Index

_

__add__() (jax_dna.energy.base.BaseEnergyFunction method) (jax_dna.energy.base.ComposedEnergyFunction method) (jax_dna.simulators.io.SimulatorTrajectory method) __call__() (jax_dna.energy.base.BaseEnergyFunction method) (jax_dna.energy.base.ComposedEnergyFunction method) (jax_dna.energy.dna1.bonded_excluded_volume.BondedExcludedVolume method) (jax_dna.energy.dna1.BondedExcludedVolume method) (jax_dna.energy.dna1.coaxial_stacking.CoaxialStacking method) (jax_dna.energy.dna1.CoaxialStacking method) (jax_dna.energy.dna1.cross_stacking.CrossStacking method) (jax_dna.energy.dna1.CrossStacking method) (jax_dna.energy.dna1.expected_hydrogen_bonding.ExpectedHydrogenBonding method) (jax_dna.energy.dna1.expected_stacking.ExpectedStacking method) (jax_dna.energy.dna1.ExpectedHydrogenBonding method) (jax_dna.energy.dna1.ExpectedStacking method) (jax_dna.energy.dna1.Fene method) (jax_dna.energy.dna1.fene.Fene method) (jax_dna.energy.dna1.hydrogen_bonding.HydrogenBonding method) (jax_dna.energy.dna1.HydrogenBonding method) (jax_dna.energy.dna1.Stacking method) (jax_dna.energy.dna1.stacking.Stacking method) (jax_dna.energy.dna1.unbonded_excluded_volume.UnbondedExcludedVolume method) (jax_dna.energy.dna1.UnbondedExcludedVolume method) (jax_dna.energy.dna2.BondedExcludedVolume method) (jax_dna.energy.dna2.coaxial_stacking.CoaxialStacking method) (jax_dna.energy.dna2.CoaxialStacking method) (jax_dna.energy.dna2.CrossStacking method) (jax_dna.energy.dna2.Debye method) (jax_dna.energy.dna2.debye.Debye method) (jax_dna.energy.dna2.Fene method) (jax_dna.energy.dna2.HydrogenBonding method) (jax_dna.energy.dna2.Stacking method) (jax_dna.energy.dna2.stacking.Stacking method) (jax_dna.energy.dna2.UnbondedExcludedVolume method) (jax_dna.energy.na1.bonded_excluded_volume.BondedExcludedVolume method) (jax_dna.energy.na1.BondedExcludedVolume method) (jax_dna.energy.na1.coaxial_stacking.CoaxialStacking method) (jax_dna.energy.na1.CoaxialStacking method) (jax_dna.energy.na1.cross_stacking.CrossStacking method) (jax_dna.energy.na1.CrossStacking method) (jax_dna.energy.na1.Debye method) (jax_dna.energy.na1.debye.Debye method) (jax_dna.energy.na1.Fene method) (jax_dna.energy.na1.fene.Fene method) (jax_dna.energy.na1.hydrogen_bonding.HydrogenBonding method) (jax_dna.energy.na1.HydrogenBonding method) (jax_dna.energy.na1.Stacking method) (jax_dna.energy.na1.stacking.Stacking method) (jax_dna.energy.na1.unbonded_excluded_volume.UnbondedExcludedVolume method) (jax_dna.energy.na1.UnbondedExcludedVolume method) (jax_dna.energy.rna2.cross_stacking.CrossStacking method) (jax_dna.energy.rna2.CrossStacking method) (jax_dna.energy.rna2.Stacking method) (jax_dna.energy.rna2.stacking.Stacking method) (jax_dna.gradient_estimators.difftre.DiffTRe method) (jax_dna.losses.observable_wrappers.LossFn method) (jax_dna.losses.observable_wrappers.ObservableLossFn method) (jax_dna.losses.observable_wrappers.RootMeanSquaredError method) (jax_dna.losses.observable_wrappers.SquaredError method) (jax_dna.observables.base.BaseObservable method) (jax_dna.observables.diameter.Diameter method) (jax_dna.observables.persistence_length.LpMetadata method) (jax_dna.observables.pitch.PitchAngle method) (jax_dna.observables.propeller.PropellerTwist method) (jax_dna.observables.rise.Rise method) (jax_dna.observables.rmse.RMSE method) (jax_dna.observables.stretch_torsion.ExtensionZ method) (jax_dna.observables.stretch_torsion.TwistXY method) __merge__baseconfig() (jax_dna.energy.configuration.BaseConfiguration method) __merge__dict() (jax_dna.energy.configuration.BaseConfiguration method) __mul__() (jax_dna.energy.base.BaseEnergyFunction method) __or__() (jax_dna.energy.configuration.BaseConfiguration method) __post_init__() (jax_dna.energy.base.ComposedEnergyFunction method) (jax_dna.energy.configuration.BaseConfiguration method) (jax_dna.input.sequence_constraints.SequenceConstraints method) (jax_dna.input.topology.Topology method) (jax_dna.input.trajectory.NucleotideState method) (jax_dna.input.trajectory.Trajectory method) (jax_dna.observables.diameter.Diameter method) (jax_dna.observables.persistence_length.LpMetadata method) (jax_dna.observables.pitch.PitchAngle method) (jax_dna.observables.propeller.PropellerTwist method) (jax_dna.observables.rise.Rise method) (jax_dna.observables.rmse.RMSE method) (jax_dna.observables.stretch_torsion.ExtensionZ method) (jax_dna.observables.stretch_torsion.TwistXY method) (jax_dna.optimization.optimization.Optimization method) (jax_dna.simulators.jax_md.jaxmd.JaxMDSimulator method) (jax_dna.simulators.jax_md.JaxMDSimulator method) (jax_dna.simulators.jax_md.NeighborList method) (jax_dna.simulators.jax_md.utils.NeighborList method) (jax_dna.simulators.oxdna.oxdna.oxDNASimulator method) (jax_dna.simulators.oxdna.oxDNASimulator method)

