StackingConfiguration attribute) (mythos.energy.rna2.stacking.StackingConfiguration attribute) (mythos.energy.rna2.StackingConfiguration attribute) b_low_coax (mythos.energy.dna1.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.dna1.CoaxialStackingConfiguration attribute) (mythos.energy.dna2.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.dna2.CoaxialStackingConfiguration attribute) b_low_cross (mythos.energy.dna1.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.dna1.CrossStackingConfiguration attribute) (mythos.energy.dna2.CrossStackingConfiguration attribute) (mythos.energy.rna2.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.rna2.CrossStackingConfiguration attribute) b_low_hb (mythos.energy.dna1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.dna1.HydrogenBondingConfiguration attribute) (mythos.energy.dna2.HydrogenBondingConfiguration attribute)

b_low_stack (mythos.energy.dna1.stacking.StackingConfiguration attribute) (mythos.energy.dna1.StackingConfiguration attribute) (mythos.energy.dna2.StackingConfiguration attribute) (mythos.energy.rna2.stacking.StackingConfiguration attribute) (mythos.energy.rna2.StackingConfiguration attribute) b_neg_cos_phi1_stack (mythos.energy.dna1.stacking.StackingConfiguration attribute) (mythos.energy.dna1.StackingConfiguration attribute) (mythos.energy.dna2.StackingConfiguration attribute) (mythos.energy.rna2.stacking.StackingConfiguration attribute) (mythos.energy.rna2.StackingConfiguration attribute) b_neg_cos_phi2_stack (mythos.energy.dna1.stacking.StackingConfiguration attribute) (mythos.energy.dna1.StackingConfiguration attribute) (mythos.energy.dna2.StackingConfiguration attribute) (mythos.energy.rna2.stacking.StackingConfiguration attribute) (mythos.energy.rna2.StackingConfiguration attribute) b_stack_10 (mythos.energy.rna2.stacking.StackingConfiguration attribute) (mythos.energy.rna2.StackingConfiguration attribute) b_stack_4 (mythos.energy.dna1.stacking.StackingConfiguration attribute) (mythos.energy.dna1.StackingConfiguration attribute) (mythos.energy.dna2.StackingConfiguration attribute) b_stack_5 (mythos.energy.dna1.stacking.StackingConfiguration attribute) (mythos.energy.dna1.StackingConfiguration attribute) (mythos.energy.dna2.StackingConfiguration attribute) (mythos.energy.rna2.stacking.StackingConfiguration attribute) (mythos.energy.rna2.StackingConfiguration attribute) b_stack_6 (mythos.energy.dna1.stacking.StackingConfiguration attribute) (mythos.energy.dna1.StackingConfiguration attribute) (mythos.energy.dna2.StackingConfiguration attribute) (mythos.energy.rna2.stacking.StackingConfiguration attribute) (mythos.energy.rna2.StackingConfiguration attribute) b_stack_9 (mythos.energy.rna2.stacking.StackingConfiguration attribute) (mythos.energy.rna2.StackingConfiguration attribute) back_base_vector (mythos.input.trajectory.NucleotideState property) back_base_vectors (mythos.energy.base.BaseNucleotide attribute) (mythos.energy.dna1.Nucleotide attribute) (mythos.energy.dna1.nucleotide.Nucleotide attribute) (mythos.energy.dna2.Nucleotide attribute) (mythos.energy.dna2.nucleotide.Nucleotide attribute) (mythos.energy.rna2.Nucleotide attribute) (mythos.energy.rna2.nucleotide.Nucleotide attribute) back_sites (mythos.energy.base.BaseNucleotide attribute) (mythos.energy.dna1.Nucleotide attribute) (mythos.energy.dna1.nucleotide.Nucleotide attribute) (mythos.energy.dna2.Nucleotide attribute) (mythos.energy.dna2.nucleotide.Nucleotide attribute) (mythos.energy.rna2.Nucleotide attribute) (mythos.energy.rna2.nucleotide.Nucleotide attribute) back_sites_dna1 (mythos.energy.dna2.Nucleotide attribute) (mythos.energy.dna2.nucleotide.Nucleotide attribute) base_normal (mythos.input.trajectory.NucleotideState property) base_normals (mythos.energy.base.BaseNucleotide attribute) (mythos.energy.dna1.Nucleotide attribute) (mythos.energy.dna1.nucleotide.Nucleotide attribute) (mythos.energy.dna2.Nucleotide attribute) (mythos.energy.dna2.nucleotide.Nucleotide attribute) (mythos.energy.rna2.Nucleotide attribute) (mythos.energy.rna2.nucleotide.Nucleotide attribute) base_sites (mythos.energy.base.BaseNucleotide attribute) (mythos.energy.dna1.Nucleotide attribute) (mythos.energy.dna1.nucleotide.Nucleotide attribute) (mythos.energy.dna2.Nucleotide attribute) (mythos.energy.dna2.nucleotide.Nucleotide attribute) (mythos.energy.rna2.Nucleotide attribute) (mythos.energy.rna2.nucleotide.Nucleotide attribute) BaseConfiguration (class in mythos.energy.configuration) BaseEnergyFunction (class in mythos.energy.base) BaseNucleotide (class in mythos.energy.base) BaseObservable (class in mythos.observables.base) batched() (in module mythos.utils.helpers) bb_p3_sites (mythos.energy.rna2.Nucleotide attribute) (mythos.energy.rna2.nucleotide.Nucleotide attribute) bb_p5_sites (mythos.energy.rna2.Nucleotide attribute) (mythos.energy.rna2.nucleotide.Nucleotide attribute) beta (mythos.optimization.objective.DiffTReObjective attribute), [1] binary_path (mythos.simulators.gromacs.gromacs.GromacsSimulator attribute) (mythos.simulators.gromacs.GromacsSimulator attribute) (mythos.simulators.oxdna.oxdna.oxDNASimulator attribute) (mythos.simulators.oxdna.oxDNASimulator attribute) Bond (class in mythos.energy.martini.m2) (class in mythos.energy.martini.m2.bond) BOND_K_PREFIX (in module mythos.energy.martini.m2.bond) bond_names (mythos.energy.martini.base.MartiniEnergyFunction property) BOND_R0_PREFIX (in module mythos.energy.martini.m2.bond) BondConfiguration (class in mythos.energy.martini.m2) (class in mythos.energy.martini.m2.bond) bonded_neighbors (mythos.energy.base.BaseEnergyFunction attribute) (mythos.energy.martini.base.MartiniTopology attribute), [1] (mythos.input.topology.Topology attribute) (mythos.simulators.jax_md.StaticSimulatorParams attribute) (mythos.simulators.jax_md.utils.StaticSimulatorParams attribute) BondedExcludedVolume (class in mythos.energy.dna1) (class in mythos.energy.dna1.bonded_excluded_volume) (class in mythos.energy.dna2) (class in mythos.energy.na1) (class in mythos.energy.na1.bonded_excluded_volume) BondedExcludedVolumeConfiguration (class in mythos.energy.dna1) (class in mythos.energy.dna1.bonded_excluded_volume) (class in mythos.energy.dna2) (class in mythos.energy.na1) (class in mythos.energy.na1.bonded_excluded_volume) box_size (mythos.input.trajectory.Trajectory attribute) (mythos.simulators.io.SimulatorTrajectory attribute) (mythos.simulators.jax_md.NeighborList attribute) (mythos.simulators.jax_md.utils.NeighborList attribute) bp1 (mythos.observables.stretch_torsion.ExtensionZ attribute) bp2 (mythos.observables.stretch_torsion.ExtensionZ attribute) BP_IDX_MAP (in module mythos.utils.constants) BP_IDXS (in module mythos.utils.constants) BP_TYPES (in module mythos.utils.constants) bps (mythos.input.sequence_constraints.SequenceConstraints attribute) btn_map (mythos.ui.loggers.jupyter.JupyterLogger attribute) build() (mythos.simulators.oxdna.oxdna.oxDNASimulator method) (mythos.simulators.oxdna.oxDNASimulator method) build_run_fn() (in module mythos.simulators.jax_md.jaxmd)

C

calc_rows_and_columns() (in module mythos.ui.loggers.jupyter) calculate() (mythos.optimization.objective.DiffTReObjective method) (mythos.optimization.objective.Objective method) calculate_extension() (in module mythos.observables.wlc) center (mythos.energy.base.BaseNucleotide attribute) (mythos.energy.dna1.Nucleotide attribute) (mythos.energy.dna1.nucleotide.Nucleotide attribute) (mythos.energy.dna2.Nucleotide attribute) (mythos.energy.dna2.nucleotide.Nucleotide attribute) (mythos.energy.rna2.Nucleotide attribute) (mythos.energy.rna2.nucleotide.Nucleotide attribute) change_size() (mythos.ui.loggers.jupyter.PlotlyLogger method) check_consistent_constraints() (in module mythos.input.sequence_constraints) check_cover() (in module mythos.input.sequence_constraints) check_valid_seq() (in module mythos.input.topology) checkpoint_every (mythos.simulators.jax_md.StaticSimulatorParams attribute) (mythos.simulators.jax_md.utils.StaticSimulatorParams attribute) checkpoint_scan() (in module mythos.simulators.jax_md.utils) clamp() (in module mythos.utils.math) CLASSIC (mythos.utils.types.oxDNAFormat attribute) CMAKE_BIN_ENV_VAR (in module mythos.simulators.oxdna) (in module mythos.simulators.oxdna.oxdna) coaxial_stacking() (in module mythos.energy.dna1.interactions) (in module mythos.energy.dna2.interactions) CoaxialStacking (class in mythos.energy.dna1) (class in mythos.energy.dna1.coaxial_stacking) (class in mythos.energy.dna2) (class in mythos.energy.dna2.coaxial_stacking) (class in mythos.energy.na1) (class in mythos.energy.na1.coaxial_stacking) CoaxialStackingConfiguration (class in mythos.energy.dna1) (class in mythos.energy.dna1.coaxial_stacking) (class in mythos.energy.dna2) (class in mythos.energy.dna2.coaxial_stacking) (class in mythos.energy.na1) (class in mythos.energy.na1.coaxial_stacking) com (mythos.input.trajectory.NucleotideState property) commit_id (in module mythos._version) COMPLETE (mythos.ui.loggers.logger.Status attribute) component_state (mythos.optimization.optimization.OptimizerState attribute) ComposedEnergyFunction (class in mythos.energy.base) compute_angle() (in module mythos.energy.martini.m2.angle) compute_curve_width() (in module mythos.observables.melting_temp) compute_energy() (mythos.energy.base.BaseEnergyFunction method) (mythos.energy.dna1.bonded_excluded_volume.BondedExcludedVolume method) (mythos.energy.dna1.BondedExcludedVolume method) (mythos.energy.dna1.coaxial_stacking.CoaxialStacking method) (mythos.energy.dna1.CoaxialStacking method) (mythos.energy.dna1.cross_stacking.CrossStacking method) (mythos.energy.dna1.CrossStacking method) (mythos.energy.dna1.Fene method) (mythos.energy.dna1.fene.Fene method) (mythos.energy.dna1.hydrogen_bonding.HydrogenBonding method) (mythos.energy.dna1.HydrogenBonding method) (mythos.energy.dna1.Stacking method) (mythos.energy.dna1.stacking.Stacking method) (mythos.energy.dna1.unbonded_excluded_volume.UnbondedExcludedVolume method) (mythos.energy.dna1.UnbondedExcludedVolume method) (mythos.energy.dna2.BondedExcludedVolume method) (mythos.energy.dna2.coaxial_stacking.CoaxialStacking method) (mythos.energy.dna2.CoaxialStacking method) (mythos.energy.dna2.CrossStacking method) (mythos.energy.dna2.Debye method) (mythos.energy.dna2.debye.Debye method) (mythos.energy.dna2.Fene method) (mythos.energy.dna2.HydrogenBonding method) (mythos.energy.dna2.Stacking method) (mythos.energy.dna2.stacking.Stacking method) (mythos.energy.dna2.UnbondedExcludedVolume method) (mythos.energy.martini.m2.Angle method) (mythos.energy.martini.m2.angle.Angle method) (mythos.energy.martini.m2.Bond method) (mythos.energy.martini.m2.bond.Bond method) (mythos.energy.martini.m2.LJ method) (mythos.energy.martini.m2.lj.LJ method) (mythos.energy.na1.bonded_excluded_volume.BondedExcludedVolume method) (mythos.energy.na1.BondedExcludedVolume method) (mythos.energy.na1.coaxial_stacking.CoaxialStacking method) (mythos.energy.na1.CoaxialStacking method) (mythos.energy.na1.cross_stacking.CrossStacking method) (mythos.energy.na1.CrossStacking method) (mythos.energy.na1.Debye method) (mythos.energy.na1.debye.Debye method) (mythos.energy.na1.Fene method) (mythos.energy.na1.fene.Fene method) (mythos.energy.na1.hydrogen_bonding.HydrogenBonding method) (mythos.energy.na1.HydrogenBonding method) (mythos.energy.na1.Stacking method) (mythos.energy.na1.stacking.Stacking method) (mythos.energy.na1.unbonded_excluded_volume.UnbondedExcludedVolume method) (mythos.energy.na1.UnbondedExcludedVolume method) (mythos.energy.rna2.cross_stacking.CrossStacking method) (mythos.energy.rna2.CrossStacking method) (mythos.energy.rna2.Stacking method) (mythos.energy.rna2.stacking.Stacking method)

compute_finf() (in module mythos.observables.melting_temp) compute_loss() (in module mythos.optimization.objective) compute_loss_and_grad (in module mythos.optimization.objective) compute_metadata() (in module mythos.observables.persistence_length) compute_pitch() (in module mythos.observables.pitch) compute_seq_dep_weight() (in module mythos.energy.utils) compute_terms() (mythos.energy.base.ComposedEnergyFunction method) compute_v_hb() (mythos.energy.dna1.hydrogen_bonding.HydrogenBonding method) (mythos.energy.dna1.HydrogenBonding method) (mythos.energy.dna2.HydrogenBonding method) compute_v_stack() (mythos.energy.dna1.Stacking method) (mythos.energy.dna1.stacking.Stacking method) (mythos.energy.rna2.Stacking method) (mythos.energy.rna2.stacking.Stacking method) compute_weights_and_neff() (in module mythos.optimization.objective) ConsoleLogger (class in mythos.ui.loggers.console) convert_to_fname() (in module mythos.ui.loggers.disk) copy_inputs() (mythos.simulators.base.InputDirSimulator method) cos_phi3_c_coax (mythos.energy.dna1.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.dna1.CoaxialStackingConfiguration attribute) cos_phi3_star_coax (mythos.energy.dna1.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.dna1.CoaxialStackingConfiguration attribute) cos_phi4_c_coax (mythos.energy.dna1.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.dna1.CoaxialStackingConfiguration attribute) cos_phi4_star_coax (mythos.energy.dna1.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.dna1.CoaxialStackingConfiguration attribute) coth() (in module mythos.observables.wlc) couplings (mythos.energy.martini.base.MartiniEnergyConfiguration attribute) create_default_energy_fn() (in module mythos.energy.dna2) create_from() (mythos.energy.base.BaseEnergyFunction class method) create_n() (mythos.simulators.base.Simulator class method) cross_prods (mythos.energy.base.BaseNucleotide attribute) (mythos.energy.dna1.Nucleotide attribute) (mythos.energy.dna1.nucleotide.Nucleotide attribute) (mythos.energy.dna2.Nucleotide attribute) (mythos.energy.dna2.nucleotide.Nucleotide attribute) (mythos.energy.rna2.Nucleotide attribute) (mythos.energy.rna2.nucleotide.Nucleotide attribute) cross_stacking() (in module mythos.energy.dna1.interactions) (in module mythos.energy.rna2.interactions) CrossStacking (class in mythos.energy.dna1) (class in mythos.energy.dna1.cross_stacking) (class in mythos.energy.dna2) (class in mythos.energy.na1) (class in mythos.energy.na1.cross_stacking) (class in mythos.energy.rna2) (class in mythos.energy.rna2.cross_stacking) CrossStackingConfiguration (class in mythos.energy.dna1) (class in mythos.energy.dna1.cross_stacking) (class in mythos.energy.dna2) (class in mythos.energy.na1) (class in mythos.energy.na1.cross_stacking) (class in mythos.energy.rna2) (class in mythos.energy.rna2.cross_stacking) custom (mythos.utils.scheduler.SchedulerHints attribute), [1]

D

dashboard (mythos.ui.loggers.jupyter.JupyterLogger attribute) Debye (class in mythos.energy.dna2) (class in mythos.energy.dna2.debye) (class in mythos.energy.na1) (class in mythos.energy.na1.debye) debye() (in module mythos.energy.dna2.interactions) DebyeConfiguration (class in mythos.energy.dna2) (class in mythos.energy.dna2.debye) (class in mythos.energy.na1) (class in mythos.energy.na1.debye) default_configs() (in module mythos.energy.dna1) (in module mythos.energy.dna2) default_configs_for() (in module mythos.energy.utils) DEFAULT_DISPLACEMENT (in module mythos.energy) default_energy_configs() (in module mythos.energy.dna2) default_energy_fns() (in module mythos.energy.dna1) (in module mythos.energy.dna2) DEFAULT_OXDNA_VARIABLE_MAPPER (in module mythos.simulators.oxdna.utils) DEFAULT_TEMP (in module mythos.utils.constants) default_transform_fn() (in module mythos.energy.dna2) delta_backbone (mythos.energy.dna1.fene.FeneConfiguration attribute) (mythos.energy.dna1.FeneConfiguration attribute) (mythos.energy.dna2.FeneConfiguration attribute) delta_theta_coax_1_c (mythos.energy.dna1.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.dna1.CoaxialStackingConfiguration attribute) (mythos.energy.dna2.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.dna2.CoaxialStackingConfiguration attribute) delta_theta_coax_4_c (mythos.energy.dna1.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.dna1.CoaxialStackingConfiguration attribute) (mythos.energy.dna2.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.dna2.CoaxialStackingConfiguration attribute) delta_theta_coax_5_c (mythos.energy.dna1.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.dna1.CoaxialStackingConfiguration attribute) (mythos.energy.dna2.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.dna2.CoaxialStackingConfiguration attribute) delta_theta_coax_6_c (mythos.energy.dna1.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.dna1.CoaxialStackingConfiguration attribute) (mythos.energy.dna2.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.dna2.CoaxialStackingConfiguration attribute) delta_theta_cross_1_c (mythos.energy.dna1.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.dna1.CrossStackingConfiguration attribute) (mythos.energy.dna2.CrossStackingConfiguration attribute) (mythos.energy.rna2.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.rna2.CrossStackingConfiguration attribute) delta_theta_cross_2_c (mythos.energy.dna1.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.dna1.CrossStackingConfiguration attribute) (mythos.energy.dna2.CrossStackingConfiguration attribute) (mythos.energy.rna2.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.rna2.CrossStackingConfiguration attribute) delta_theta_cross_3_c (mythos.energy.dna1.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.dna1.CrossStackingConfiguration attribute) (mythos.energy.dna2.CrossStackingConfiguration attribute) (mythos.energy.rna2.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.rna2.CrossStackingConfiguration attribute) delta_theta_cross_4_c (mythos.energy.dna1.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.dna1.CrossStackingConfiguration attribute) (mythos.energy.dna2.CrossStackingConfiguration attribute) delta_theta_cross_7_c (mythos.energy.dna1.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.dna1.CrossStackingConfiguration attribute) (mythos.energy.dna2.CrossStackingConfiguration attribute) (mythos.energy.rna2.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.rna2.CrossStackingConfiguration attribute) delta_theta_cross_8_c (mythos.energy.dna1.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.dna1.CrossStackingConfiguration attribute) (mythos.energy.dna2.CrossStackingConfiguration attribute) (mythos.energy.rna2.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.rna2.CrossStackingConfiguration attribute) delta_theta_hb_1_c (mythos.energy.dna1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.dna1.HydrogenBondingConfiguration attribute) (mythos.energy.dna2.HydrogenBondingConfiguration attribute) delta_theta_hb_2_c (mythos.energy.dna1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.dna1.HydrogenBondingConfiguration attribute) (mythos.energy.dna2.HydrogenBondingConfiguration attribute) delta_theta_hb_3_c (mythos.energy.dna1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.dna1.HydrogenBondingConfiguration attribute) (mythos.energy.dna2.HydrogenBondingConfiguration attribute) delta_theta_hb_4_c (mythos.energy.dna1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.dna1.HydrogenBondingConfiguration attribute) (mythos.energy.dna2.HydrogenBondingConfiguration attribute) delta_theta_hb_7_c (mythos.energy.dna1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.dna1.HydrogenBondingConfiguration attribute) (mythos.energy.dna2.HydrogenBondingConfiguration attribute) delta_theta_hb_8_c (mythos.energy.dna1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.dna1.HydrogenBondingConfiguration attribute) (mythos.energy.dna2.HydrogenBondingConfiguration attribute) delta_theta_stack_10_c (mythos.energy.rna2.stacking.StackingConfiguration attribute) (mythos.energy.rna2.StackingConfiguration attribute) delta_theta_stack_4_c (mythos.energy.dna1.stacking.StackingConfiguration attribute) (mythos.energy.dna1.StackingConfiguration attribute) (mythos.energy.dna2.StackingConfiguration attribute) delta_theta_stack_5_c (mythos.energy.dna1.stacking.StackingConfiguration attribute) (mythos.energy.dna1.StackingConfiguration attribute) (mythos.energy.dna2.StackingConfiguration attribute) (mythos.energy.rna2.stacking.StackingConfiguration attribute) (mythos.energy.rna2.StackingConfiguration attribute) delta_theta_stack_6_c (mythos.energy.dna1.stacking.StackingConfiguration attribute) (mythos.energy.dna1.StackingConfiguration attribute) (mythos.energy.dna2.StackingConfiguration attribute) (mythos.energy.rna2.stacking.StackingConfiguration attribute) (mythos.energy.rna2.StackingConfiguration attribute) delta_theta_stack_9_c (mythos.energy.rna2.stacking.StackingConfiguration attribute) (mythos.energy.rna2.StackingConfiguration attribute) delta_theta_star_coax_1 (mythos.energy.dna1.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.dna1.CoaxialStackingConfiguration attribute) (mythos.energy.dna2.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.dna2.CoaxialStackingConfiguration attribute) delta_theta_star_coax_4 (mythos.energy.dna1.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.dna1.CoaxialStackingConfiguration attribute) (mythos.energy.dna2.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.dna2.CoaxialStackingConfiguration attribute) delta_theta_star_coax_5 (mythos.energy.dna1.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.dna1.CoaxialStackingConfiguration attribute) (mythos.energy.dna2.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.dna2.CoaxialStackingConfiguration attribute) delta_theta_star_coax_6 (mythos.energy.dna1.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.dna1.CoaxialStackingConfiguration attribute) (mythos.energy.dna2.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.dna2.CoaxialStackingConfiguration attribute) delta_theta_star_cross_1 (mythos.energy.dna1.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.dna1.CrossStackingConfiguration attribute) (mythos.energy.dna2.CrossStackingConfiguration attribute) (mythos.energy.rna2.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.rna2.CrossStackingConfiguration attribute) delta_theta_star_cross_2 (mythos.energy.dna1.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.dna1.CrossStackingConfiguration attribute) (mythos.energy.dna2.CrossStackingConfiguration attribute) (mythos.energy.rna2.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.rna2.CrossStackingConfiguration attribute) delta_theta_star_cross_3 (mythos.energy.dna1.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.dna1.CrossStackingConfiguration attribute) (mythos.energy.dna2.CrossStackingConfiguration attribute) (mythos.energy.rna2.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.rna2.CrossStackingConfiguration attribute) delta_theta_star_cross_4 (mythos.energy.dna1.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.dna1.CrossStackingConfiguration attribute) (mythos.energy.dna2.CrossStackingConfiguration attribute) delta_theta_star_cross_7 (mythos.energy.dna1.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.dna1.CrossStackingConfiguration attribute) (mythos.energy.dna2.CrossStackingConfiguration attribute) (mythos.energy.rna2.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.rna2.CrossStackingConfiguration attribute) delta_theta_star_cross_8 (mythos.energy.dna1.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.dna1.CrossStackingConfiguration attribute) (mythos.energy.dna2.CrossStackingConfiguration attribute) (mythos.energy.rna2.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.rna2.CrossStackingConfiguration attribute) delta_theta_star_hb_1 (mythos.energy.dna1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.dna1.HydrogenBondingConfiguration attribute) (mythos.energy.dna2.HydrogenBondingConfiguration attribute) delta_theta_star_hb_2 (mythos.energy.dna1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.dna1.HydrogenBondingConfiguration attribute) (mythos.energy.dna2.HydrogenBondingConfiguration attribute) delta_theta_star_hb_3 (mythos.energy.dna1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.dna1.HydrogenBondingConfiguration attribute) (mythos.energy.dna2.HydrogenBondingConfiguration attribute) delta_theta_star_hb_4 (mythos.energy.dna1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.dna1.HydrogenBondingConfiguration attribute) (mythos.energy.dna2.HydrogenBondingConfiguration attribute) delta_theta_star_hb_7 (mythos.energy.dna1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.dna1.HydrogenBondingConfiguration attribute) (mythos.energy.dna2.HydrogenBondingConfiguration attribute) delta_theta_star_hb_8 (mythos.energy.dna1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.dna1.HydrogenBondingConfiguration attribute) (mythos.energy.dna2.HydrogenBondingConfiguration attribute) delta_theta_star_stack_10 (mythos.energy.rna2.stacking.StackingConfiguration attribute) (mythos.energy.rna2.StackingConfiguration attribute) delta_theta_star_stack_4 (mythos.energy.dna1.stacking.StackingConfiguration attribute) (mythos.energy.dna1.StackingConfiguration attribute) (mythos.energy.dna2.StackingConfiguration attribute) delta_theta_star_stack_5 (mythos.energy.dna1.stacking.StackingConfiguration attribute) (mythos.energy.dna1.StackingConfiguration attribute) (mythos.energy.dna2.StackingConfiguration attribute) (mythos.energy.rna2.stacking.StackingConfiguration attribute) (mythos.energy.rna2.StackingConfiguration attribute) delta_theta_star_stack_6 (mythos.energy.dna1.stacking.StackingConfiguration attribute) (mythos.energy.dna1.StackingConfiguration attribute) (mythos.energy.dna2.StackingConfiguration attribute) (mythos.energy.rna2.stacking.StackingConfiguration attribute) (mythos.energy.rna2.StackingConfiguration attribute) delta_theta_star_stack_9 (mythos.energy.rna2.stacking.StackingConfiguration attribute) (mythos.energy.rna2.StackingConfiguration attribute) dependent_params (mythos.energy.configuration.BaseConfiguration attribute) (mythos.energy.dna1.bonded_excluded_volume.BondedExcludedVolumeConfiguration attribute) (mythos.energy.dna1.BondedExcludedVolumeConfiguration attribute) (mythos.energy.dna1.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.dna1.CoaxialStackingConfiguration attribute) (mythos.energy.dna1.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.dna1.CrossStackingConfiguration attribute) (mythos.energy.dna1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.dna1.HydrogenBondingConfiguration attribute) (mythos.energy.dna1.stacking.StackingConfiguration attribute) (mythos.energy.dna1.StackingConfiguration attribute) (mythos.energy.dna1.unbonded_excluded_volume.UnbondedExcludedVolumeConfiguration attribute) (mythos.energy.dna1.UnbondedExcludedVolumeConfiguration attribute) (mythos.energy.dna2.BondedExcludedVolumeConfiguration attribute) (mythos.energy.dna2.CrossStackingConfiguration attribute) (mythos.energy.dna2.HydrogenBondingConfiguration attribute) (mythos.energy.dna2.StackingConfiguration attribute) (mythos.energy.dna2.UnbondedExcludedVolumeConfiguration attribute) Diameter (class in mythos.observables.diameter) DiffTReObjective (class in mythos.optimization.objective) Discrete_Sequence (in module mythos.utils.types) displacement_fn (mythos.energy.base.BaseEnergyFunction attribute) (mythos.energy.martini.base.MartiniEnergyFunction attribute) (mythos.observables.diameter.Diameter attribute) (mythos.observables.persistence_length.PersistenceLength attribute) (mythos.observables.pitch.PitchAngle attribute) (mythos.observables.rise.Rise attribute) (mythos.observables.stretch_torsion.ExtensionZ attribute) (mythos.observables.stretch_torsion.TwistXY attribute) (mythos.simulators.jax_md.NeighborList attribute) (mythos.simulators.jax_md.utils.NeighborList attribute) displacement_mapped (mythos.energy.base.BaseEnergyFunction property) dna (mythos.energy.na1.HybridNucleotide attribute) (mythos.energy.na1.nucleotide.HybridNucleotide attribute) DNA (mythos.input.topology.NucleotideType attribute) DNA1 (mythos.utils.types.oxDNASimulatorType attribute) DNA2 (mythos.utils.types.oxDNASimulatorType attribute) dna_a_coax_1 (mythos.energy.na1.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.na1.CoaxialStackingConfiguration attribute) dna_a_coax_1_f6 (mythos.energy.na1.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.na1.CoaxialStackingConfiguration attribute) dna_a_coax_4 (mythos.energy.na1.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.na1.CoaxialStackingConfiguration attribute) dna_a_coax_5 (mythos.energy.na1.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.na1.CoaxialStackingConfiguration attribute) dna_a_coax_6 (mythos.energy.na1.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.na1.CoaxialStackingConfiguration attribute) dna_a_cross_1 (mythos.energy.na1.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.na1.CrossStackingConfiguration attribute) dna_a_cross_2 (mythos.energy.na1.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.na1.CrossStackingConfiguration attribute) dna_a_cross_3 (mythos.energy.na1.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.na1.CrossStackingConfiguration attribute) dna_a_cross_4 (mythos.energy.na1.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.na1.CrossStackingConfiguration attribute) dna_a_cross_7 (mythos.energy.na1.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.na1.CrossStackingConfiguration attribute) dna_a_cross_8 (mythos.energy.na1.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.na1.CrossStackingConfiguration attribute) dna_a_hb (mythos.energy.na1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.na1.HydrogenBondingConfiguration attribute) dna_a_hb_1 (mythos.energy.na1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.na1.HydrogenBondingConfiguration attribute) dna_a_hb_2 (mythos.energy.na1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.na1.HydrogenBondingConfiguration attribute) dna_a_hb_3 (mythos.energy.na1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.na1.HydrogenBondingConfiguration attribute) dna_a_hb_4 (mythos.energy.na1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.na1.HydrogenBondingConfiguration attribute) dna_a_hb_7 (mythos.energy.na1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.na1.HydrogenBondingConfiguration attribute) dna_a_hb_8 (mythos.energy.na1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.na1.HydrogenBondingConfiguration attribute) dna_a_stack (mythos.energy.na1.stacking.StackingConfiguration attribute) (mythos.energy.na1.StackingConfiguration attribute) dna_a_stack_1 (mythos.energy.na1.stacking.StackingConfiguration attribute) (mythos.energy.na1.StackingConfiguration attribute) dna_a_stack_2 (mythos.energy.na1.stacking.StackingConfiguration attribute) (mythos.energy.na1.StackingConfiguration attribute) dna_a_stack_4 (mythos.energy.na1.stacking.StackingConfiguration attribute) (mythos.energy.na1.StackingConfiguration attribute) dna_a_stack_5 (mythos.energy.na1.stacking.StackingConfiguration attribute) (mythos.energy.na1.StackingConfiguration attribute) dna_a_stack_6 (mythos.energy.na1.stacking.StackingConfiguration attribute) (mythos.energy.na1.StackingConfiguration attribute) DNA_ALPHA (in module mythos.utils.constants) dna_b_coax_1_f6 (mythos.energy.na1.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.na1.CoaxialStackingConfiguration attribute) dna_config (mythos.energy.na1.bonded_excluded_volume.BondedExcludedVolumeConfiguration attribute) (mythos.energy.na1.BondedExcludedVolumeConfiguration attribute) (mythos.energy.na1.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.na1.CoaxialStackingConfiguration attribute) (mythos.energy.na1.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.na1.CrossStackingConfiguration attribute) (mythos.energy.na1.debye.DebyeConfiguration attribute) (mythos.energy.na1.DebyeConfiguration attribute) (mythos.energy.na1.fene.FeneConfiguration attribute) (mythos.energy.na1.FeneConfiguration attribute) (mythos.energy.na1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.na1.HydrogenBondingConfiguration attribute) (mythos.energy.na1.stacking.StackingConfiguration attribute) (mythos.energy.na1.StackingConfiguration attribute) (mythos.energy.na1.unbonded_excluded_volume.UnbondedExcludedVolumeConfiguration attribute) (mythos.energy.na1.UnbondedExcludedVolumeConfiguration attribute) dna_delta_backbone (mythos.energy.na1.fene.FeneConfiguration attribute) (mythos.energy.na1.FeneConfiguration attribute) dna_delta_theta_star_coax_1 (mythos.energy.na1.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.na1.CoaxialStackingConfiguration attribute) dna_delta_theta_star_coax_4 (mythos.energy.na1.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.na1.CoaxialStackingConfiguration attribute) dna_delta_theta_star_coax_5 (mythos.energy.na1.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.na1.CoaxialStackingConfiguration attribute) dna_delta_theta_star_coax_6 (mythos.energy.na1.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.na1.CoaxialStackingConfiguration attribute) dna_delta_theta_star_cross_1 (mythos.energy.na1.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.na1.CrossStackingConfiguration attribute) dna_delta_theta_star_cross_2 (mythos.energy.na1.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.na1.CrossStackingConfiguration attribute) dna_delta_theta_star_cross_3 (mythos.energy.na1.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.na1.CrossStackingConfiguration attribute) dna_delta_theta_star_cross_4 (mythos.energy.na1.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.na1.CrossStackingConfiguration attribute) dna_delta_theta_star_cross_7 (mythos.energy.na1.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.na1.CrossStackingConfiguration attribute) dna_delta_theta_star_cross_8 (mythos.energy.na1.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.na1.CrossStackingConfiguration attribute) dna_delta_theta_star_hb_1 (mythos.energy.na1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.na1.HydrogenBondingConfiguration attribute) dna_delta_theta_star_hb_2 (mythos.energy.na1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.na1.HydrogenBondingConfiguration attribute) dna_delta_theta_star_hb_3 (mythos.energy.na1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.na1.HydrogenBondingConfiguration attribute) dna_delta_theta_star_hb_4 (mythos.energy.na1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.na1.HydrogenBondingConfiguration attribute) dna_delta_theta_star_hb_7 (mythos.energy.na1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.na1.HydrogenBondingConfiguration attribute) dna_delta_theta_star_hb_8 (mythos.energy.na1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.na1.HydrogenBondingConfiguration attribute) dna_delta_theta_star_stack_4 (mythos.energy.na1.stacking.StackingConfiguration attribute) (mythos.energy.na1.StackingConfiguration attribute) dna_delta_theta_star_stack_5 (mythos.energy.na1.stacking.StackingConfiguration attribute) (mythos.energy.na1.StackingConfiguration attribute) dna_delta_theta_star_stack_6 (mythos.energy.na1.stacking.StackingConfiguration attribute) (mythos.energy.na1.StackingConfiguration attribute) dna_dr0_coax (mythos.energy.na1.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.na1.CoaxialStackingConfiguration attribute) dna_dr0_hb (mythos.energy.na1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.na1.HydrogenBondingConfiguration attribute) dna_dr0_stack (mythos.energy.na1.stacking.StackingConfiguration attribute) (mythos.energy.na1.StackingConfiguration attribute) dna_dr_c_coax (mythos.energy.na1.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.na1.CoaxialStackingConfiguration attribute) dna_dr_c_cross (mythos.energy.na1.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.na1.CrossStackingConfiguration attribute) dna_dr_c_hb (mythos.energy.na1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.na1.HydrogenBondingConfiguration attribute) dna_dr_c_stack (mythos.energy.na1.stacking.StackingConfiguration attribute) (mythos.energy.na1.StackingConfiguration attribute) dna_dr_high_coax (mythos.energy.na1.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.na1.CoaxialStackingConfiguration attribute) dna_dr_high_cross (mythos.energy.na1.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.na1.CrossStackingConfiguration attribute) dna_dr_high_hb (mythos.energy.na1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.na1.HydrogenBondingConfiguration attribute) dna_dr_high_stack (mythos.energy.na1.stacking.StackingConfiguration attribute) (mythos.energy.na1.StackingConfiguration attribute) dna_dr_low_coax (mythos.energy.na1.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.na1.CoaxialStackingConfiguration attribute) dna_dr_low_cross (mythos.energy.na1.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.na1.CrossStackingConfiguration attribute) dna_dr_low_hb (mythos.energy.na1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.na1.HydrogenBondingConfiguration attribute) dna_dr_low_stack (mythos.energy.na1.stacking.StackingConfiguration attribute) (mythos.energy.na1.StackingConfiguration attribute) dna_dr_star_back_base (mythos.energy.na1.bonded_excluded_volume.BondedExcludedVolumeConfiguration attribute) (mythos.energy.na1.BondedExcludedVolumeConfiguration attribute) (mythos.energy.na1.unbonded_excluded_volume.UnbondedExcludedVolumeConfiguration attribute) (mythos.energy.na1.UnbondedExcludedVolumeConfiguration attribute) dna_dr_star_backbone (mythos.energy.na1.unbonded_excluded_volume.UnbondedExcludedVolumeConfiguration attribute) (mythos.energy.na1.UnbondedExcludedVolumeConfiguration attribute) dna_dr_star_base (mythos.energy.na1.bonded_excluded_volume.BondedExcludedVolumeConfiguration attribute) (mythos.energy.na1.BondedExcludedVolumeConfiguration attribute) (mythos.energy.na1.unbonded_excluded_volume.UnbondedExcludedVolumeConfiguration attribute) (mythos.energy.na1.UnbondedExcludedVolumeConfiguration attribute) dna_dr_star_base_back (mythos.energy.na1.bonded_excluded_volume.BondedExcludedVolumeConfiguration attribute) (mythos.energy.na1.BondedExcludedVolumeConfiguration attribute) (mythos.energy.na1.unbonded_excluded_volume.UnbondedExcludedVolumeConfiguration attribute) (mythos.energy.na1.UnbondedExcludedVolumeConfiguration attribute) dna_eps_backbone (mythos.energy.na1.fene.FeneConfiguration attribute) (mythos.energy.na1.FeneConfiguration attribute) dna_eps_exc (mythos.energy.na1.bonded_excluded_volume.BondedExcludedVolumeConfiguration attribute) (mythos.energy.na1.BondedExcludedVolumeConfiguration attribute) (mythos.energy.na1.unbonded_excluded_volume.UnbondedExcludedVolumeConfiguration attribute) (mythos.energy.na1.UnbondedExcludedVolumeConfiguration attribute) dna_eps_hb (mythos.energy.na1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.na1.HydrogenBondingConfiguration attribute) dna_eps_stack_base (mythos.energy.na1.stacking.StackingConfiguration attribute) (mythos.energy.na1.StackingConfiguration attribute) dna_eps_stack_kt_coeff (mythos.energy.na1.stacking.StackingConfiguration attribute) (mythos.energy.na1.StackingConfiguration attribute) dna_finf (mythos.energy.na1.fene.FeneConfiguration attribute) (mythos.energy.na1.FeneConfiguration attribute) dna_fmax (mythos.energy.na1.fene.FeneConfiguration attribute) (mythos.energy.na1.FeneConfiguration attribute) dna_k_coax (mythos.energy.na1.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.na1.CoaxialStackingConfiguration attribute)