__project__ (in module jax_dna) __radd__() (jax_dna.energy.base.ComposedEnergyFunction method) __repr__() (jax_dna.input.trajectory.Trajectory method) __update_status() (jax_dna.ui.loggers.console.ConsoleLogger method) (jax_dna.ui.loggers.logger.Logger method) __version__ (in module jax_dna) (in module jax_dna._version) __version_tuple__ (in module jax_dna._version) _beta (jax_dna.optimization.objective.DiffTReObjective attribute) _compute_loss() (in module jax_dna.gradient_estimators.difftre) _compute_states_energies() (in module jax_dna.gradient_estimators.difftre) _default_build_ready() (in module jax_dna.simulators.oxdna.oxdna) _default_set_build_ready() (in module jax_dna.simulators.oxdna.oxdna) _determine_oxdna_format() (in module jax_dna.input.topology) _energy_fn_builder (jax_dna.optimization.objective.DiffTReObjective attribute) _exposes (jax_dna.optimization.simulator.BaseSimulator attribute) _fn (jax_dna.optimization.simulator.BaseSimulator attribute) _from_file_oxdna_classic() (in module jax_dna.input.topology) _from_file_oxdna_new() (in module jax_dna.input.topology) _get_bonded_neighbors() (in module jax_dna.input.topology) _get_unbonded_neighbors() (in module jax_dna.input.topology) _grad_or_loss_fn (jax_dna.optimization.objective.Objective attribute) _guess_binary_location() (in module jax_dna.simulators.oxdna) (in module jax_dna.simulators.oxdna.oxdna) _initialize_logger() (jax_dna.simulators.oxdna.oxdna.oxDNASimulator method) (jax_dna.simulators.oxdna.oxDNASimulator method) _logger (jax_dna.optimization.objective.Objective attribute) _logging_observables (jax_dna.optimization.objective.Objective attribute) _loss_w_grads (in module jax_dna.gradient_estimators.difftre) _max_valid_opt_steps (jax_dna.optimization.objective.DiffTReObjective attribute) _meta_data (jax_dna.optimization.simulator.BaseSimulator attribute) _n_eff_factor (jax_dna.optimization.objective.DiffTReObjective attribute) _n_eq_steps (jax_dna.optimization.objective.DiffTReObjective attribute) _name (jax_dna.optimization.objective.Objective attribute) (jax_dna.optimization.simulator.BaseSimulator attribute) _needed_observables (jax_dna.optimization.objective.Objective attribute) _obtained_observables (jax_dna.optimization.objective.Objective attribute) _opt_params (jax_dna.optimization.objective.DiffTReObjective attribute) _opt_steps (jax_dna.optimization.objective.DiffTReObjective attribute) _parse_boolean() (in module jax_dna.input.oxdna_input) _parse_dict() (in module jax_dna.input.oxdna_input) _parse_numeric() (in module jax_dna.input.oxdna_input) _parse_value() (in module jax_dna.input.oxdna_input) _parse_value_in() (in module jax_dna.simulators.oxdna.utils) _parse_value_out() (in module jax_dna.simulators.oxdna.utils) _read_file() (in module jax_dna.input.trajectory) _read_file_process_wrapper() (in module jax_dna.input.trajectory) _ready (jax_dna.simulators.oxdna.oxdna.oxDNABinarySemaphore attribute) (jax_dna.simulators.oxdna.oxDNABinarySemaphore attribute) _ref_energies (jax_dna.gradient_estimators.difftre.DiffTRe attribute) _ref_states (jax_dna.gradient_estimators.difftre.DiffTRe attribute) _reference_energies (jax_dna.optimization.objective.DiffTReObjective attribute) _reference_states (jax_dna.optimization.objective.DiffTReObjective attribute) _required_observables (jax_dna.optimization.objective.Objective attribute) _restore_params() (jax_dna.simulators.oxdna.oxdna.oxDNASimulator method) (jax_dna.simulators.oxdna.oxDNASimulator method) _solve_f1_b() (in module jax_dna.energy.dna1.base_smoothing_functions) _solve_f1_xc_star() (in module jax_dna.energy.dna1.base_smoothing_functions) _solve_f2_b() (in module jax_dna.energy.dna1.base_smoothing_functions) _solve_f2_xc_star() (in module jax_dna.energy.dna1.base_smoothing_functions) _solve_f3_b() (in module jax_dna.energy.dna1.base_smoothing_functions) _solve_f3_xc() (in module jax_dna.energy.dna1.base_smoothing_functions) _solve_f4_b() (in module jax_dna.energy.dna1.base_smoothing_functions) _solve_f4_xc() (in module jax_dna.energy.dna1.base_smoothing_functions) _solve_f5_b() (in module jax_dna.energy.dna1.base_smoothing_functions) _solve_f5_xc() (in module jax_dna.energy.dna1.base_smoothing_functions) _trajectory (jax_dna.gradient_estimators.difftre.DiffTRe attribute) _update_params() (jax_dna.simulators.oxdna.oxdna.oxDNASimulator method) (jax_dna.simulators.oxdna.oxDNASimulator method) _update_status() (jax_dna.ui.loggers.jupyter.JupyterLogger method)