dna_k_cross (mythos.energy.na1.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.na1.CrossStackingConfiguration attribute) dna_lambda_factor (mythos.energy.na1.debye.DebyeConfiguration attribute) (mythos.energy.na1.DebyeConfiguration attribute) dna_neg_cos_phi1_star_stack (mythos.energy.na1.stacking.StackingConfiguration attribute) (mythos.energy.na1.StackingConfiguration attribute) dna_neg_cos_phi2_star_stack (mythos.energy.na1.stacking.StackingConfiguration attribute) (mythos.energy.na1.StackingConfiguration attribute) dna_prefactor_coeff (mythos.energy.na1.debye.DebyeConfiguration attribute) (mythos.energy.na1.DebyeConfiguration attribute) dna_q_eff (mythos.energy.na1.debye.DebyeConfiguration attribute) (mythos.energy.na1.DebyeConfiguration attribute) dna_r0_backbone (mythos.energy.na1.fene.FeneConfiguration attribute) (mythos.energy.na1.FeneConfiguration attribute) dna_r0_cross (mythos.energy.na1.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.na1.CrossStackingConfiguration attribute) dna_sigma_back_base (mythos.energy.na1.bonded_excluded_volume.BondedExcludedVolumeConfiguration attribute) (mythos.energy.na1.BondedExcludedVolumeConfiguration attribute) (mythos.energy.na1.unbonded_excluded_volume.UnbondedExcludedVolumeConfiguration attribute) (mythos.energy.na1.UnbondedExcludedVolumeConfiguration attribute) dna_sigma_backbone (mythos.energy.na1.unbonded_excluded_volume.UnbondedExcludedVolumeConfiguration attribute) (mythos.energy.na1.UnbondedExcludedVolumeConfiguration attribute) dna_sigma_base (mythos.energy.na1.bonded_excluded_volume.BondedExcludedVolumeConfiguration attribute) (mythos.energy.na1.BondedExcludedVolumeConfiguration attribute) (mythos.energy.na1.unbonded_excluded_volume.UnbondedExcludedVolumeConfiguration attribute) (mythos.energy.na1.UnbondedExcludedVolumeConfiguration attribute) dna_sigma_base_back (mythos.energy.na1.bonded_excluded_volume.BondedExcludedVolumeConfiguration attribute) (mythos.energy.na1.BondedExcludedVolumeConfiguration attribute) (mythos.energy.na1.unbonded_excluded_volume.UnbondedExcludedVolumeConfiguration attribute) (mythos.energy.na1.UnbondedExcludedVolumeConfiguration attribute) dna_ss_hb_weights (mythos.energy.na1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.na1.HydrogenBondingConfiguration attribute) dna_ss_stack_weights (mythos.energy.na1.stacking.StackingConfiguration attribute) (mythos.energy.na1.StackingConfiguration attribute) dna_theta0_coax_1 (mythos.energy.na1.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.na1.CoaxialStackingConfiguration attribute) dna_theta0_coax_4 (mythos.energy.na1.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.na1.CoaxialStackingConfiguration attribute) dna_theta0_coax_5 (mythos.energy.na1.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.na1.CoaxialStackingConfiguration attribute) dna_theta0_coax_6 (mythos.energy.na1.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.na1.CoaxialStackingConfiguration attribute) dna_theta0_cross_1 (mythos.energy.na1.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.na1.CrossStackingConfiguration attribute) dna_theta0_cross_2 (mythos.energy.na1.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.na1.CrossStackingConfiguration attribute) dna_theta0_cross_3 (mythos.energy.na1.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.na1.CrossStackingConfiguration attribute) dna_theta0_cross_4 (mythos.energy.na1.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.na1.CrossStackingConfiguration attribute) dna_theta0_cross_7 (mythos.energy.na1.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.na1.CrossStackingConfiguration attribute) dna_theta0_cross_8 (mythos.energy.na1.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.na1.CrossStackingConfiguration attribute) dna_theta0_hb_1 (mythos.energy.na1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.na1.HydrogenBondingConfiguration attribute) dna_theta0_hb_2 (mythos.energy.na1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.na1.HydrogenBondingConfiguration attribute) dna_theta0_hb_3 (mythos.energy.na1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.na1.HydrogenBondingConfiguration attribute) dna_theta0_hb_4 (mythos.energy.na1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.na1.HydrogenBondingConfiguration attribute) dna_theta0_hb_7 (mythos.energy.na1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.na1.HydrogenBondingConfiguration attribute) dna_theta0_hb_8 (mythos.energy.na1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.na1.HydrogenBondingConfiguration attribute) dna_theta0_stack_4 (mythos.energy.na1.stacking.StackingConfiguration attribute) (mythos.energy.na1.StackingConfiguration attribute) dna_theta0_stack_5 (mythos.energy.na1.stacking.StackingConfiguration attribute) (mythos.energy.na1.StackingConfiguration attribute) dna_theta0_stack_6 (mythos.energy.na1.stacking.StackingConfiguration attribute) (mythos.energy.na1.StackingConfiguration attribute) dr0_coax (mythos.energy.dna1.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.dna1.CoaxialStackingConfiguration attribute) (mythos.energy.dna2.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.dna2.CoaxialStackingConfiguration attribute) dr0_hb (mythos.energy.dna1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.dna1.HydrogenBondingConfiguration attribute) (mythos.energy.dna2.HydrogenBondingConfiguration attribute) dr0_stack (mythos.energy.dna1.stacking.StackingConfiguration attribute) (mythos.energy.dna1.StackingConfiguration attribute) (mythos.energy.dna2.StackingConfiguration attribute) (mythos.energy.rna2.stacking.StackingConfiguration attribute) (mythos.energy.rna2.StackingConfiguration attribute) dr_c_back_base (mythos.energy.dna1.bonded_excluded_volume.BondedExcludedVolumeConfiguration attribute) (mythos.energy.dna1.BondedExcludedVolumeConfiguration attribute) (mythos.energy.dna1.unbonded_excluded_volume.UnbondedExcludedVolumeConfiguration attribute) (mythos.energy.dna1.UnbondedExcludedVolumeConfiguration attribute) (mythos.energy.dna2.BondedExcludedVolumeConfiguration attribute) (mythos.energy.dna2.UnbondedExcludedVolumeConfiguration attribute) dr_c_backbone (mythos.energy.dna1.unbonded_excluded_volume.UnbondedExcludedVolumeConfiguration attribute) (mythos.energy.dna1.UnbondedExcludedVolumeConfiguration attribute) (mythos.energy.dna2.UnbondedExcludedVolumeConfiguration attribute) dr_c_base (mythos.energy.dna1.bonded_excluded_volume.BondedExcludedVolumeConfiguration attribute) (mythos.energy.dna1.BondedExcludedVolumeConfiguration attribute) (mythos.energy.dna1.unbonded_excluded_volume.UnbondedExcludedVolumeConfiguration attribute) (mythos.energy.dna1.UnbondedExcludedVolumeConfiguration attribute) (mythos.energy.dna2.BondedExcludedVolumeConfiguration attribute) (mythos.energy.dna2.UnbondedExcludedVolumeConfiguration attribute) dr_c_base_back (mythos.energy.dna1.bonded_excluded_volume.BondedExcludedVolumeConfiguration attribute) (mythos.energy.dna1.BondedExcludedVolumeConfiguration attribute) (mythos.energy.dna1.unbonded_excluded_volume.UnbondedExcludedVolumeConfiguration attribute) (mythos.energy.dna1.UnbondedExcludedVolumeConfiguration attribute) (mythos.energy.dna2.BondedExcludedVolumeConfiguration attribute) (mythos.energy.dna2.UnbondedExcludedVolumeConfiguration attribute) dr_c_coax (mythos.energy.dna1.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.dna1.CoaxialStackingConfiguration attribute) (mythos.energy.dna2.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.dna2.CoaxialStackingConfiguration attribute) dr_c_cross (mythos.energy.dna1.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.dna1.CrossStackingConfiguration attribute) (mythos.energy.dna2.CrossStackingConfiguration attribute) (mythos.energy.rna2.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.rna2.CrossStackingConfiguration attribute) dr_c_hb (mythos.energy.dna1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.dna1.HydrogenBondingConfiguration attribute) (mythos.energy.dna2.HydrogenBondingConfiguration attribute) dr_c_high_coax (mythos.energy.dna1.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.dna1.CoaxialStackingConfiguration attribute) (mythos.energy.dna2.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.dna2.CoaxialStackingConfiguration attribute) dr_c_high_cross (mythos.energy.dna1.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.dna1.CrossStackingConfiguration attribute) (mythos.energy.dna2.CrossStackingConfiguration attribute) (mythos.energy.rna2.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.rna2.CrossStackingConfiguration attribute) dr_c_high_hb (mythos.energy.dna1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.dna1.HydrogenBondingConfiguration attribute) (mythos.energy.dna2.HydrogenBondingConfiguration attribute) dr_c_high_stack (mythos.energy.dna1.stacking.StackingConfiguration attribute) (mythos.energy.dna1.StackingConfiguration attribute) (mythos.energy.dna2.StackingConfiguration attribute) (mythos.energy.rna2.stacking.StackingConfiguration attribute) (mythos.energy.rna2.StackingConfiguration attribute) dr_c_low_coax (mythos.energy.dna1.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.dna1.CoaxialStackingConfiguration attribute) (mythos.energy.dna2.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.dna2.CoaxialStackingConfiguration attribute) dr_c_low_cross (mythos.energy.dna1.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.dna1.CrossStackingConfiguration attribute) (mythos.energy.dna2.CrossStackingConfiguration attribute) (mythos.energy.rna2.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.rna2.CrossStackingConfiguration attribute) dr_c_low_hb (mythos.energy.dna1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.dna1.HydrogenBondingConfiguration attribute) (mythos.energy.dna2.HydrogenBondingConfiguration attribute) dr_c_low_stack (mythos.energy.dna1.stacking.StackingConfiguration attribute) (mythos.energy.dna1.StackingConfiguration attribute) (mythos.energy.dna2.StackingConfiguration attribute) (mythos.energy.rna2.stacking.StackingConfiguration attribute) (mythos.energy.rna2.StackingConfiguration attribute) dr_c_stack (mythos.energy.dna1.stacking.StackingConfiguration attribute) (mythos.energy.dna1.StackingConfiguration attribute) (mythos.energy.dna2.StackingConfiguration attribute) (mythos.energy.rna2.stacking.StackingConfiguration attribute) (mythos.energy.rna2.StackingConfiguration attribute) dr_high_coax (mythos.energy.dna1.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.dna1.CoaxialStackingConfiguration attribute) (mythos.energy.dna2.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.dna2.CoaxialStackingConfiguration attribute) dr_high_cross (mythos.energy.dna1.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.dna1.CrossStackingConfiguration attribute) (mythos.energy.dna2.CrossStackingConfiguration attribute) (mythos.energy.rna2.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.rna2.CrossStackingConfiguration attribute) dr_high_hb (mythos.energy.dna1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.dna1.HydrogenBondingConfiguration attribute) (mythos.energy.dna2.HydrogenBondingConfiguration attribute) dr_high_stack (mythos.energy.dna1.stacking.StackingConfiguration attribute) (mythos.energy.dna1.StackingConfiguration attribute) (mythos.energy.dna2.StackingConfiguration attribute) (mythos.energy.rna2.stacking.StackingConfiguration attribute) (mythos.energy.rna2.StackingConfiguration attribute) dr_low_coax (mythos.energy.dna1.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.dna1.CoaxialStackingConfiguration attribute) (mythos.energy.dna2.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.dna2.CoaxialStackingConfiguration attribute) dr_low_cross (mythos.energy.dna1.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.dna1.CrossStackingConfiguration attribute) (mythos.energy.dna2.CrossStackingConfiguration attribute) (mythos.energy.rna2.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.rna2.CrossStackingConfiguration attribute) dr_low_hb (mythos.energy.dna1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.dna1.HydrogenBondingConfiguration attribute) (mythos.energy.dna2.HydrogenBondingConfiguration attribute) dr_low_stack (mythos.energy.dna1.stacking.StackingConfiguration attribute) (mythos.energy.dna1.StackingConfiguration attribute) (mythos.energy.dna2.StackingConfiguration attribute) (mythos.energy.rna2.stacking.StackingConfiguration attribute) (mythos.energy.rna2.StackingConfiguration attribute) dr_star_back_base (mythos.energy.dna1.bonded_excluded_volume.BondedExcludedVolumeConfiguration attribute) (mythos.energy.dna1.BondedExcludedVolumeConfiguration attribute) (mythos.energy.dna1.unbonded_excluded_volume.UnbondedExcludedVolumeConfiguration attribute) (mythos.energy.dna1.UnbondedExcludedVolumeConfiguration attribute) (mythos.energy.dna2.BondedExcludedVolumeConfiguration attribute) (mythos.energy.dna2.UnbondedExcludedVolumeConfiguration attribute) dr_star_backbone (mythos.energy.dna1.unbonded_excluded_volume.UnbondedExcludedVolumeConfiguration attribute) (mythos.energy.dna1.UnbondedExcludedVolumeConfiguration attribute) (mythos.energy.dna2.UnbondedExcludedVolumeConfiguration attribute) dr_star_base (mythos.energy.dna1.bonded_excluded_volume.BondedExcludedVolumeConfiguration attribute) (mythos.energy.dna1.BondedExcludedVolumeConfiguration attribute) (mythos.energy.dna1.unbonded_excluded_volume.UnbondedExcludedVolumeConfiguration attribute) (mythos.energy.dna1.UnbondedExcludedVolumeConfiguration attribute) (mythos.energy.dna2.BondedExcludedVolumeConfiguration attribute) (mythos.energy.dna2.UnbondedExcludedVolumeConfiguration attribute) dr_star_base_back (mythos.energy.dna1.bonded_excluded_volume.BondedExcludedVolumeConfiguration attribute) (mythos.energy.dna1.BondedExcludedVolumeConfiguration attribute) (mythos.energy.dna1.unbonded_excluded_volume.UnbondedExcludedVolumeConfiguration attribute) (mythos.energy.dna1.UnbondedExcludedVolumeConfiguration attribute) (mythos.energy.dna2.BondedExcludedVolumeConfiguration attribute) (mythos.energy.dna2.UnbondedExcludedVolumeConfiguration attribute) dr_threshold (mythos.simulators.jax_md.NeighborList attribute) (mythos.simulators.jax_md.utils.NeighborList attribute) drh_a_coax_1 (mythos.energy.na1.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.na1.CoaxialStackingConfiguration attribute) drh_a_coax_3p (mythos.energy.na1.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.na1.CoaxialStackingConfiguration attribute) drh_a_coax_4 (mythos.energy.na1.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.na1.CoaxialStackingConfiguration attribute) drh_a_coax_4p (mythos.energy.na1.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.na1.CoaxialStackingConfiguration attribute) drh_a_coax_5 (mythos.energy.na1.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.na1.CoaxialStackingConfiguration attribute) drh_a_coax_6 (mythos.energy.na1.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.na1.CoaxialStackingConfiguration attribute) drh_a_cross_1 (mythos.energy.na1.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.na1.CrossStackingConfiguration attribute) drh_a_cross_2 (mythos.energy.na1.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.na1.CrossStackingConfiguration attribute) drh_a_cross_3 (mythos.energy.na1.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.na1.CrossStackingConfiguration attribute) drh_a_cross_4 (mythos.energy.na1.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.na1.CrossStackingConfiguration attribute) drh_a_cross_7 (mythos.energy.na1.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.na1.CrossStackingConfiguration attribute) drh_a_cross_8 (mythos.energy.na1.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.na1.CrossStackingConfiguration attribute) drh_a_hb (mythos.energy.na1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.na1.HydrogenBondingConfiguration attribute) drh_a_hb_1 (mythos.energy.na1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.na1.HydrogenBondingConfiguration attribute) drh_a_hb_2 (mythos.energy.na1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.na1.HydrogenBondingConfiguration attribute) drh_a_hb_3 (mythos.energy.na1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.na1.HydrogenBondingConfiguration attribute) drh_a_hb_4 (mythos.energy.na1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.na1.HydrogenBondingConfiguration attribute) drh_a_hb_7 (mythos.energy.na1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.na1.HydrogenBondingConfiguration attribute) drh_a_hb_8 (mythos.energy.na1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.na1.HydrogenBondingConfiguration attribute) drh_config (mythos.energy.na1.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.na1.CoaxialStackingConfiguration attribute) (mythos.energy.na1.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.na1.CrossStackingConfiguration attribute) (mythos.energy.na1.debye.DebyeConfiguration attribute) (mythos.energy.na1.DebyeConfiguration attribute) (mythos.energy.na1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.na1.HydrogenBondingConfiguration attribute) (mythos.energy.na1.unbonded_excluded_volume.UnbondedExcludedVolumeConfiguration attribute) (mythos.energy.na1.UnbondedExcludedVolumeConfiguration attribute) drh_cos_phi3_star_coax (mythos.energy.na1.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.na1.CoaxialStackingConfiguration attribute) drh_cos_phi4_star_coax (mythos.energy.na1.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.na1.CoaxialStackingConfiguration attribute) drh_delta_theta_star_coax_1 (mythos.energy.na1.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.na1.CoaxialStackingConfiguration attribute) drh_delta_theta_star_coax_4 (mythos.energy.na1.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.na1.CoaxialStackingConfiguration attribute) drh_delta_theta_star_coax_5 (mythos.energy.na1.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.na1.CoaxialStackingConfiguration attribute) drh_delta_theta_star_coax_6 (mythos.energy.na1.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.na1.CoaxialStackingConfiguration attribute) drh_delta_theta_star_cross_1 (mythos.energy.na1.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.na1.CrossStackingConfiguration attribute) drh_delta_theta_star_cross_2 (mythos.energy.na1.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.na1.CrossStackingConfiguration attribute) drh_delta_theta_star_cross_3 (mythos.energy.na1.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.na1.CrossStackingConfiguration attribute) drh_delta_theta_star_cross_4 (mythos.energy.na1.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.na1.CrossStackingConfiguration attribute) drh_delta_theta_star_cross_7 (mythos.energy.na1.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.na1.CrossStackingConfiguration attribute) drh_delta_theta_star_cross_8 (mythos.energy.na1.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.na1.CrossStackingConfiguration attribute) drh_delta_theta_star_hb_1 (mythos.energy.na1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.na1.HydrogenBondingConfiguration attribute) drh_delta_theta_star_hb_2 (mythos.energy.na1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.na1.HydrogenBondingConfiguration attribute) drh_delta_theta_star_hb_3 (mythos.energy.na1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.na1.HydrogenBondingConfiguration attribute) drh_delta_theta_star_hb_4 (mythos.energy.na1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.na1.HydrogenBondingConfiguration attribute) drh_delta_theta_star_hb_7 (mythos.energy.na1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.na1.HydrogenBondingConfiguration attribute) drh_delta_theta_star_hb_8 (mythos.energy.na1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.na1.HydrogenBondingConfiguration attribute) drh_dr0_coax (mythos.energy.na1.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.na1.CoaxialStackingConfiguration attribute) drh_dr0_hb (mythos.energy.na1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.na1.HydrogenBondingConfiguration attribute) drh_dr_c_coax (mythos.energy.na1.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.na1.CoaxialStackingConfiguration attribute) drh_dr_c_cross (mythos.energy.na1.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.na1.CrossStackingConfiguration attribute) drh_dr_c_hb (mythos.energy.na1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.na1.HydrogenBondingConfiguration attribute) drh_dr_high_coax (mythos.energy.na1.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.na1.CoaxialStackingConfiguration attribute) drh_dr_high_cross (mythos.energy.na1.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.na1.CrossStackingConfiguration attribute) drh_dr_high_hb (mythos.energy.na1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.na1.HydrogenBondingConfiguration attribute) drh_dr_low_coax (mythos.energy.na1.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.na1.CoaxialStackingConfiguration attribute) drh_dr_low_cross (mythos.energy.na1.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.na1.CrossStackingConfiguration attribute) drh_dr_low_hb (mythos.energy.na1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.na1.HydrogenBondingConfiguration attribute) drh_dr_star_back_base (mythos.energy.na1.unbonded_excluded_volume.UnbondedExcludedVolumeConfiguration attribute) (mythos.energy.na1.UnbondedExcludedVolumeConfiguration attribute) drh_dr_star_backbone (mythos.energy.na1.unbonded_excluded_volume.UnbondedExcludedVolumeConfiguration attribute) (mythos.energy.na1.UnbondedExcludedVolumeConfiguration attribute) drh_dr_star_base (mythos.energy.na1.unbonded_excluded_volume.UnbondedExcludedVolumeConfiguration attribute) (mythos.energy.na1.UnbondedExcludedVolumeConfiguration attribute) drh_dr_star_base_back (mythos.energy.na1.unbonded_excluded_volume.UnbondedExcludedVolumeConfiguration attribute) (mythos.energy.na1.UnbondedExcludedVolumeConfiguration attribute) drh_eps_exc (mythos.energy.na1.unbonded_excluded_volume.UnbondedExcludedVolumeConfiguration attribute) (mythos.energy.na1.UnbondedExcludedVolumeConfiguration attribute) drh_eps_hb (mythos.energy.na1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.na1.HydrogenBondingConfiguration attribute) drh_k_coax (mythos.energy.na1.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.na1.CoaxialStackingConfiguration attribute) drh_k_cross (mythos.energy.na1.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.na1.CrossStackingConfiguration attribute) drh_lambda_factor (mythos.energy.na1.debye.DebyeConfiguration attribute) (mythos.energy.na1.DebyeConfiguration attribute) drh_prefactor_coeff (mythos.energy.na1.debye.DebyeConfiguration attribute) (mythos.energy.na1.DebyeConfiguration attribute) drh_q_eff (mythos.energy.na1.debye.DebyeConfiguration attribute) (mythos.energy.na1.DebyeConfiguration attribute) drh_r0_cross (mythos.energy.na1.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.na1.CrossStackingConfiguration attribute) drh_sigma_back_base (mythos.energy.na1.unbonded_excluded_volume.UnbondedExcludedVolumeConfiguration attribute) (mythos.energy.na1.UnbondedExcludedVolumeConfiguration attribute) drh_sigma_backbone (mythos.energy.na1.unbonded_excluded_volume.UnbondedExcludedVolumeConfiguration attribute) (mythos.energy.na1.UnbondedExcludedVolumeConfiguration attribute) drh_sigma_base (mythos.energy.na1.unbonded_excluded_volume.UnbondedExcludedVolumeConfiguration attribute) (mythos.energy.na1.UnbondedExcludedVolumeConfiguration attribute) drh_sigma_base_back (mythos.energy.na1.unbonded_excluded_volume.UnbondedExcludedVolumeConfiguration attribute) (mythos.energy.na1.UnbondedExcludedVolumeConfiguration attribute) drh_ss_hb_weights (mythos.energy.na1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.na1.HydrogenBondingConfiguration attribute) drh_theta0_coax_1 (mythos.energy.na1.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.na1.CoaxialStackingConfiguration attribute) drh_theta0_coax_4 (mythos.energy.na1.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.na1.CoaxialStackingConfiguration attribute) drh_theta0_coax_5 (mythos.energy.na1.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.na1.CoaxialStackingConfiguration attribute) drh_theta0_coax_6 (mythos.energy.na1.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.na1.CoaxialStackingConfiguration attribute) drh_theta0_cross_1 (mythos.energy.na1.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.na1.CrossStackingConfiguration attribute) drh_theta0_cross_2 (mythos.energy.na1.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.na1.CrossStackingConfiguration attribute) drh_theta0_cross_3 (mythos.energy.na1.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.na1.CrossStackingConfiguration attribute) drh_theta0_cross_4 (mythos.energy.na1.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.na1.CrossStackingConfiguration attribute) drh_theta0_cross_7 (mythos.energy.na1.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.na1.CrossStackingConfiguration attribute) drh_theta0_cross_8 (mythos.energy.na1.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.na1.CrossStackingConfiguration attribute) drh_theta0_hb_1 (mythos.energy.na1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.na1.HydrogenBondingConfiguration attribute) drh_theta0_hb_2 (mythos.energy.na1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.na1.HydrogenBondingConfiguration attribute) drh_theta0_hb_3 (mythos.energy.na1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.na1.HydrogenBondingConfiguration attribute) drh_theta0_hb_4 (mythos.energy.na1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.na1.HydrogenBondingConfiguration attribute) drh_theta0_hb_7 (mythos.energy.na1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.na1.HydrogenBondingConfiguration attribute) drh_theta0_hb_8 (mythos.energy.na1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.na1.HydrogenBondingConfiguration attribute) dseq_to_pseq() (in module mythos.input.sequence_constraints) dt (mythos.simulators.jax_md.StaticSimulatorParams attribute) (mythos.simulators.jax_md.utils.StaticSimulatorParams attribute)

E

empty_dict (in module mythos.optimization.objective) energies (mythos.input.trajectory.Trajectory attribute) energy_fn (mythos.observables.melting_temp.MeltingTemp attribute) (mythos.optimization.objective.DiffTReObjective attribute), [1] (mythos.simulators.gromacs.gromacs.GromacsSimulator attribute) (mythos.simulators.gromacs.GromacsSimulator attribute) (mythos.simulators.jax_md.jaxmd.JaxMDSimulator attribute) (mythos.simulators.jax_md.JaxMDSimulator attribute) (mythos.simulators.lammps.lammps_oxdna.LAMMPSoxDNASimulator attribute) (mythos.simulators.oxdna.oxdna.oxDNASimulator attribute) (mythos.simulators.oxdna.oxDNASimulator attribute) energy_fn_builder() (in module mythos.energy) energy_fns (mythos.energy.base.ComposedEnergyFunction attribute) EnergyFn (in module mythos.optimization.objective) EnergyFunction (class in mythos.energy.base) eps_backbone (mythos.energy.dna1.fene.FeneConfiguration attribute) (mythos.energy.dna1.FeneConfiguration attribute) (mythos.energy.dna2.FeneConfiguration attribute) eps_exc (mythos.energy.dna1.bonded_excluded_volume.BondedExcludedVolumeConfiguration attribute) (mythos.energy.dna1.BondedExcludedVolumeConfiguration attribute) (mythos.energy.dna1.unbonded_excluded_volume.UnbondedExcludedVolumeConfiguration attribute) (mythos.energy.dna1.UnbondedExcludedVolumeConfiguration attribute) (mythos.energy.dna2.BondedExcludedVolumeConfiguration attribute) (mythos.energy.dna2.UnbondedExcludedVolumeConfiguration attribute) eps_hb (mythos.energy.dna1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.dna1.HydrogenBondingConfiguration attribute) (mythos.energy.dna2.HydrogenBondingConfiguration attribute) eps_hb_weights (mythos.energy.dna1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.dna1.HydrogenBondingConfiguration attribute) (mythos.energy.dna2.HydrogenBondingConfiguration attribute) eps_stack (mythos.energy.dna1.stacking.StackingConfiguration attribute) (mythos.energy.dna1.StackingConfiguration attribute) (mythos.energy.dna2.StackingConfiguration attribute) (mythos.energy.rna2.stacking.StackingConfiguration attribute) (mythos.energy.rna2.StackingConfiguration attribute) eps_stack_base (mythos.energy.dna1.stacking.StackingConfiguration attribute) (mythos.energy.dna1.StackingConfiguration attribute) (mythos.energy.dna2.StackingConfiguration attribute) (mythos.energy.rna2.stacking.StackingConfiguration attribute) (mythos.energy.rna2.StackingConfiguration attribute) eps_stack_kt_coeff (mythos.energy.dna1.stacking.StackingConfiguration attribute) (mythos.energy.dna1.StackingConfiguration attribute) (mythos.energy.dna2.StackingConfiguration attribute) (mythos.energy.rna2.stacking.StackingConfiguration attribute) (mythos.energy.rna2.StackingConfiguration attribute) equilibration_steps (mythos.simulators.gromacs.gromacs.GromacsSimulator attribute) (mythos.simulators.gromacs.GromacsSimulator attribute) ERR_BATCHED_N (in module mythos.utils.helpers) ERR_BP_ARR_CONTAINS_DUPLICATES (in module mythos.input.sequence_constraints) ERR_BUILD_SETUP_FAILED (in module mythos.simulators.oxdna) (in module mythos.simulators.oxdna.oxdna) ERR_CALL_NOT_IMPLEMENTED (in module mythos.energy.base) ERR_CANNOT_PROCESS_SRC_H (in module mythos.simulators.oxdna.utils) ERR_CHKPNT_SCN (in module mythos.simulators.jax_md.utils) ERR_COMPOSED_ENERGY_FN_LEN_MISMATCH (in module mythos.energy.base) ERR_COMPOSED_ENERGY_FN_TYPE_ENERGY_FNS (in module mythos.energy.base) ERR_DIFFTRE_MISSING_KWARGS (in module mythos.optimization.objective) ERR_DISPLACEMENT_FN_REQUIRED (in module mythos.observables.diameter) ERR_DSEQ_TO_PSEQ_INVALID_BP (in module mythos.input.sequence_constraints) ERR_FILE_NOT_FOUND (in module mythos.input.topology) ERR_FIXED_BOX_SIZE (in module mythos.input.trajectory) ERR_INPUT_FILE_NOT_FOUND (in module mythos.simulators.oxdna) (in module mythos.simulators.oxdna.oxdna) ERR_INVALID_BP_INDICES (in module mythos.input.sequence_constraints) ERR_INVALID_BP_SHAPE (in module mythos.input.sequence_constraints) ERR_INVALID_HEADER_TYPE (in module mythos.simulators.oxdna.utils) ERR_INVALID_OXDNA_FORMAT (in module mythos.input.topology)

ERR_MISSING_AGG_GRAD_FN (in module mythos.optimization.optimization) ERR_MISSING_ARG (in module mythos.optimization.objective) ERR_MISSING_OBJECTIVES (in module mythos.optimization.optimization) ERR_MISSING_OPTIMIZER (in module mythos.optimization.optimization) ERR_MISSING_REQUIRED_KEYS (in module mythos.simulators.oxdna) (in module mythos.simulators.oxdna.oxdna) ERR_MISSING_REQUIRED_PARAMS (in module mythos.energy.configuration) ERR_MISSING_SIMULATORS (in module mythos.optimization.optimization) ERR_MISSING_TOML_ENTRY (in module mythos.input.toml) ERR_NEIGHBORS_INVALID_BONDED_NEIGHBORS (in module mythos.utils.neighbors) ERR_NUCLEOTIDE_STATE_SHAPE (in module mythos.input.trajectory) ERR_NUCLEOTIDE_STATE_TYPE (in module mythos.input.trajectory) ERR_OBJECTIVE_NOT_READY (in module mythos.optimization.objective) ERR_OPT_DEPENDENT_PARAMS (in module mythos.energy.configuration) ERR_ORIG_MODEL_H_NOT_FOUND (in module mythos.simulators.oxdna.oxdna) ERR_OXDNA_FAILED (in module mythos.simulators.oxdna.oxdna) ERR_OXDNA_NOT_FOUND (in module mythos.simulators.oxdna.oxdna) ERR_PARAM_NOT_FOUND (in module mythos.energy.base) ERR_RIGID_BODY_TRANSFORM_FN_REQUIRED (in module mythos.observables.base) ERR_SEQ_CONSTRAINTS_INCOMPLETE_BP_MAPPED_IDXS (in module mythos.input.sequence_constraints) ERR_SEQ_CONSTRAINTS_INCOMPLETE_UNPAIRED_MAPPED_IDXS (in module mythos.input.sequence_constraints) ERR_SEQ_CONSTRAINTS_INVALID_BP_MAPPER_SHAPE (in module mythos.input.sequence_constraints) ERR_SEQ_CONSTRAINTS_INVALID_COVER (in module mythos.input.sequence_constraints) ERR_SEQ_CONSTRAINTS_INVALID_IS_UNPAIRED (in module mythos.input.sequence_constraints) ERR_SEQ_CONSTRAINTS_INVALID_IS_UNPAIRED_SHAPE (in module mythos.input.sequence_constraints) ERR_SEQ_CONSTRAINTS_INVALID_NUMBER_NUCLEOTIDES (in module mythos.input.sequence_constraints) ERR_SEQ_CONSTRAINTS_INVALID_UNPAIRED_MAPPER_SHAPE (in module mythos.input.sequence_constraints) ERR_SEQ_CONSTRAINTS_INVALID_UNPAIRED_SHAPE (in module mythos.input.sequence_constraints) ERR_SEQ_CONSTRAINTS_IS_UNPAIRED_INVALID_VALUES (in module mythos.input.sequence_constraints) ERR_SEQ_CONSTRAINTS_MISMATCH_NUM_TYPES (in module mythos.input.sequence_constraints) ERR_SEQ_CONSTRAINTS_PAIRED_NT_MAPPED_TO_UNPAIRED (in module mythos.input.sequence_constraints) ERR_SEQ_CONSTRAINTS_UNPAIRED_NT_MAPPED_TO_PAIRED (in module mythos.input.sequence_constraints) ERR_SINGLE_TARGET_STATE_REQUIRED (in module mythos.observables.rmse) ERR_STRAND_COUNTS_CIRCULAR_MISMATCH (in module mythos.input.topology) ERR_TARGET_STATE_DIM (in module mythos.observables.rmse) ERR_TOPOLOGY_BONDED_NEIGHBORS_INVALID_SHAPE (in module mythos.input.topology) ERR_TOPOLOGY_INVALID_BP_PSEQ_SHAPE (in module mythos.input.topology) ERR_TOPOLOGY_INVALID_DISCRETE_SEQUENCE_SHAPE (in module mythos.input.topology) ERR_TOPOLOGY_INVALID_NUMBER_NUCLEOTIDES (in module mythos.input.topology) ERR_TOPOLOGY_INVALID_PROBABILITIES (in module mythos.input.topology) ERR_TOPOLOGY_INVALID_SEQUENCE_LENGTH (in module mythos.input.topology) ERR_TOPOLOGY_INVALID_SEQUENCE_NUCLEOTIDES (in module mythos.input.topology) ERR_TOPOLOGY_INVALID_SEQUENCE_TYPE (in module mythos.input.topology) ERR_TOPOLOGY_INVALID_STRAND_COUNTS (in module mythos.input.topology) ERR_TOPOLOGY_INVALID_UNPAIRED_PSEQ_SHAPE (in module mythos.input.topology) ERR_TOPOLOGY_MISMATCH_PSEQ_SHAPE_NUM_NUCLEOTIDES (in module mythos.input.topology) ERR_TOPOLOGY_PSEQ_NOT_NORMALIZED (in module mythos.input.topology) ERR_TOPOLOGY_SEQ_NOT_MATCH_NUCLEOTIDES (in module mythos.input.topology) ERR_TOPOLOGY_STRAND_COUNTS_NOT_MATCH (in module mythos.input.topology) ERR_TOPOLOGY_UNBONDED_NEIGHBORS_INVALID_SHAPE (in module mythos.input.topology) ERR_TRAJECTORY_ENERGIES_SHAPE (in module mythos.input.trajectory) ERR_TRAJECTORY_ENERGIES_TYPE (in module mythos.input.trajectory) ERR_TRAJECTORY_FILE_NOT_FOUND (in module mythos.input.trajectory) ERR_TRAJECTORY_N_NUCLEOTIDE_STRAND_LEGNTHS (in module mythos.input.trajectory) ERR_TRAJECTORY_T_E_S_LENGTHS (in module mythos.input.trajectory) ERR_TRAJECTORY_TIMES_DIMS (in module mythos.input.trajectory) ERR_TRAJECTORY_TIMES_TYPE (in module mythos.input.trajectory) ERROR (mythos.ui.loggers.logger.Status attribute) euler_angles (mythos.input.trajectory.NucleotideState property) euler_angles_to_quaternion() (in module mythos.utils.math) exc_vol_bonded() (in module mythos.energy.dna1.interactions) exc_vol_unbonded() (in module mythos.energy.dna1.interactions) exposed_observables (mythos.simulators.base.Simulator attribute) (mythos.simulators.oxdna.oxdna.oxDNAUmbrellaSampler attribute) (mythos.simulators.oxdna.oxDNAUmbrellaSampler attribute) exposes() (mythos.simulators.base.Simulator method) ExtensionZ (class in mythos.observables.stretch_torsion)

F

f1() (in module mythos.energy.dna1.base_functions) (in module mythos.energy.dna2.base_functions) f2() (in module mythos.energy.dna1.base_functions) (in module mythos.energy.dna2.base_functions) f3() (in module mythos.energy.dna1.base_functions) (in module mythos.energy.dna2.base_functions) f4() (in module mythos.energy.dna1.base_functions) (in module mythos.energy.dna2.base_functions) f5() (in module mythos.energy.dna1.base_functions) (in module mythos.energy.dna2.base_functions) f6() (in module mythos.energy.dna2.base_functions) Fene (class in mythos.energy.dna1) (class in mythos.energy.dna1.fene) (class in mythos.energy.dna2) (class in mythos.energy.na1) (class in mythos.energy.na1.fene) FeneConfiguration (class in mythos.energy.dna1) (class in mythos.energy.dna1.fene) (class in mythos.energy.dna2) (class in mythos.energy.na1) (class in mythos.energy.na1.fene) fig (mythos.ui.loggers.jupyter.PlotlyLogger attribute) figure_widget_f (in module mythos.ui.loggers.jupyter) file (mythos.input.gromacs_input.GromacsParamsParser attribute) file_handles (mythos.ui.loggers.disk.PerMetricFileLogger attribute) FileLogger (class in mythos.ui.loggers.disk) filter() (mythos.simulators.io.SimulatorTrajectory method) find_melting_temp() (in module mythos.observables.melting_temp)

finf (mythos.energy.dna1.fene.FeneConfiguration attribute) (mythos.energy.dna1.FeneConfiguration attribute) (mythos.energy.dna2.FeneConfiguration attribute) fit_wlc() (in module mythos.observables.wlc) flatten_n() (in module mythos.simulators.jax_md.utils) FLOAT (mythos.utils.types.oxDNAModelHType attribute) fmax (mythos.energy.dna1.fene.FeneConfiguration attribute) (mythos.energy.dna1.FeneConfiguration attribute) (mythos.energy.dna2.FeneConfiguration attribute) from_bps() (in module mythos.input.sequence_constraints) from_dict() (mythos.energy.configuration.BaseConfiguration class method) from_file() (in module mythos.input.trajectory) from_kt() (in module mythos.utils.units) from_lists() (mythos.energy.base.ComposedEnergyFunction class method) from_oxdna_file() (in module mythos.input.topology) from_rigid_body() (mythos.energy.base.BaseNucleotide static method) (mythos.energy.dna1.Nucleotide static method) (mythos.energy.dna1.nucleotide.Nucleotide static method) (mythos.energy.dna2.Nucleotide static method) (mythos.energy.dna2.nucleotide.Nucleotide static method) (mythos.energy.na1.HybridNucleotide static method) (mythos.energy.na1.nucleotide.HybridNucleotide static method) (mythos.energy.rna2.Nucleotide static method) (mythos.energy.rna2.nucleotide.Nucleotide static method) (mythos.simulators.io.SimulatorTrajectory class method) from_topology() (mythos.energy.martini.base.MartiniEnergyFunction class method) from_tpr() (mythos.energy.martini.base.MartiniTopology class method) from_universe() (mythos.energy.martini.base.MartiniTopology class method)

G

gamma (mythos.simulators.jax_md.StaticSimulatorParams attribute) (mythos.simulators.jax_md.utils.StaticSimulatorParams attribute) get_all_corrs_and_l0s() (mythos.observables.persistence_length.PersistenceLength method) get_all_l_vectors (in module mythos.observables.persistence_length) get_duplex_quartets() (in module mythos.observables.base) get_extrap_ratios() (mythos.observables.melting_temp.MeltingTemp method) get_f1_smoothing_params() (in module mythos.energy.dna1.base_smoothing_functions) get_f2_smoothing_params() (in module mythos.energy.dna1.base_smoothing_functions) get_f3_smoothing_params() (in module mythos.energy.dna1.base_smoothing_functions) get_f4_smoothing_params() (in module mythos.energy.dna1.base_smoothing_functions) get_f5_smoothing_params() (in module mythos.energy.dna1.base_smoothing_functions) get_kt() (in module mythos.utils.units) get_kt_from_c() (in module mythos.utils.units) get_kt_from_string() (in module mythos.utils.units)

get_logging_observables() (mythos.optimization.objective.Objective method) get_melting_curve() (mythos.observables.melting_temp.MeltingTemp method) get_melting_curve_width() (mythos.observables.melting_temp.MeltingTemp method) get_melting_temperature() (mythos.observables.melting_temp.MeltingTemp method) get_neighbor_list_fn() (in module mythos.utils.neighbors) get_pair_probs() (in module mythos.energy.utils) get_periodic() (in module mythos.energy.martini.base) grad_or_loss_fn (mythos.optimization.objective.Objective attribute), [1] Grads (in module mythos.utils.types) grads (mythos.optimization.objective.ObjectiveOutput attribute), [1] (mythos.optimization.optimization.OptimizerOutput attribute), [1] GromacsParamsParser (class in mythos.input.gromacs_input) GromacsSimulator (class in mythos.simulators.gromacs) (class in mythos.simulators.gromacs.gromacs)

H

h_bonded_base_pairs (mythos.observables.diameter.Diameter attribute) (mythos.observables.propeller.PropellerTwist attribute) half_charged_ends (mythos.energy.dna2.debye.DebyeConfiguration attribute) (mythos.energy.dna2.DebyeConfiguration attribute) (mythos.energy.na1.debye.DebyeConfiguration attribute) (mythos.energy.na1.DebyeConfiguration attribute) HB_WEIGHTS_SA (in module mythos.energy.dna1.hydrogen_bonding) HybridNucleotide (class in mythos.energy.na1) (class in mythos.energy.na1.nucleotide) hydrogen_bonding() (in module mythos.energy.dna1.interactions)

HydrogenBonding (class in mythos.energy.dna1) (class in mythos.energy.dna1.hydrogen_bonding) (class in mythos.energy.dna2) (class in mythos.energy.na1) (class in mythos.energy.na1.hydrogen_bonding) HydrogenBondingConfiguration (class in mythos.energy.dna1) (class in mythos.energy.dna1.hydrogen_bonding) (class in mythos.energy.dna2) (class in mythos.energy.na1) (class in mythos.energy.na1.hydrogen_bonding)

I

idx (mythos.simulators.jax_md.NeighborList property) (mythos.simulators.jax_md.NoNeighborList property) (mythos.simulators.jax_md.utils.NeighborHelper property) (mythos.simulators.jax_md.utils.NeighborList property) (mythos.simulators.jax_md.utils.NoNeighborList property) idx_to_bp_idx (mythos.input.sequence_constraints.SequenceConstraints attribute) idx_to_unpaired_idx (mythos.input.sequence_constraints.SequenceConstraints attribute) ignore_params (mythos.simulators.oxdna.oxdna.oxDNASimulator attribute) (mythos.simulators.oxdna.oxDNASimulator attribute) increment_prog_bar() (mythos.ui.loggers.jupyter.JupyterLogger method) index_file (mythos.simulators.gromacs.gromacs.GromacsSimulator attribute) (mythos.simulators.gromacs.GromacsSimulator attribute) init_fn (mythos.simulators.jax_md.StaticSimulatorParams property) (mythos.simulators.jax_md.utils.StaticSimulatorParams property) init_params() (mythos.energy.configuration.BaseConfiguration method) (mythos.energy.dna1.bonded_excluded_volume.BondedExcludedVolumeConfiguration method) (mythos.energy.dna1.BondedExcludedVolumeConfiguration method) (mythos.energy.dna1.coaxial_stacking.CoaxialStackingConfiguration method) (mythos.energy.dna1.CoaxialStackingConfiguration method) (mythos.energy.dna1.cross_stacking.CrossStackingConfiguration method) (mythos.energy.dna1.CrossStackingConfiguration method) (mythos.energy.dna1.fene.FeneConfiguration method) (mythos.energy.dna1.FeneConfiguration method) (mythos.energy.dna1.hydrogen_bonding.HydrogenBondingConfiguration method) (mythos.energy.dna1.HydrogenBondingConfiguration method) (mythos.energy.dna1.stacking.StackingConfiguration method) (mythos.energy.dna1.StackingConfiguration method) (mythos.energy.dna1.unbonded_excluded_volume.UnbondedExcludedVolumeConfiguration method) (mythos.energy.dna1.UnbondedExcludedVolumeConfiguration method) (mythos.energy.dna2.BondedExcludedVolumeConfiguration method) (mythos.energy.dna2.coaxial_stacking.CoaxialStackingConfiguration method) (mythos.energy.dna2.CoaxialStackingConfiguration method) (mythos.energy.dna2.CrossStackingConfiguration method) (mythos.energy.dna2.debye.DebyeConfiguration method) (mythos.energy.dna2.DebyeConfiguration method) (mythos.energy.dna2.FeneConfiguration method) (mythos.energy.dna2.HydrogenBondingConfiguration method) (mythos.energy.dna2.StackingConfiguration method) (mythos.energy.dna2.UnbondedExcludedVolumeConfiguration method) (mythos.energy.martini.base.MartiniEnergyConfiguration method) (mythos.energy.na1.bonded_excluded_volume.BondedExcludedVolumeConfiguration method) (mythos.energy.na1.BondedExcludedVolumeConfiguration method) (mythos.energy.na1.coaxial_stacking.CoaxialStackingConfiguration method) (mythos.energy.na1.CoaxialStackingConfiguration method) (mythos.energy.na1.cross_stacking.CrossStackingConfiguration method) (mythos.energy.na1.CrossStackingConfiguration method) (mythos.energy.na1.debye.DebyeConfiguration method) (mythos.energy.na1.DebyeConfiguration method) (mythos.energy.na1.fene.FeneConfiguration method) (mythos.energy.na1.FeneConfiguration method) (mythos.energy.na1.hydrogen_bonding.HydrogenBondingConfiguration method) (mythos.energy.na1.HydrogenBondingConfiguration method) (mythos.energy.na1.stacking.StackingConfiguration method) (mythos.energy.na1.StackingConfiguration method) (mythos.energy.na1.unbonded_excluded_volume.UnbondedExcludedVolumeConfiguration method) (mythos.energy.na1.UnbondedExcludedVolumeConfiguration method) (mythos.energy.rna2.cross_stacking.CrossStackingConfiguration method) (mythos.energy.rna2.CrossStackingConfiguration method) (mythos.energy.rna2.stacking.StackingConfiguration method) (mythos.energy.rna2.StackingConfiguration method)

init_positions (mythos.simulators.jax_md.NeighborList attribute) (mythos.simulators.jax_md.utils.NeighborList attribute) input_dir (mythos.simulators.base.InputDirSimulator attribute) input_file_name (mythos.simulators.lammps.lammps_oxdna.LAMMPSoxDNASimulator attribute) input_overrides (mythos.simulators.gromacs.gromacs.GromacsSimulator attribute) (mythos.simulators.gromacs.GromacsSimulator attribute) (mythos.simulators.oxdna.oxdna.oxDNASimulator attribute) (mythos.simulators.oxdna.oxDNASimulator attribute) InputDirSimulator (class in mythos.simulators.base) INTEGER (mythos.utils.types.oxDNAModelHType attribute) INVALID_DICT_LINE (in module mythos.input.oxdna_input) INVALID_LINE (in module mythos.input.gromacs_input) is_dna_rna_pair() (in module mythos.energy.na1.utils) is_end (mythos.energy.dna2.Debye attribute) (mythos.energy.dna2.debye.Debye attribute) (mythos.input.topology.Topology attribute) is_ready (mythos.optimization.objective.ObjectiveOutput attribute), [1] is_rna_pair() (in module mythos.energy.na1.utils) is_unpaired (mythos.input.sequence_constraints.SequenceConstraints attribute)

J

jax_interp1d() (in module mythos.observables.melting_temp) JaxMDSimulator (class in mythos.simulators.jax_md) (class in mythos.simulators.jax_md.jaxmd)

JOULES_PER_OXDNA_ENERGY (in module mythos.utils.units) JupyterLogger (class in mythos.ui.loggers.jupyter)

K

k_coax (mythos.energy.dna1.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.dna1.CoaxialStackingConfiguration attribute) (mythos.energy.dna2.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.dna2.CoaxialStackingConfiguration attribute) k_cross (mythos.energy.dna1.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.dna1.CrossStackingConfiguration attribute) (mythos.energy.dna2.CrossStackingConfiguration attribute) (mythos.energy.rna2.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.rna2.CrossStackingConfiguration attribute) kappa (mythos.energy.dna2.debye.DebyeConfiguration attribute) (mythos.energy.dna2.DebyeConfiguration attribute) kt (mythos.energy.dna1.stacking.StackingConfiguration attribute) (mythos.energy.dna1.StackingConfiguration attribute) (mythos.energy.dna2.debye.DebyeConfiguration attribute) (mythos.energy.dna2.DebyeConfiguration attribute) (mythos.energy.dna2.StackingConfiguration attribute) (mythos.energy.na1.debye.DebyeConfiguration attribute) (mythos.energy.na1.DebyeConfiguration attribute) (mythos.energy.na1.stacking.StackingConfiguration attribute) (mythos.energy.na1.StackingConfiguration attribute) (mythos.energy.rna2.stacking.StackingConfiguration attribute) (mythos.energy.rna2.StackingConfiguration attribute)

kT (mythos.simulators.jax_md.StaticSimulatorParams attribute) (mythos.simulators.jax_md.utils.StaticSimulatorParams attribute)

L

l2_loss() (in module mythos.losses.observable_wrappers) lambda_ (mythos.energy.dna2.debye.DebyeConfiguration attribute) (mythos.energy.dna2.DebyeConfiguration attribute) lambda_factor (mythos.energy.dna2.debye.DebyeConfiguration attribute) (mythos.energy.dna2.DebyeConfiguration attribute) LAMMPS_REQUIRED_FIELDS (in module mythos.simulators.lammps.lammps_oxdna) LAMMPSoxDNASimulator (class in mythos.simulators.lammps.lammps_oxdna) LBL_OBJ_HEADER (in module mythos.ui.loggers.jupyter) LBL_OBS_HEADER (in module mythos.ui.loggers.jupyter) LBL_PROG_BAR (in module mythos.ui.loggers.jupyter) LBL_SIM_HEADER (in module mythos.ui.loggers.jupyter) LBL_TOP_HEADER (in module mythos.ui.loggers.jupyter) length() (mythos.simulators.io.SimulatorTrajectory method) lennard_jones() (in module mythos.energy.martini.m2.lj) lipid_sel (mythos.observables.area_per_lipid.AreaPerLipid attribute) (mythos.observables.membrane_thickness.MembraneThickness attribute) LJ (class in mythos.energy.martini.m2) (class in mythos.energy.martini.m2.lj) LJ_EPSILON_PREFIX (in module mythos.energy.martini.m2.lj) LJ_SIGMA_PREFIX (in module mythos.energy.martini.m2.lj) LJConfiguration (class in mythos.energy.martini.m2) (class in mythos.energy.martini.m2.lj) load_pytree() (in module mythos.input.tree) local_helical_axis() (in module mythos.observables.base) local_helical_axis_with_norm() (in module mythos.observables.base) log_dir (mythos.ui.loggers.disk.PerMetricFileLogger attribute)

log_file (mythos.ui.loggers.disk.FileLogger attribute) log_metric() (mythos.ui.loggers.aim.AimLogger method) (mythos.ui.loggers.console.ConsoleLogger method) (mythos.ui.loggers.disk.FileLogger method) (mythos.ui.loggers.disk.PerMetricFileLogger method) (mythos.ui.loggers.jupyter.JupyterLogger method) (mythos.ui.loggers.jupyter.PlotlyLogger method) (mythos.ui.loggers.logger.Logger method) (mythos.ui.loggers.logger.NullLogger method) (mythos.ui.loggers.multilogger.MultiLogger method) Logger (class in mythos.ui.loggers.logger) logger (in module mythos.input.gromacs_input) (in module mythos.simulators.gromacs.gromacs) (in module mythos.simulators.gromacs.utils) (in module mythos.simulators.oxdna.oxdna) (mythos.optimization.optimization.RayOptimizer attribute) (mythos.optimization.optimization.SimpleOptimizer attribute) logger_config (mythos.simulators.oxdna.oxdna.oxDNASimulator attribute) (mythos.simulators.oxdna.oxDNASimulator attribute) loggers (mythos.ui.loggers.multilogger.MultiLogger attribute) logging_observables (mythos.optimization.objective.Objective attribute), [1] loss() (in module mythos.observables.wlc) loss_fn (mythos.losses.observable_wrappers.ObservableLossFn attribute) loss_input (in module mythos.losses.observable_wrappers) LossFn (class in mythos.losses.observable_wrappers) lp_fit() (mythos.observables.persistence_length.PersistenceLength method)

M

MAKE_BIN_ENV_VAR (in module mythos.simulators.oxdna) (in module mythos.simulators.oxdna.oxdna) make_subplots_f (in module mythos.ui.loggers.jupyter) map() (mythos.energy.base.EnergyFunction method) MartiniEnergyConfiguration (class in mythos.energy.martini.base) MartiniEnergyFunction (class in mythos.energy.martini.base) MartiniTopology (class in mythos.energy.martini.base) mass (mythos.simulators.jax_md.SimulationState attribute) (mythos.simulators.jax_md.StaticSimulatorParams attribute) (mythos.simulators.jax_md.utils.SimulationState attribute) (mythos.simulators.jax_md.utils.StaticSimulatorParams attribute) MatrixSq (in module mythos.utils.types) max_retries (mythos.utils.scheduler.SchedulerHints attribute), [1] max_valid_opt_steps (mythos.optimization.objective.DiffTReObjective attribute), [1] mdp_file (mythos.simulators.gromacs.gromacs.GromacsSimulator attribute) (mythos.simulators.gromacs.GromacsSimulator attribute) MeltingTemp (class in mythos.observables.melting_temp) mem_mb (mythos.utils.scheduler.SchedulerHints attribute), [1] MembraneThickness (class in mythos.observables.membrane_thickness) MetaData (in module mythos.utils.types) metadata (mythos.simulators.io.SimulatorTrajectory attribute) min_n_eff_factor (mythos.optimization.objective.DiffTReObjective attribute), [1] MIN_VALID_HEADER_TOKEN_COUNT (in module mythos.simulators.oxdna.utils) MISSING_LOGDIR_WANING (in module mythos.ui.loggers.logger) MISSING_LOGDIR_WARNING (in module mythos.ui.loggers.disk) module mythos mythos._version mythos.energy mythos.energy.base mythos.energy.configuration mythos.energy.dna1 mythos.energy.dna1.base_functions mythos.energy.dna1.base_smoothing_functions mythos.energy.dna1.bonded_excluded_volume mythos.energy.dna1.coaxial_stacking mythos.energy.dna1.cross_stacking mythos.energy.dna1.fene mythos.energy.dna1.hydrogen_bonding mythos.energy.dna1.interactions mythos.energy.dna1.nucleotide mythos.energy.dna1.stacking mythos.energy.dna1.unbonded_excluded_volume mythos.energy.dna2 mythos.energy.dna2.base_functions mythos.energy.dna2.coaxial_stacking mythos.energy.dna2.debye mythos.energy.dna2.interactions mythos.energy.dna2.nucleotide mythos.energy.dna2.stacking mythos.energy.martini mythos.energy.martini.base mythos.energy.martini.m2 mythos.energy.martini.m2.angle mythos.energy.martini.m2.bond mythos.energy.martini.m2.lj mythos.energy.na1 mythos.energy.na1.bonded_excluded_volume mythos.energy.na1.coaxial_stacking mythos.energy.na1.cross_stacking mythos.energy.na1.debye mythos.energy.na1.fene mythos.energy.na1.hydrogen_bonding mythos.energy.na1.nucleotide mythos.energy.na1.stacking mythos.energy.na1.unbonded_excluded_volume mythos.energy.na1.utils mythos.energy.potentials mythos.energy.rna2 mythos.energy.rna2.cross_stacking mythos.energy.rna2.interactions mythos.energy.rna2.nucleotide mythos.energy.rna2.stacking mythos.energy.utils mythos.input mythos.input.dna1 mythos.input.gromacs_input mythos.input.oxdna_input mythos.input.sequence_constraints mythos.input.sequence_dependence mythos.input.toml mythos.input.topology mythos.input.trajectory mythos.input.tree mythos.losses mythos.losses.observable_wrappers mythos.observables mythos.observables.area_per_lipid mythos.observables.base mythos.observables.diameter mythos.observables.martini_utils mythos.observables.melting_temp mythos.observables.membrane_thickness mythos.observables.persistence_length mythos.observables.pitch mythos.observables.propeller mythos.observables.rise mythos.observables.rmse mythos.observables.stretch_torsion mythos.observables.wlc mythos.optimization mythos.optimization.objective mythos.optimization.optimization mythos.simulators mythos.simulators.base mythos.simulators.gromacs mythos.simulators.gromacs.gromacs mythos.simulators.gromacs.utils mythos.simulators.io mythos.simulators.jax_md mythos.simulators.jax_md.jaxmd mythos.simulators.jax_md.utils mythos.simulators.lammps mythos.simulators.lammps.lammps_oxdna mythos.simulators.oxdna mythos.simulators.oxdna.oxdna mythos.simulators.oxdna.utils mythos.ui mythos.ui.loggers mythos.ui.loggers.aim mythos.ui.loggers.console mythos.ui.loggers.disk mythos.ui.loggers.jupyter mythos.ui.loggers.logger mythos.ui.loggers.multilogger mythos.utils mythos.utils.constants mythos.utils.helpers mythos.utils.math mythos.utils.neighbors mythos.utils.scheduler mythos.utils.types mythos.utils.units mult() (in module mythos.utils.math) MultiLogger (class in mythos.ui.loggers.multilogger) mythos module mythos._version module mythos.energy module mythos.energy.base module mythos.energy.configuration module mythos.energy.dna1 module mythos.energy.dna1.base_functions module mythos.energy.dna1.base_smoothing_functions module mythos.energy.dna1.bonded_excluded_volume module mythos.energy.dna1.coaxial_stacking module mythos.energy.dna1.cross_stacking module mythos.energy.dna1.fene module mythos.energy.dna1.hydrogen_bonding module mythos.energy.dna1.interactions module mythos.energy.dna1.nucleotide module mythos.energy.dna1.stacking module mythos.energy.dna1.unbonded_excluded_volume module mythos.energy.dna2 module mythos.energy.dna2.base_functions module mythos.energy.dna2.coaxial_stacking module

mythos.energy.dna2.debye module mythos.energy.dna2.interactions module mythos.energy.dna2.nucleotide module mythos.energy.dna2.stacking module mythos.energy.martini module mythos.energy.martini.base module mythos.energy.martini.m2 module mythos.energy.martini.m2.angle module mythos.energy.martini.m2.bond module mythos.energy.martini.m2.lj module mythos.energy.na1 module mythos.energy.na1.bonded_excluded_volume module mythos.energy.na1.coaxial_stacking module mythos.energy.na1.cross_stacking module mythos.energy.na1.debye module mythos.energy.na1.fene module mythos.energy.na1.hydrogen_bonding module mythos.energy.na1.nucleotide module mythos.energy.na1.stacking module mythos.energy.na1.unbonded_excluded_volume module mythos.energy.na1.utils module mythos.energy.potentials module mythos.energy.rna2 module mythos.energy.rna2.cross_stacking module mythos.energy.rna2.interactions module mythos.energy.rna2.nucleotide module mythos.energy.rna2.stacking module mythos.energy.utils module mythos.input module mythos.input.dna1 module mythos.input.gromacs_input module mythos.input.oxdna_input module mythos.input.sequence_constraints module mythos.input.sequence_dependence module mythos.input.toml module mythos.input.topology module mythos.input.trajectory module mythos.input.tree module mythos.losses module mythos.losses.observable_wrappers module mythos.observables module mythos.observables.area_per_lipid module mythos.observables.base module mythos.observables.diameter module mythos.observables.martini_utils module mythos.observables.melting_temp module mythos.observables.membrane_thickness module mythos.observables.persistence_length module mythos.observables.pitch module mythos.observables.propeller module mythos.observables.rise module mythos.observables.rmse module mythos.observables.stretch_torsion module mythos.observables.wlc module mythos.optimization module mythos.optimization.objective module mythos.optimization.optimization module mythos.simulators module mythos.simulators.base module mythos.simulators.gromacs module mythos.simulators.gromacs.gromacs module mythos.simulators.gromacs.utils module mythos.simulators.io module mythos.simulators.jax_md module mythos.simulators.jax_md.jaxmd module mythos.simulators.jax_md.utils module mythos.simulators.lammps module mythos.simulators.lammps.lammps_oxdna module mythos.simulators.oxdna module mythos.simulators.oxdna.oxdna module mythos.simulators.oxdna.utils module mythos.ui module mythos.ui.loggers module mythos.ui.loggers.aim module mythos.ui.loggers.console module mythos.ui.loggers.disk module mythos.ui.loggers.jupyter module mythos.ui.loggers.logger module mythos.ui.loggers.multilogger module mythos.utils module mythos.utils.constants module mythos.utils.helpers module mythos.utils.math module mythos.utils.neighbors module mythos.utils.scheduler module mythos.utils.types module mythos.utils.units module

N

N_1ST_LINE_OXDNA_CLASSIC (in module mythos.input.topology) N_1ST_LINE_OXDNA_NEW (in module mythos.input.topology) n_bp (mythos.input.sequence_constraints.SequenceConstraints attribute) N_BP_TYPES (in module mythos.utils.constants) n_build_threads (mythos.simulators.oxdna.oxdna.oxDNASimulator attribute) (mythos.simulators.oxdna.oxDNASimulator attribute) N_DIMS_NUCLEOTIDES_POSITION (in module mythos.observables.rmse) n_equilibration_steps (mythos.optimization.objective.DiffTReObjective attribute), [1] N_NT (in module mythos.utils.constants) N_NT_PER_BP (in module mythos.utils.constants) n_nucleotides (mythos.input.sequence_constraints.SequenceConstraints attribute) (mythos.input.topology.Topology attribute) (mythos.input.trajectory.Trajectory attribute) n_unpaired (mythos.input.sequence_constraints.SequenceConstraints attribute) name (mythos.optimization.objective.Objective attribute), [1] (mythos.simulators.base.Simulator attribute) needs_update (mythos.optimization.objective.ObjectiveOutput attribute), [1] neg_cos_phi1_c_stack (mythos.energy.dna1.stacking.StackingConfiguration attribute) (mythos.energy.dna1.StackingConfiguration attribute) (mythos.energy.dna2.StackingConfiguration attribute) (mythos.energy.rna2.stacking.StackingConfiguration attribute) (mythos.energy.rna2.StackingConfiguration attribute) neg_cos_phi1_star_stack (mythos.energy.dna1.stacking.StackingConfiguration attribute) (mythos.energy.dna1.StackingConfiguration attribute) (mythos.energy.dna2.StackingConfiguration attribute) (mythos.energy.rna2.stacking.StackingConfiguration attribute) (mythos.energy.rna2.StackingConfiguration attribute) neg_cos_phi2_c_stack (mythos.energy.dna1.stacking.StackingConfiguration attribute) (mythos.energy.dna1.StackingConfiguration attribute) (mythos.energy.dna2.StackingConfiguration attribute) (mythos.energy.rna2.stacking.StackingConfiguration attribute) (mythos.energy.rna2.StackingConfiguration attribute) neg_cos_phi2_star_stack (mythos.energy.dna1.stacking.StackingConfiguration attribute) (mythos.energy.dna1.StackingConfiguration attribute) (mythos.energy.dna2.StackingConfiguration attribute) (mythos.energy.rna2.stacking.StackingConfiguration attribute) (mythos.energy.rna2.StackingConfiguration attribute) NeighborHelper (class in mythos.simulators.jax_md.utils) NeighborList (class in mythos.simulators.jax_md) (class in mythos.simulators.jax_md.utils)

neighbors (mythos.simulators.jax_md.jaxmd.JaxMDSimulator attribute) (mythos.simulators.jax_md.JaxMDSimulator attribute) NEW (mythos.utils.types.oxDNAFormat attribute) NM_PER_OXDNA_LENGTH (in module mythos.utils.units) NM_TO_ANGSTROMS (in module mythos.observables.martini_utils) non_optimizable_required_params (mythos.energy.configuration.BaseConfiguration attribute) NoNeighborList (class in mythos.simulators.jax_md) (class in mythos.simulators.jax_md.utils) nt_type (mythos.energy.na1.bonded_excluded_volume.BondedExcludedVolumeConfiguration attribute) (mythos.energy.na1.BondedExcludedVolumeConfiguration attribute) (mythos.energy.na1.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.na1.CoaxialStackingConfiguration attribute) (mythos.energy.na1.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.na1.CrossStackingConfiguration attribute) (mythos.energy.na1.debye.DebyeConfiguration attribute) (mythos.energy.na1.DebyeConfiguration attribute) (mythos.energy.na1.fene.FeneConfiguration attribute) (mythos.energy.na1.FeneConfiguration attribute) (mythos.energy.na1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.na1.HydrogenBondingConfiguration attribute) (mythos.energy.na1.stacking.StackingConfiguration attribute) (mythos.energy.na1.StackingConfiguration attribute) (mythos.energy.na1.unbonded_excluded_volume.UnbondedExcludedVolumeConfiguration attribute) (mythos.energy.na1.UnbondedExcludedVolumeConfiguration attribute) (mythos.input.topology.Topology attribute) Nucleotide (class in mythos.energy.dna1) (class in mythos.energy.dna1.nucleotide) (class in mythos.energy.dna2) (class in mythos.energy.dna2.nucleotide) (class in mythos.energy.rna2) (class in mythos.energy.rna2.nucleotide) NUCLEOTIDE_STATE_SHAPE (in module mythos.input.trajectory) NUCLEOTIDES_IDX (in module mythos.utils.constants) NucleotideState (class in mythos.input.trajectory) NucleotideType (class in mythos.input.topology) NullLogger (class in mythos.ui.loggers.logger) num_cpus (mythos.utils.scheduler.SchedulerHints attribute), [1] num_gpus (mythos.utils.scheduler.SchedulerHints attribute), [1]

O

obj_btns (mythos.ui.loggers.jupyter.JupyterLogger attribute) Objective (class in mythos.optimization.objective) objective (mythos.optimization.optimization.SimpleOptimizer attribute) OBJECTIVE (mythos.ui.loggers.logger.StatusKind attribute) OBJECTIVE_PER_STEP_CALL_LIMIT (in module mythos.optimization.optimization) ObjectiveOutput (class in mythos.optimization.objective) objectives (mythos.optimization.optimization.RayOptimizer attribute) obs_btns (mythos.ui.loggers.jupyter.JupyterLogger attribute) observable (mythos.losses.observable_wrappers.ObservableLossFn attribute) OBSERVABLE (mythos.ui.loggers.logger.StatusKind attribute) observable_plots (mythos.ui.loggers.jupyter.PlotlyLogger attribute) ObservableLossFn (class in mythos.losses.observable_wrappers) observables (mythos.optimization.objective.ObjectiveOutput attribute), [1] (mythos.optimization.optimization.OptimizerOutput attribute), [1] (mythos.optimization.optimization.OptimizerState attribute), [1] (mythos.simulators.base.SimulatorOutput attribute) OPT_ALL (mythos.energy.configuration.BaseConfiguration attribute) opt_params (mythos.energy.configuration.BaseConfiguration property) (mythos.energy.martini.base.MartiniEnergyConfiguration property) (mythos.optimization.optimization.OptimizerOutput attribute), [1] opt_params() (mythos.energy.base.BaseEnergyFunction method) (mythos.energy.base.ComposedEnergyFunction method) (mythos.energy.base.EnergyFunction method)

Optimizer (class in mythos.optimization.optimization) optimizer (mythos.optimization.optimization.RayOptimizer attribute) (mythos.optimization.optimization.SimpleOptimizer attribute) optimizer_state (mythos.optimization.optimization.OptimizerState attribute), [1] OptimizerOutput (class in mythos.optimization.optimization) OptimizerState (class in mythos.optimization.optimization) orientation (mythos.energy.base.BaseNucleotide attribute) (mythos.energy.dna1.Nucleotide attribute) (mythos.energy.dna1.nucleotide.Nucleotide attribute) (mythos.energy.dna2.Nucleotide attribute) (mythos.energy.dna2.nucleotide.Nucleotide attribute) (mythos.energy.rna2.Nucleotide attribute) (mythos.energy.rna2.nucleotide.Nucleotide attribute) OUTPUT_PREFIX (in module mythos.simulators.gromacs.gromacs) overwrite_input (mythos.simulators.base.InputDirSimulator attribute) OXDNA_TOPOLOGY_FILE_KEY (in module mythos.simulators.oxdna.oxdna) OXDNA_TRAJECTORY_FILE_KEY (in module mythos.simulators.oxdna.oxdna) oxDNAFormat (class in mythos.utils.types) oxDNAModelHType (class in mythos.utils.types) oxDNASimulator (class in mythos.simulators.oxdna) (class in mythos.simulators.oxdna.oxdna) oxDNASimulatorType (class in mythos.utils.types) oxDNAUmbrellaSampler (class in mythos.simulators.oxdna) (class in mythos.simulators.oxdna.oxdna)

P

pair_bond() (in module mythos.energy.martini.m2.bond) pair_lj() (in module mythos.energy.martini.m2.lj) pairwise_energies() (mythos.energy.dna1.bonded_excluded_volume.BondedExcludedVolume method) (mythos.energy.dna1.BondedExcludedVolume method) (mythos.energy.dna1.coaxial_stacking.CoaxialStacking method) (mythos.energy.dna1.CoaxialStacking method) (mythos.energy.dna1.cross_stacking.CrossStacking method) (mythos.energy.dna1.CrossStacking method) (mythos.energy.dna1.Fene method) (mythos.energy.dna1.fene.Fene method) (mythos.energy.dna1.hydrogen_bonding.HydrogenBonding method) (mythos.energy.dna1.HydrogenBonding method) (mythos.energy.dna1.Stacking method) (mythos.energy.dna1.stacking.Stacking method) (mythos.energy.dna1.unbonded_excluded_volume.UnbondedExcludedVolume method) (mythos.energy.dna1.UnbondedExcludedVolume method) (mythos.energy.dna2.BondedExcludedVolume method) (mythos.energy.dna2.coaxial_stacking.CoaxialStacking method) (mythos.energy.dna2.CoaxialStacking method) (mythos.energy.dna2.CrossStacking method) (mythos.energy.dna2.Debye method) (mythos.energy.dna2.debye.Debye method) (mythos.energy.dna2.Fene method) (mythos.energy.dna2.HydrogenBonding method) (mythos.energy.dna2.Stacking method) (mythos.energy.dna2.stacking.Stacking method) (mythos.energy.dna2.UnbondedExcludedVolume method) (mythos.energy.rna2.cross_stacking.CrossStacking method) (mythos.energy.rna2.CrossStacking method) (mythos.energy.rna2.Stacking method) (mythos.energy.rna2.stacking.Stacking method) Params (in module mythos.utils.types) params (mythos.energy.base.BaseEnergyFunction attribute) (mythos.energy.dna1.bonded_excluded_volume.BondedExcludedVolume attribute) (mythos.energy.dna1.BondedExcludedVolume attribute) (mythos.energy.dna1.coaxial_stacking.CoaxialStacking attribute) (mythos.energy.dna1.CoaxialStacking attribute) (mythos.energy.dna1.cross_stacking.CrossStacking attribute) (mythos.energy.dna1.CrossStacking attribute) (mythos.energy.dna1.Fene attribute) (mythos.energy.dna1.fene.Fene attribute) (mythos.energy.dna1.hydrogen_bonding.HydrogenBonding attribute) (mythos.energy.dna1.HydrogenBonding attribute) (mythos.energy.dna1.Stacking attribute) (mythos.energy.dna1.stacking.Stacking attribute) (mythos.energy.dna1.unbonded_excluded_volume.UnbondedExcludedVolume attribute) (mythos.energy.dna1.UnbondedExcludedVolume attribute) (mythos.energy.dna2.BondedExcludedVolume attribute) (mythos.energy.dna2.coaxial_stacking.CoaxialStacking attribute) (mythos.energy.dna2.CoaxialStacking attribute) (mythos.energy.dna2.CrossStacking attribute) (mythos.energy.dna2.Debye attribute) (mythos.energy.dna2.debye.Debye attribute) (mythos.energy.dna2.Fene attribute) (mythos.energy.dna2.HydrogenBonding attribute) (mythos.energy.dna2.Stacking attribute) (mythos.energy.dna2.stacking.Stacking attribute) (mythos.energy.dna2.UnbondedExcludedVolume attribute) (mythos.energy.martini.base.MartiniEnergyConfiguration attribute) (mythos.energy.martini.m2.Angle attribute) (mythos.energy.martini.m2.angle.Angle attribute) (mythos.energy.martini.m2.Bond attribute) (mythos.energy.martini.m2.bond.Bond attribute) (mythos.energy.martini.m2.LJ attribute) (mythos.energy.martini.m2.lj.LJ attribute) (mythos.energy.na1.bonded_excluded_volume.BondedExcludedVolume attribute) (mythos.energy.na1.BondedExcludedVolume attribute) (mythos.energy.na1.coaxial_stacking.CoaxialStacking attribute) (mythos.energy.na1.CoaxialStacking attribute) (mythos.energy.na1.cross_stacking.CrossStacking attribute) (mythos.energy.na1.CrossStacking attribute) (mythos.energy.na1.Debye attribute) (mythos.energy.na1.debye.Debye attribute) (mythos.energy.na1.Fene attribute) (mythos.energy.na1.fene.Fene attribute) (mythos.energy.na1.hydrogen_bonding.HydrogenBonding attribute) (mythos.energy.na1.HydrogenBonding attribute) (mythos.energy.na1.Stacking attribute) (mythos.energy.na1.stacking.Stacking attribute) (mythos.energy.na1.unbonded_excluded_volume.UnbondedExcludedVolume attribute) (mythos.energy.na1.UnbondedExcludedVolume attribute) (mythos.energy.rna2.cross_stacking.CrossStacking attribute) (mythos.energy.rna2.CrossStacking attribute) (mythos.energy.rna2.Stacking attribute) (mythos.energy.rna2.stacking.Stacking attribute)

params_dict() (mythos.energy.base.BaseEnergyFunction method) (mythos.energy.base.ComposedEnergyFunction method) (mythos.energy.base.EnergyFunction method) params_to_optimize (mythos.energy.configuration.BaseConfiguration attribute) ParamsDict (in module mythos.input.gromacs_input) parse() (mythos.input.gromacs_input.GromacsParamsParser method) parse_str() (in module mythos.input.toml) parse_toml() (in module mythos.input.toml) parse_value() (in module mythos.input.toml) PathOrStr (in module mythos.utils.types) percent_complete (mythos.ui.loggers.jupyter.JupyterLogger attribute) PerMetricFileLogger (class in mythos.ui.loggers.disk) persistence_length_fit() (in module mythos.observables.persistence_length) PersistenceLength (class in mythos.observables.persistence_length) PitchAngle (class in mythos.observables.pitch) PlotlyLogger (class in mythos.ui.loggers.jupyter) plots (mythos.ui.loggers.jupyter.JupyterLogger attribute) PN_PER_OXDNA_FORCE (in module mythos.utils.units) position (mythos.simulators.jax_md.SimulationState attribute) (mythos.simulators.jax_md.utils.SimulationState attribute) prefactor (mythos.energy.dna2.debye.DebyeConfiguration attribute) (mythos.energy.dna2.DebyeConfiguration attribute) prefactor_coeff (mythos.energy.dna2.debye.DebyeConfiguration attribute) (mythos.energy.dna2.DebyeConfiguration attribute) PREPROCESSED_TOPOLOGY_FILE (in module mythos.simulators.gromacs.gromacs) principal_axes_to_euler_angles() (in module mythos.utils.math) Probabilistic_Sequence (in module mythos.utils.types) prog_bar (mythos.ui.loggers.jupyter.JupyterLogger attribute) propeller_twist_rad (in module mythos.observables.propeller) PropellerTwist (class in mythos.observables.propeller) pseq (mythos.energy.dna1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.dna1.HydrogenBondingConfiguration attribute) (mythos.energy.dna1.stacking.StackingConfiguration attribute) (mythos.energy.dna1.StackingConfiguration attribute) (mythos.energy.dna2.HydrogenBondingConfiguration attribute) (mythos.energy.dna2.StackingConfiguration attribute) (mythos.energy.na1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.na1.HydrogenBondingConfiguration attribute) (mythos.energy.rna2.stacking.StackingConfiguration attribute) (mythos.energy.rna2.StackingConfiguration attribute) pseq_constraints (mythos.energy.dna1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.dna1.HydrogenBondingConfiguration attribute) (mythos.energy.dna1.stacking.StackingConfiguration attribute) (mythos.energy.dna1.StackingConfiguration attribute) (mythos.energy.dna2.HydrogenBondingConfiguration attribute) (mythos.energy.dna2.StackingConfiguration attribute) (mythos.energy.na1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.na1.HydrogenBondingConfiguration attribute) (mythos.energy.rna2.stacking.StackingConfiguration attribute) (mythos.energy.rna2.StackingConfiguration attribute) pseq_weights() (mythos.energy.dna1.Stacking method) (mythos.energy.dna1.stacking.Stacking method) (mythos.energy.rna2.Stacking method) (mythos.energy.rna2.stacking.Stacking method) PyTree (in module mythos.utils.types)

Q

q_eff (mythos.energy.dna2.debye.DebyeConfiguration attribute) (mythos.energy.dna2.DebyeConfiguration attribute) q_to_back_base() (in module mythos.energy.utils) q_to_base_normal() (in module mythos.energy.utils) q_to_cross_prod() (in module mythos.energy.utils)

QualifiedComposedEnergyFunction (class in mythos.energy.base) quartets (mythos.observables.persistence_length.PersistenceLength attribute) (mythos.observables.pitch.PitchAngle attribute) (mythos.observables.rise.Rise attribute) (mythos.observables.stretch_torsion.TwistXY attribute) quaternions (mythos.input.trajectory.NucleotideState property)

R

r0_backbone (mythos.energy.dna1.fene.FeneConfiguration attribute) (mythos.energy.dna1.FeneConfiguration attribute) (mythos.energy.dna2.FeneConfiguration attribute) r0_cross (mythos.energy.dna1.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.dna1.CrossStackingConfiguration attribute) (mythos.energy.dna2.CrossStackingConfiguration attribute) (mythos.energy.rna2.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.rna2.CrossStackingConfiguration attribute) r_cut (mythos.energy.dna2.debye.DebyeConfiguration attribute) (mythos.energy.dna2.DebyeConfiguration attribute) r_cutoff (mythos.simulators.jax_md.NeighborList attribute) (mythos.simulators.jax_md.utils.NeighborList attribute) r_high (mythos.energy.dna2.debye.DebyeConfiguration attribute) (mythos.energy.dna2.DebyeConfiguration attribute) RawTrajectory (in module mythos.input.trajectory) RayOptimizer (class in mythos.optimization.optimization) read() (in module mythos.input.oxdna_input) read_energy() (in module mythos.simulators.oxdna.utils) read_last_hist() (in module mythos.simulators.oxdna.utils) read_mdp() (in module mythos.input.gromacs_input) read_output_trajectory() (in module mythos.simulators.oxdna.utils) read_params_from_topology() (in module mythos.input.gromacs_input) read_src_h() (in module mythos.simulators.oxdna.utils) read_ss_weights() (in module mythos.input.sequence_dependence) read_trajectory_mdanalysis() (in module mythos.simulators.gromacs.utils) remote_options_default (mythos.optimization.optimization.RayOptimizer attribute) replace() (mythos.input.gromacs_input.GromacsParamsParser method) replace_params_in_topology() (in module mythos.input.gromacs_input) REPLACEMENT_MAP (in module mythos.simulators.lammps.lammps_oxdna), [1] required_observables (mythos.optimization.objective.Objective attribute), [1] required_params (mythos.energy.configuration.BaseConfiguration attribute) (mythos.energy.dna1.bonded_excluded_volume.BondedExcludedVolumeConfiguration attribute) (mythos.energy.dna1.BondedExcludedVolumeConfiguration attribute) (mythos.energy.dna1.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.dna1.CoaxialStackingConfiguration attribute) (mythos.energy.dna1.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.dna1.CrossStackingConfiguration attribute) (mythos.energy.dna1.fene.FeneConfiguration attribute) (mythos.energy.dna1.FeneConfiguration attribute) (mythos.energy.dna1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.dna1.HydrogenBondingConfiguration attribute) (mythos.energy.dna1.stacking.StackingConfiguration attribute) (mythos.energy.dna1.StackingConfiguration attribute) (mythos.energy.dna1.unbonded_excluded_volume.UnbondedExcludedVolumeConfiguration attribute) (mythos.energy.dna1.UnbondedExcludedVolumeConfiguration attribute) (mythos.energy.dna2.BondedExcludedVolumeConfiguration attribute) (mythos.energy.dna2.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.dna2.CoaxialStackingConfiguration attribute) (mythos.energy.dna2.CrossStackingConfiguration attribute) (mythos.energy.dna2.debye.DebyeConfiguration attribute) (mythos.energy.dna2.DebyeConfiguration attribute) (mythos.energy.dna2.FeneConfiguration attribute) (mythos.energy.dna2.HydrogenBondingConfiguration attribute) (mythos.energy.dna2.StackingConfiguration attribute) (mythos.energy.dna2.UnbondedExcludedVolumeConfiguration attribute) (mythos.energy.na1.bonded_excluded_volume.BondedExcludedVolumeConfiguration attribute) (mythos.energy.na1.BondedExcludedVolumeConfiguration attribute) (mythos.energy.na1.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.na1.CoaxialStackingConfiguration attribute) (mythos.energy.na1.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.na1.CrossStackingConfiguration attribute) (mythos.energy.na1.debye.DebyeConfiguration attribute) (mythos.energy.na1.DebyeConfiguration attribute) (mythos.energy.na1.fene.FeneConfiguration attribute) (mythos.energy.na1.FeneConfiguration attribute) (mythos.energy.na1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.na1.HydrogenBondingConfiguration attribute) (mythos.energy.na1.stacking.StackingConfiguration attribute) (mythos.energy.na1.StackingConfiguration attribute) (mythos.energy.na1.unbonded_excluded_volume.UnbondedExcludedVolumeConfiguration attribute) (mythos.energy.na1.UnbondedExcludedVolumeConfiguration attribute) (mythos.energy.rna2.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.rna2.CrossStackingConfiguration attribute) (mythos.energy.rna2.stacking.StackingConfiguration attribute) (mythos.energy.rna2.StackingConfiguration attribute) residue_names (mythos.energy.martini.base.MartiniEnergyFunction attribute) (mythos.energy.martini.base.MartiniTopology attribute) return_observable (mythos.losses.observable_wrappers.ObservableLossFn attribute) reversed_couplings (mythos.energy.martini.base.MartiniEnergyConfiguration attribute) rigid_body_transform_fn (mythos.observables.base.BaseObservable attribute) Rise (class in mythos.observables.rise) RMSE (class in mythos.observables.rmse) rna (mythos.energy.na1.HybridNucleotide attribute) (mythos.energy.na1.nucleotide.HybridNucleotide attribute) RNA (mythos.input.topology.NucleotideType attribute) rna_a_coax_1 (mythos.energy.na1.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.na1.CoaxialStackingConfiguration attribute) rna_a_coax_3p (mythos.energy.na1.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.na1.CoaxialStackingConfiguration attribute) rna_a_coax_4 (mythos.energy.na1.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.na1.CoaxialStackingConfiguration attribute) rna_a_coax_4p (mythos.energy.na1.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.na1.CoaxialStackingConfiguration attribute) rna_a_coax_5 (mythos.energy.na1.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.na1.CoaxialStackingConfiguration attribute) rna_a_coax_6 (mythos.energy.na1.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.na1.CoaxialStackingConfiguration attribute) rna_a_cross_1 (mythos.energy.na1.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.na1.CrossStackingConfiguration attribute) rna_a_cross_2 (mythos.energy.na1.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.na1.CrossStackingConfiguration attribute) rna_a_cross_3 (mythos.energy.na1.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.na1.CrossStackingConfiguration attribute) rna_a_cross_7 (mythos.energy.na1.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.na1.CrossStackingConfiguration attribute) rna_a_cross_8 (mythos.energy.na1.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.na1.CrossStackingConfiguration attribute) rna_a_hb (mythos.energy.na1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.na1.HydrogenBondingConfiguration attribute) rna_a_hb_1 (mythos.energy.na1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.na1.HydrogenBondingConfiguration attribute) rna_a_hb_2 (mythos.energy.na1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.na1.HydrogenBondingConfiguration attribute) rna_a_hb_3 (mythos.energy.na1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.na1.HydrogenBondingConfiguration attribute) rna_a_hb_4 (mythos.energy.na1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.na1.HydrogenBondingConfiguration attribute) rna_a_hb_7 (mythos.energy.na1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.na1.HydrogenBondingConfiguration attribute) rna_a_hb_8 (mythos.energy.na1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.na1.HydrogenBondingConfiguration attribute) rna_a_stack (mythos.energy.na1.stacking.StackingConfiguration attribute) (mythos.energy.na1.StackingConfiguration attribute) rna_a_stack_1 (mythos.energy.na1.stacking.StackingConfiguration attribute) (mythos.energy.na1.StackingConfiguration attribute) rna_a_stack_10 (mythos.energy.na1.stacking.StackingConfiguration attribute) (mythos.energy.na1.StackingConfiguration attribute) rna_a_stack_2 (mythos.energy.na1.stacking.StackingConfiguration attribute) (mythos.energy.na1.StackingConfiguration attribute) rna_a_stack_5 (mythos.energy.na1.stacking.StackingConfiguration attribute) (mythos.energy.na1.StackingConfiguration attribute) rna_a_stack_6 (mythos.energy.na1.stacking.StackingConfiguration attribute) (mythos.energy.na1.StackingConfiguration attribute) rna_a_stack_9 (mythos.energy.na1.stacking.StackingConfiguration attribute) (mythos.energy.na1.StackingConfiguration attribute) RNA_ALPHA (in module mythos.utils.constants) rna_config (mythos.energy.na1.bonded_excluded_volume.BondedExcludedVolumeConfiguration attribute) (mythos.energy.na1.BondedExcludedVolumeConfiguration attribute) (mythos.energy.na1.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.na1.CoaxialStackingConfiguration attribute) (mythos.energy.na1.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.na1.CrossStackingConfiguration attribute) (mythos.energy.na1.debye.DebyeConfiguration attribute) (mythos.energy.na1.DebyeConfiguration attribute) (mythos.energy.na1.fene.FeneConfiguration attribute) (mythos.energy.na1.FeneConfiguration attribute) (mythos.energy.na1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.na1.HydrogenBondingConfiguration attribute) (mythos.energy.na1.stacking.StackingConfiguration attribute) (mythos.energy.na1.StackingConfiguration attribute) (mythos.energy.na1.unbonded_excluded_volume.UnbondedExcludedVolumeConfiguration attribute) (mythos.energy.na1.UnbondedExcludedVolumeConfiguration attribute) rna_cos_phi3_star_coax (mythos.energy.na1.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.na1.CoaxialStackingConfiguration attribute) rna_cos_phi4_star_coax (mythos.energy.na1.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.na1.CoaxialStackingConfiguration attribute) rna_delta_backbone (mythos.energy.na1.fene.FeneConfiguration attribute) (mythos.energy.na1.FeneConfiguration attribute) rna_delta_theta_star_coax_1 (mythos.energy.na1.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.na1.CoaxialStackingConfiguration attribute) rna_delta_theta_star_coax_4 (mythos.energy.na1.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.na1.CoaxialStackingConfiguration attribute) rna_delta_theta_star_coax_5 (mythos.energy.na1.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.na1.CoaxialStackingConfiguration attribute) rna_delta_theta_star_coax_6 (mythos.energy.na1.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.na1.CoaxialStackingConfiguration attribute) rna_delta_theta_star_cross_1 (mythos.energy.na1.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.na1.CrossStackingConfiguration attribute) rna_delta_theta_star_cross_2 (mythos.energy.na1.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.na1.CrossStackingConfiguration attribute) rna_delta_theta_star_cross_3 (mythos.energy.na1.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.na1.CrossStackingConfiguration attribute)

rna_delta_theta_star_cross_7 (mythos.energy.na1.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.na1.CrossStackingConfiguration attribute) rna_delta_theta_star_cross_8 (mythos.energy.na1.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.na1.CrossStackingConfiguration attribute) rna_delta_theta_star_hb_1 (mythos.energy.na1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.na1.HydrogenBondingConfiguration attribute) rna_delta_theta_star_hb_2 (mythos.energy.na1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.na1.HydrogenBondingConfiguration attribute) rna_delta_theta_star_hb_3 (mythos.energy.na1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.na1.HydrogenBondingConfiguration attribute) rna_delta_theta_star_hb_4 (mythos.energy.na1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.na1.HydrogenBondingConfiguration attribute) rna_delta_theta_star_hb_7 (mythos.energy.na1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.na1.HydrogenBondingConfiguration attribute) rna_delta_theta_star_hb_8 (mythos.energy.na1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.na1.HydrogenBondingConfiguration attribute) rna_delta_theta_star_stack_10 (mythos.energy.na1.stacking.StackingConfiguration attribute) (mythos.energy.na1.StackingConfiguration attribute) rna_delta_theta_star_stack_5 (mythos.energy.na1.stacking.StackingConfiguration attribute) (mythos.energy.na1.StackingConfiguration attribute) rna_delta_theta_star_stack_6 (mythos.energy.na1.stacking.StackingConfiguration attribute) (mythos.energy.na1.StackingConfiguration attribute) rna_delta_theta_star_stack_9 (mythos.energy.na1.stacking.StackingConfiguration attribute) (mythos.energy.na1.StackingConfiguration attribute) rna_dr0_coax (mythos.energy.na1.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.na1.CoaxialStackingConfiguration attribute) rna_dr0_hb (mythos.energy.na1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.na1.HydrogenBondingConfiguration attribute) rna_dr0_stack (mythos.energy.na1.stacking.StackingConfiguration attribute) (mythos.energy.na1.StackingConfiguration attribute) rna_dr_c_coax (mythos.energy.na1.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.na1.CoaxialStackingConfiguration attribute) rna_dr_c_cross (mythos.energy.na1.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.na1.CrossStackingConfiguration attribute) rna_dr_c_hb (mythos.energy.na1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.na1.HydrogenBondingConfiguration attribute) rna_dr_c_stack (mythos.energy.na1.stacking.StackingConfiguration attribute) (mythos.energy.na1.StackingConfiguration attribute) rna_dr_high_coax (mythos.energy.na1.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.na1.CoaxialStackingConfiguration attribute) rna_dr_high_cross (mythos.energy.na1.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.na1.CrossStackingConfiguration attribute) rna_dr_high_hb (mythos.energy.na1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.na1.HydrogenBondingConfiguration attribute) rna_dr_high_stack (mythos.energy.na1.stacking.StackingConfiguration attribute) (mythos.energy.na1.StackingConfiguration attribute) rna_dr_low_coax (mythos.energy.na1.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.na1.CoaxialStackingConfiguration attribute) rna_dr_low_cross (mythos.energy.na1.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.na1.CrossStackingConfiguration attribute) rna_dr_low_hb (mythos.energy.na1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.na1.HydrogenBondingConfiguration attribute) rna_dr_low_stack (mythos.energy.na1.stacking.StackingConfiguration attribute) (mythos.energy.na1.StackingConfiguration attribute) rna_dr_star_back_base (mythos.energy.na1.bonded_excluded_volume.BondedExcludedVolumeConfiguration attribute) (mythos.energy.na1.BondedExcludedVolumeConfiguration attribute) (mythos.energy.na1.unbonded_excluded_volume.UnbondedExcludedVolumeConfiguration attribute) (mythos.energy.na1.UnbondedExcludedVolumeConfiguration attribute) rna_dr_star_backbone (mythos.energy.na1.unbonded_excluded_volume.UnbondedExcludedVolumeConfiguration attribute) (mythos.energy.na1.UnbondedExcludedVolumeConfiguration attribute) rna_dr_star_base (mythos.energy.na1.bonded_excluded_volume.BondedExcludedVolumeConfiguration attribute) (mythos.energy.na1.BondedExcludedVolumeConfiguration attribute) (mythos.energy.na1.unbonded_excluded_volume.UnbondedExcludedVolumeConfiguration attribute) (mythos.energy.na1.UnbondedExcludedVolumeConfiguration attribute) rna_dr_star_base_back (mythos.energy.na1.bonded_excluded_volume.BondedExcludedVolumeConfiguration attribute) (mythos.energy.na1.BondedExcludedVolumeConfiguration attribute) (mythos.energy.na1.unbonded_excluded_volume.UnbondedExcludedVolumeConfiguration attribute) (mythos.energy.na1.UnbondedExcludedVolumeConfiguration attribute) rna_eps_backbone (mythos.energy.na1.fene.FeneConfiguration attribute) (mythos.energy.na1.FeneConfiguration attribute) rna_eps_exc (mythos.energy.na1.bonded_excluded_volume.BondedExcludedVolumeConfiguration attribute) (mythos.energy.na1.BondedExcludedVolumeConfiguration attribute) (mythos.energy.na1.unbonded_excluded_volume.UnbondedExcludedVolumeConfiguration attribute) (mythos.energy.na1.UnbondedExcludedVolumeConfiguration attribute) rna_eps_hb (mythos.energy.na1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.na1.HydrogenBondingConfiguration attribute) rna_eps_stack_base (mythos.energy.na1.stacking.StackingConfiguration attribute) (mythos.energy.na1.StackingConfiguration attribute) rna_eps_stack_kt_coeff (mythos.energy.na1.stacking.StackingConfiguration attribute) (mythos.energy.na1.StackingConfiguration attribute) rna_finf (mythos.energy.na1.fene.FeneConfiguration attribute) (mythos.energy.na1.FeneConfiguration attribute) rna_fmax (mythos.energy.na1.fene.FeneConfiguration attribute) (mythos.energy.na1.FeneConfiguration attribute) rna_k_coax (mythos.energy.na1.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.na1.CoaxialStackingConfiguration attribute) rna_k_cross (mythos.energy.na1.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.na1.CrossStackingConfiguration attribute) rna_lambda_factor (mythos.energy.na1.debye.DebyeConfiguration attribute) (mythos.energy.na1.DebyeConfiguration attribute) rna_neg_cos_phi1_star_stack (mythos.energy.na1.stacking.StackingConfiguration attribute) (mythos.energy.na1.StackingConfiguration attribute) rna_neg_cos_phi2_star_stack (mythos.energy.na1.stacking.StackingConfiguration attribute) (mythos.energy.na1.StackingConfiguration attribute) rna_prefactor_coeff (mythos.energy.na1.debye.DebyeConfiguration attribute) (mythos.energy.na1.DebyeConfiguration attribute) rna_q_eff (mythos.energy.na1.debye.DebyeConfiguration attribute) (mythos.energy.na1.DebyeConfiguration attribute) rna_r0_backbone (mythos.energy.na1.fene.FeneConfiguration attribute) (mythos.energy.na1.FeneConfiguration attribute) rna_r0_cross (mythos.energy.na1.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.na1.CrossStackingConfiguration attribute) rna_sigma_back_base (mythos.energy.na1.bonded_excluded_volume.BondedExcludedVolumeConfiguration attribute) (mythos.energy.na1.BondedExcludedVolumeConfiguration attribute) (mythos.energy.na1.unbonded_excluded_volume.UnbondedExcludedVolumeConfiguration attribute) (mythos.energy.na1.UnbondedExcludedVolumeConfiguration attribute) rna_sigma_backbone (mythos.energy.na1.unbonded_excluded_volume.UnbondedExcludedVolumeConfiguration attribute) (mythos.energy.na1.UnbondedExcludedVolumeConfiguration attribute) rna_sigma_base (mythos.energy.na1.bonded_excluded_volume.BondedExcludedVolumeConfiguration attribute) (mythos.energy.na1.BondedExcludedVolumeConfiguration attribute) (mythos.energy.na1.unbonded_excluded_volume.UnbondedExcludedVolumeConfiguration attribute) (mythos.energy.na1.UnbondedExcludedVolumeConfiguration attribute) rna_sigma_base_back (mythos.energy.na1.bonded_excluded_volume.BondedExcludedVolumeConfiguration attribute) (mythos.energy.na1.BondedExcludedVolumeConfiguration attribute) (mythos.energy.na1.unbonded_excluded_volume.UnbondedExcludedVolumeConfiguration attribute) (mythos.energy.na1.UnbondedExcludedVolumeConfiguration attribute) rna_ss_hb_weights (mythos.energy.na1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.na1.HydrogenBondingConfiguration attribute) rna_ss_stack_weights (mythos.energy.na1.stacking.StackingConfiguration attribute) (mythos.energy.na1.StackingConfiguration attribute) rna_theta0_coax_1 (mythos.energy.na1.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.na1.CoaxialStackingConfiguration attribute) rna_theta0_coax_4 (mythos.energy.na1.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.na1.CoaxialStackingConfiguration attribute) rna_theta0_coax_5 (mythos.energy.na1.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.na1.CoaxialStackingConfiguration attribute) rna_theta0_coax_6 (mythos.energy.na1.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.na1.CoaxialStackingConfiguration attribute) rna_theta0_cross_1 (mythos.energy.na1.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.na1.CrossStackingConfiguration attribute) rna_theta0_cross_2 (mythos.energy.na1.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.na1.CrossStackingConfiguration attribute) rna_theta0_cross_3 (mythos.energy.na1.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.na1.CrossStackingConfiguration attribute) rna_theta0_cross_7 (mythos.energy.na1.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.na1.CrossStackingConfiguration attribute) rna_theta0_cross_8 (mythos.energy.na1.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.na1.CrossStackingConfiguration attribute) rna_theta0_hb_1 (mythos.energy.na1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.na1.HydrogenBondingConfiguration attribute) rna_theta0_hb_2 (mythos.energy.na1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.na1.HydrogenBondingConfiguration attribute) rna_theta0_hb_3 (mythos.energy.na1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.na1.HydrogenBondingConfiguration attribute) rna_theta0_hb_4 (mythos.energy.na1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.na1.HydrogenBondingConfiguration attribute) rna_theta0_hb_7 (mythos.energy.na1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.na1.HydrogenBondingConfiguration attribute) rna_theta0_hb_8 (mythos.energy.na1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.na1.HydrogenBondingConfiguration attribute) rna_theta0_stack_10 (mythos.energy.na1.stacking.StackingConfiguration attribute) (mythos.energy.na1.StackingConfiguration attribute) rna_theta0_stack_5 (mythos.energy.na1.stacking.StackingConfiguration attribute) (mythos.energy.na1.StackingConfiguration attribute) rna_theta0_stack_6 (mythos.energy.na1.stacking.StackingConfiguration attribute) (mythos.energy.na1.StackingConfiguration attribute) rna_theta0_stack_9 (mythos.energy.na1.stacking.StackingConfiguration attribute) (mythos.energy.na1.StackingConfiguration attribute) RootMeanSquaredError (class in mythos.losses.observable_wrappers) run() (mythos.simulators.base.InputDirSimulator method) (mythos.simulators.base.Simulator method) run_command() (in module mythos.utils.helpers) run_simulation() (mythos.simulators.base.InputDirSimulator method) (mythos.simulators.gromacs.gromacs.GromacsSimulator method) (mythos.simulators.gromacs.GromacsSimulator method) (mythos.simulators.lammps.lammps_oxdna.LAMMPSoxDNASimulator method) (mythos.simulators.oxdna.oxdna.oxDNASimulator method) (mythos.simulators.oxdna.oxdna.oxDNAUmbrellaSampler method) (mythos.simulators.oxdna.oxDNASimulator method) (mythos.simulators.oxdna.oxDNAUmbrellaSampler method) RUNNING (mythos.ui.loggers.logger.Status attribute)

S

salt_conc (mythos.energy.dna2.debye.DebyeConfiguration attribute) (mythos.energy.dna2.DebyeConfiguration attribute) (mythos.energy.na1.debye.DebyeConfiguration attribute) (mythos.energy.na1.DebyeConfiguration attribute) save_pytree() (in module mythos.input.tree) Scalar (in module mythos.utils.types) scatter_f (in module mythos.ui.loggers.jupyter) scheduler_hints (mythos.optimization.objective.Objective attribute) (mythos.utils.scheduler.SchedulerUnit attribute) SchedulerHints (class in mythos.utils.scheduler) SchedulerUnit (class in mythos.utils.scheduler) seq (mythos.energy.base.BaseEnergyFunction attribute) (mythos.input.topology.Topology attribute) (mythos.simulators.jax_md.StaticSimulatorParams attribute) (mythos.simulators.jax_md.utils.StaticSimulatorParams attribute) Sequence (in module mythos.utils.types) SequenceConstraints (class in mythos.input.sequence_constraints) set_objective_complete() (mythos.ui.loggers.logger.Logger method) (mythos.ui.loggers.multilogger.MultiLogger method) set_objective_error() (mythos.ui.loggers.logger.Logger method) (mythos.ui.loggers.multilogger.MultiLogger method) set_objective_running() (mythos.ui.loggers.logger.Logger method) (mythos.ui.loggers.multilogger.MultiLogger method) set_objective_started() (mythos.ui.loggers.logger.Logger method) (mythos.ui.loggers.multilogger.MultiLogger method) set_observable_complete() (mythos.ui.loggers.logger.Logger method) (mythos.ui.loggers.multilogger.MultiLogger method) set_observable_error() (mythos.ui.loggers.logger.Logger method) (mythos.ui.loggers.multilogger.MultiLogger method) set_observable_running() (mythos.ui.loggers.logger.Logger method) (mythos.ui.loggers.multilogger.MultiLogger method) set_observable_started() (mythos.ui.loggers.logger.Logger method) (mythos.ui.loggers.multilogger.MultiLogger method) set_simulator_complete() (mythos.ui.loggers.logger.Logger method) (mythos.ui.loggers.multilogger.MultiLogger method) set_simulator_error() (mythos.ui.loggers.logger.Logger method) (mythos.ui.loggers.multilogger.MultiLogger method) set_simulator_running() (mythos.ui.loggers.logger.Logger method) (mythos.ui.loggers.multilogger.MultiLogger method) set_simulator_started() (mythos.ui.loggers.logger.Logger method) (mythos.ui.loggers.multilogger.MultiLogger method) setup_figure_layout() (in module mythos.ui.loggers.jupyter) show() (mythos.ui.loggers.jupyter.JupyterLogger method) (mythos.ui.loggers.jupyter.PlotlyLogger method) sigma_back_base (mythos.energy.dna1.bonded_excluded_volume.BondedExcludedVolumeConfiguration attribute) (mythos.energy.dna1.BondedExcludedVolumeConfiguration attribute) (mythos.energy.dna1.unbonded_excluded_volume.UnbondedExcludedVolumeConfiguration attribute) (mythos.energy.dna1.UnbondedExcludedVolumeConfiguration attribute) (mythos.energy.dna2.BondedExcludedVolumeConfiguration attribute) (mythos.energy.dna2.UnbondedExcludedVolumeConfiguration attribute) sigma_backbone (mythos.energy.dna1.unbonded_excluded_volume.UnbondedExcludedVolumeConfiguration attribute) (mythos.energy.dna1.UnbondedExcludedVolumeConfiguration attribute) (mythos.energy.dna2.UnbondedExcludedVolumeConfiguration attribute) sigma_base (mythos.energy.dna1.bonded_excluded_volume.BondedExcludedVolumeConfiguration attribute) (mythos.energy.dna1.BondedExcludedVolumeConfiguration attribute) (mythos.energy.dna1.unbonded_excluded_volume.UnbondedExcludedVolumeConfiguration attribute) (mythos.energy.dna1.UnbondedExcludedVolumeConfiguration attribute) (mythos.energy.dna2.BondedExcludedVolumeConfiguration attribute) (mythos.energy.dna2.UnbondedExcludedVolumeConfiguration attribute) sigma_base_back (mythos.energy.dna1.bonded_excluded_volume.BondedExcludedVolumeConfiguration attribute) (mythos.energy.dna1.BondedExcludedVolumeConfiguration attribute) (mythos.energy.dna1.unbonded_excluded_volume.UnbondedExcludedVolumeConfiguration attribute) (mythos.energy.dna1.UnbondedExcludedVolumeConfiguration attribute) (mythos.energy.dna2.BondedExcludedVolumeConfiguration attribute) (mythos.energy.dna2.UnbondedExcludedVolumeConfiguration attribute) sim_btns (mythos.ui.loggers.jupyter.JupyterLogger attribute) sim_init_fn (mythos.simulators.jax_md.StaticSimulatorParams property) (mythos.simulators.jax_md.utils.StaticSimulatorParams property) SIM_STATE (in module mythos.simulators.jax_md.jaxmd) sim_temperature (mythos.observables.melting_temp.MeltingTemp attribute) SimpleOptimizer (class in mythos.optimization.optimization) simulation_steps (mythos.simulators.gromacs.gromacs.GromacsSimulator attribute) (mythos.simulators.gromacs.GromacsSimulator attribute) SimulationState (class in mythos.simulators.jax_md) (class in mythos.simulators.jax_md.utils) Simulator (class in mythos.simulators.base) simulator (mythos.optimization.optimization.SimpleOptimizer attribute) SIMULATOR (mythos.ui.loggers.logger.StatusKind attribute) simulator_init (mythos.simulators.jax_md.jaxmd.JaxMDSimulator attribute) (mythos.simulators.jax_md.JaxMDSimulator attribute) simulator_params (mythos.simulators.jax_md.jaxmd.JaxMDSimulator attribute) (mythos.simulators.jax_md.JaxMDSimulator attribute) SimulatorActorOutput (in module mythos.utils.types) SimulatorOutput (class in mythos.simulators.base) simulators (mythos.optimization.optimization.RayOptimizer attribute) SimulatorTrajectory (class in mythos.simulators.io)

single_angle_xy() (in module mythos.observables.stretch_torsion) single_diameter() (in module mythos.observables.diameter) single_diameter_mapped (in module mythos.observables.diameter) single_extension_z() (in module mythos.observables.stretch_torsion) single_pitch_angle() (in module mythos.observables.pitch) single_pitch_angle_mapped (in module mythos.observables.pitch) single_propeller_twist_rad() (in module mythos.observables.propeller) single_rise() (in module mythos.observables.rise) single_rise_mapped (in module mythos.observables.rise) single_rmse() (in module mythos.observables.rmse) skip_ends (mythos.observables.persistence_length.PersistenceLength attribute) slice() (mythos.input.trajectory.Trajectory method) (mythos.simulators.io.SimulatorTrajectory method) smooth_abs() (in module mythos.utils.math) smoothing_coeff (mythos.energy.dna2.debye.DebyeConfiguration attribute) (mythos.energy.dna2.DebyeConfiguration attribute) source_path (mythos.simulators.oxdna.oxdna.oxDNASimulator attribute) (mythos.simulators.oxdna.oxDNASimulator attribute) space (mythos.simulators.jax_md.jaxmd.JaxMDSimulator attribute) (mythos.simulators.jax_md.JaxMDSimulator attribute) split_and_stack() (in module mythos.simulators.jax_md.utils) SquaredError (class in mythos.losses.observable_wrappers) ss_hb_weights (mythos.energy.dna1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.dna1.HydrogenBondingConfiguration attribute) (mythos.energy.dna2.HydrogenBondingConfiguration attribute) ss_stack_weights (mythos.energy.dna1.stacking.StackingConfiguration attribute) (mythos.energy.dna1.StackingConfiguration attribute) (mythos.energy.dna2.StackingConfiguration attribute) (mythos.energy.rna2.stacking.StackingConfiguration attribute) (mythos.energy.rna2.StackingConfiguration attribute) stack3_sites (mythos.energy.rna2.Nucleotide attribute) (mythos.energy.rna2.nucleotide.Nucleotide attribute) stack5_sites (mythos.energy.rna2.Nucleotide attribute) (mythos.energy.rna2.nucleotide.Nucleotide attribute) stack_sites (mythos.energy.base.BaseNucleotide attribute) (mythos.energy.dna1.Nucleotide attribute) (mythos.energy.dna1.nucleotide.Nucleotide attribute) (mythos.energy.dna2.Nucleotide attribute) (mythos.energy.dna2.nucleotide.Nucleotide attribute) (mythos.energy.rna2.Nucleotide attribute) (mythos.energy.rna2.nucleotide.Nucleotide attribute) STACK_WEIGHTS_SA (in module mythos.energy.dna1.stacking) Stacking (class in mythos.energy.dna1) (class in mythos.energy.dna1.stacking) (class in mythos.energy.dna2) (class in mythos.energy.dna2.stacking) (class in mythos.energy.na1) (class in mythos.energy.na1.stacking) (class in mythos.energy.rna2) (class in mythos.energy.rna2.stacking) stacking() (in module mythos.energy.dna1.interactions) (in module mythos.energy.rna2.interactions) StackingConfiguration (class in mythos.energy.dna1) (class in mythos.energy.dna1.stacking) (class in mythos.energy.dna2) (class in mythos.energy.na1) (class in mythos.energy.na1.stacking) (class in mythos.energy.rna2) (class in mythos.energy.rna2.stacking) STARTED (mythos.ui.loggers.logger.Status attribute) state (mythos.optimization.objective.ObjectiveOutput attribute), [1] (mythos.optimization.optimization.OptimizerOutput attribute), [1] (mythos.optimization.optimization.OptimizerState attribute) (mythos.simulators.base.SimulatorOutput attribute) state_rigid_bodies (mythos.input.trajectory.Trajectory property) state_rigid_body (mythos.input.trajectory.Trajectory property) states (mythos.input.trajectory.Trajectory attribute) StaticSimulatorParams (class in mythos.simulators.jax_md) (class in mythos.simulators.jax_md.utils) Status (class in mythos.ui.loggers.logger) STATUS_STYLE (mythos.ui.loggers.jupyter.JupyterLogger attribute) StatusKind (class in mythos.ui.loggers.logger) step() (mythos.optimization.optimization.Optimizer method) (mythos.optimization.optimization.RayOptimizer method) (mythos.optimization.optimization.SimpleOptimizer method) step_fn (mythos.simulators.jax_md.StaticSimulatorParams property) (mythos.simulators.jax_md.utils.StaticSimulatorParams property) strand_counts (mythos.input.topology.Topology attribute) strand_lengths (mythos.input.trajectory.Trajectory attribute) stretch() (in module mythos.observables.stretch_torsion) stretch_torsion() (in module mythos.observables.stretch_torsion) STRING (mythos.utils.types.oxDNAModelHType attribute) structure_file (mythos.simulators.gromacs.gromacs.GromacsSimulator attribute) (mythos.simulators.gromacs.GromacsSimulator attribute) svd_align() (in module mythos.observables.rmse) SYMPY_EVAL_N (in module mythos.input.toml) (in module mythos.simulators.oxdna.utils)

T

tail_file() (in module mythos.utils.helpers) target_state (mythos.observables.rmse.RMSE attribute) TARGETS (in module mythos.observables.diameter) (in module mythos.observables.melting_temp) (in module mythos.observables.persistence_length) (in module mythos.observables.pitch) (in module mythos.observables.propeller) (in module mythos.observables.rise) temperature_range (mythos.observables.melting_temp.MeltingTemp attribute) theta0_coax_1 (mythos.energy.dna1.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.dna1.CoaxialStackingConfiguration attribute) (mythos.energy.dna2.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.dna2.CoaxialStackingConfiguration attribute) theta0_coax_4 (mythos.energy.dna1.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.dna1.CoaxialStackingConfiguration attribute) (mythos.energy.dna2.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.dna2.CoaxialStackingConfiguration attribute) theta0_coax_5 (mythos.energy.dna1.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.dna1.CoaxialStackingConfiguration attribute) (mythos.energy.dna2.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.dna2.CoaxialStackingConfiguration attribute) theta0_coax_6 (mythos.energy.dna1.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.dna1.CoaxialStackingConfiguration attribute) (mythos.energy.dna2.coaxial_stacking.CoaxialStackingConfiguration attribute) (mythos.energy.dna2.CoaxialStackingConfiguration attribute) theta0_cross_1 (mythos.energy.dna1.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.dna1.CrossStackingConfiguration attribute) (mythos.energy.dna2.CrossStackingConfiguration attribute) (mythos.energy.rna2.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.rna2.CrossStackingConfiguration attribute) theta0_cross_2 (mythos.energy.dna1.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.dna1.CrossStackingConfiguration attribute) (mythos.energy.dna2.CrossStackingConfiguration attribute) (mythos.energy.rna2.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.rna2.CrossStackingConfiguration attribute) theta0_cross_3 (mythos.energy.dna1.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.dna1.CrossStackingConfiguration attribute) (mythos.energy.dna2.CrossStackingConfiguration attribute) (mythos.energy.rna2.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.rna2.CrossStackingConfiguration attribute) theta0_cross_4 (mythos.energy.dna1.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.dna1.CrossStackingConfiguration attribute) (mythos.energy.dna2.CrossStackingConfiguration attribute) theta0_cross_7 (mythos.energy.dna1.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.dna1.CrossStackingConfiguration attribute) (mythos.energy.dna2.CrossStackingConfiguration attribute) (mythos.energy.rna2.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.rna2.CrossStackingConfiguration attribute) theta0_cross_8 (mythos.energy.dna1.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.dna1.CrossStackingConfiguration attribute) (mythos.energy.dna2.CrossStackingConfiguration attribute) (mythos.energy.rna2.cross_stacking.CrossStackingConfiguration attribute) (mythos.energy.rna2.CrossStackingConfiguration attribute) theta0_hb_1 (mythos.energy.dna1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.dna1.HydrogenBondingConfiguration attribute) (mythos.energy.dna2.HydrogenBondingConfiguration attribute) theta0_hb_2 (mythos.energy.dna1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.dna1.HydrogenBondingConfiguration attribute) (mythos.energy.dna2.HydrogenBondingConfiguration attribute)

theta0_hb_3 (mythos.energy.dna1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.dna1.HydrogenBondingConfiguration attribute) (mythos.energy.dna2.HydrogenBondingConfiguration attribute) theta0_hb_4 (mythos.energy.dna1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.dna1.HydrogenBondingConfiguration attribute) (mythos.energy.dna2.HydrogenBondingConfiguration attribute) theta0_hb_7 (mythos.energy.dna1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.dna1.HydrogenBondingConfiguration attribute) (mythos.energy.dna2.HydrogenBondingConfiguration attribute) theta0_hb_8 (mythos.energy.dna1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (mythos.energy.dna1.HydrogenBondingConfiguration attribute) (mythos.energy.dna2.HydrogenBondingConfiguration attribute) theta0_stack_10 (mythos.energy.rna2.stacking.StackingConfiguration attribute) (mythos.energy.rna2.StackingConfiguration attribute) theta0_stack_4 (mythos.energy.dna1.stacking.StackingConfiguration attribute) (mythos.energy.dna1.StackingConfiguration attribute) (mythos.energy.dna2.StackingConfiguration attribute) theta0_stack_5 (mythos.energy.dna1.stacking.StackingConfiguration attribute) (mythos.energy.dna1.StackingConfiguration attribute) (mythos.energy.dna2.StackingConfiguration attribute) (mythos.energy.rna2.stacking.StackingConfiguration attribute) (mythos.energy.rna2.StackingConfiguration attribute) theta0_stack_6 (mythos.energy.dna1.stacking.StackingConfiguration attribute) (mythos.energy.dna1.StackingConfiguration attribute) (mythos.energy.dna2.StackingConfiguration attribute) (mythos.energy.rna2.stacking.StackingConfiguration attribute) (mythos.energy.rna2.StackingConfiguration attribute) theta0_stack_9 (mythos.energy.rna2.stacking.StackingConfiguration attribute) (mythos.energy.rna2.StackingConfiguration attribute) thickness_sel (mythos.observables.membrane_thickness.MembraneThickness attribute) THREE_DIMENSIONS (in module mythos.observables.rmse) times (mythos.input.trajectory.Trajectory attribute) to_dict() (mythos.utils.scheduler.SchedulerHints method) to_dictionary() (mythos.energy.configuration.BaseConfiguration method) to_file() (mythos.input.trajectory.Trajectory method) (mythos.simulators.io.SimulatorTrajectory method) to_rigid_body() (mythos.input.trajectory.NucleotideState method) Topology (class in mythos.input.topology) topology (mythos.energy.base.BaseEnergyFunction attribute) (mythos.observables.area_per_lipid.AreaPerLipid attribute) (mythos.observables.membrane_thickness.MembraneThickness attribute) (mythos.simulators.jax_md.NeighborList attribute) (mythos.simulators.jax_md.utils.NeighborList attribute) topology_file (mythos.simulators.gromacs.gromacs.GromacsSimulator attribute) (mythos.simulators.gromacs.GromacsSimulator attribute) torsion() (in module mythos.observables.stretch_torsion) Trajectory (class in mythos.input.trajectory) TRAJECTORY_ENERGIES_SHAPE (in module mythos.input.trajectory) TRAJECTORY_TIMES_DIMS (in module mythos.input.trajectory) transform_fn (mythos.energy.base.BaseEnergyFunction attribute) tree_concatenate() (in module mythos.utils.helpers) tree_stack() (in module mythos.utils.helpers) triplet_angle() (in module mythos.energy.martini.m2.angle) truncate (mythos.observables.persistence_length.PersistenceLength attribute) tsnow() (in module mythos.ui.loggers.disk) TwistXY (class in mythos.observables.stretch_torsion) TWO_DIMENSIONS (in module mythos.utils.constants)

U

UmbrellaEnergyInfo (class in mythos.simulators.oxdna) (class in mythos.simulators.oxdna.oxdna) unbonded_nbrs (mythos.simulators.jax_md.NoNeighborList attribute) (mythos.simulators.jax_md.utils.NoNeighborList attribute) unbonded_neighbors (mythos.energy.base.BaseEnergyFunction attribute) (mythos.energy.martini.base.MartiniTopology attribute), [1] (mythos.input.topology.Topology attribute) UnbondedExcludedVolume (class in mythos.energy.dna1) (class in mythos.energy.dna1.unbonded_excluded_volume) (class in mythos.energy.dna2) (class in mythos.energy.na1) (class in mythos.energy.na1.unbonded_excluded_volume) UnbondedExcludedVolumeConfiguration (class in mythos.energy.dna1) (class in mythos.energy.dna1.unbonded_excluded_volume) (class in mythos.energy.dna2) (class in mythos.energy.na1) (class in mythos.energy.na1.unbonded_excluded_volume) universe_from_trajectory() (in module mythos.observables.martini_utils) unpaired (mythos.input.sequence_constraints.SequenceConstraints attribute) UNSPECIFIED (mythos.input.topology.NucleotideType attribute) update() (mythos.simulators.jax_md.NeighborList method) (mythos.simulators.jax_md.NoNeighborList method) (mythos.simulators.jax_md.utils.NeighborHelper method) (mythos.simulators.jax_md.utils.NeighborList method) (mythos.simulators.jax_md.utils.NoNeighborList method)

update_mdp_params() (in module mythos.input.gromacs_input) update_objective_status() (mythos.ui.loggers.logger.Logger method) (mythos.ui.loggers.multilogger.MultiLogger method) update_observable_status() (mythos.ui.loggers.logger.Logger method) (mythos.ui.loggers.multilogger.MultiLogger method) update_params() (in module mythos.simulators.oxdna.utils) update_simulator_status() (mythos.ui.loggers.logger.Logger method) (mythos.ui.loggers.multilogger.MultiLogger method) update_status() (mythos.ui.loggers.aim.AimLogger method) (mythos.ui.loggers.console.ConsoleLogger method) (mythos.ui.loggers.disk.FileLogger method) (mythos.ui.loggers.disk.PerMetricFileLogger method) (mythos.ui.loggers.jupyter.JupyterLogger method) (mythos.ui.loggers.jupyter.PlotlyLogger method) (mythos.ui.loggers.logger.Logger method) (mythos.ui.loggers.logger.NullLogger method) (mythos.ui.loggers.multilogger.MultiLogger method) use_G96 (mythos.energy.martini.m2.Angle attribute) (mythos.energy.martini.m2.angle.Angle attribute)

V

v_fene() (in module mythos.energy.potentials) v_fene_smooth() (in module mythos.energy.dna1.interactions) v_harmonic() (in module mythos.energy.potentials) v_lj() (in module mythos.energy.potentials) v_mod() (in module mythos.energy.potentials) v_morse() (in module mythos.energy.potentials) v_smooth() (in module mythos.energy.potentials) VALID_NEIGHBOR_SECOND_DIM (in module mythos.input.topology)

validate_box_size() (in module mythos.input.trajectory) variables (mythos.simulators.lammps.lammps_oxdna.LAMMPSoxDNASimulator attribute) Vector2D (in module mythos.utils.types) Vector3D (in module mythos.utils.types) Vector4D (in module mythos.utils.types) vector_autocorrelate() (in module mythos.observables.persistence_length) velocity (mythos.input.trajectory.NucleotideState property) version (in module mythos._version) version_tuple (in module mythos._version)

W

WARN_CLASSIC_UNSPECIFIED_NT_TYPE (in module mythos.input.topology) WARN_DEPENDENT_PARAMS_NOT_INITIALIZED (in module mythos.energy.configuration) WARN_INIT_PARAMS_NOT_IMPLEMENTED (in module mythos.energy.configuration) WARN_INVALID_NCOLS_NROWS (in module mythos.ui.loggers.jupyter) WARN_NEW_UNSPECIFIED_NT_TYPE (in module mythos.input.topology) weight() (mythos.energy.dna1.hydrogen_bonding.HydrogenBonding method) (mythos.energy.dna1.HydrogenBonding method) (mythos.energy.dna2.HydrogenBonding method) weights (mythos.energy.base.ComposedEnergyFunction attribute) with_cached_build() (mythos.simulators.oxdna.oxdna.oxDNASimulator method) (mythos.simulators.oxdna.oxDNASimulator method) with_noopt() (mythos.energy.base.BaseEnergyFunction method) (mythos.energy.base.ComposedEnergyFunction method) (mythos.energy.base.EnergyFunction method)

with_params() (mythos.energy.base.BaseEnergyFunction method) (mythos.energy.base.ComposedEnergyFunction method) (mythos.energy.base.EnergyFunction method) with_props() (mythos.energy.base.BaseEnergyFunction method) (mythos.energy.base.ComposedEnergyFunction method) (mythos.energy.base.EnergyFunction method) with_state_metadata() (mythos.simulators.io.SimulatorTrajectory method) without_terms() (mythos.energy.base.ComposedEnergyFunction method) write() (in module mythos.input.oxdna_input) write_mdp() (in module mythos.input.gromacs_input) write_mdp_to() (in module mythos.input.gromacs_input) write_src_h() (in module mythos.simulators.oxdna.utils) write_to() (in module mythos.input.oxdna_input)