A

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

a_hb_8 (jax_dna.energy.dna1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (jax_dna.energy.dna1.HydrogenBondingConfiguration attribute) (jax_dna.energy.dna2.HydrogenBondingConfiguration attribute) a_stack (jax_dna.energy.dna1.stacking.StackingConfiguration attribute) (jax_dna.energy.dna1.StackingConfiguration attribute) (jax_dna.energy.dna2.StackingConfiguration attribute) (jax_dna.energy.rna2.stacking.StackingConfiguration attribute) (jax_dna.energy.rna2.StackingConfiguration attribute) a_stack_1 (jax_dna.energy.dna1.stacking.StackingConfiguration attribute) (jax_dna.energy.dna1.StackingConfiguration attribute) (jax_dna.energy.dna2.StackingConfiguration attribute) (jax_dna.energy.rna2.stacking.StackingConfiguration attribute) (jax_dna.energy.rna2.StackingConfiguration attribute) a_stack_10 (jax_dna.energy.rna2.stacking.StackingConfiguration attribute) (jax_dna.energy.rna2.StackingConfiguration attribute) a_stack_2 (jax_dna.energy.dna1.stacking.StackingConfiguration attribute) (jax_dna.energy.dna1.StackingConfiguration attribute) (jax_dna.energy.dna2.StackingConfiguration attribute) (jax_dna.energy.rna2.stacking.StackingConfiguration attribute) (jax_dna.energy.rna2.StackingConfiguration attribute) a_stack_4 (jax_dna.energy.dna1.stacking.StackingConfiguration attribute) (jax_dna.energy.dna1.StackingConfiguration attribute) (jax_dna.energy.dna2.StackingConfiguration attribute) a_stack_5 (jax_dna.energy.dna1.stacking.StackingConfiguration attribute) (jax_dna.energy.dna1.StackingConfiguration attribute) (jax_dna.energy.dna2.StackingConfiguration attribute) (jax_dna.energy.rna2.stacking.StackingConfiguration attribute) (jax_dna.energy.rna2.StackingConfiguration attribute) a_stack_6 (jax_dna.energy.dna1.stacking.StackingConfiguration attribute) (jax_dna.energy.dna1.StackingConfiguration attribute) (jax_dna.energy.dna2.StackingConfiguration attribute) (jax_dna.energy.rna2.stacking.StackingConfiguration attribute) (jax_dna.energy.rna2.StackingConfiguration attribute) a_stack_9 (jax_dna.energy.rna2.stacking.StackingConfiguration attribute) (jax_dna.energy.rna2.StackingConfiguration attribute) add_composable_energy_fn() (jax_dna.energy.base.ComposedEnergyFunction method) add_energy_fn() (jax_dna.energy.base.ComposedEnergyFunction method) aggregate_grad_fn (jax_dna.optimization.optimization.Optimization attribute) allocate() (jax_dna.simulators.jax_md.NeighborList method) (jax_dna.simulators.jax_md.NoNeighborList method) (jax_dna.simulators.jax_md.utils.NeighborHelper method) (jax_dna.simulators.jax_md.utils.NeighborList method) (jax_dna.simulators.jax_md.utils.NoNeighborList method) ANGSTROMS_PER_NM (in module jax_dna.utils.units) ANGSTROMS_PER_OXDNA_LENGTH (in module jax_dna.utils.units) angular_velocity (jax_dna.input.trajectory.NucleotideState property) Arr_Bonded_Neighbors (in module jax_dna.utils.types) Arr_Bonded_Neighbors_2 (in module jax_dna.utils.types) Arr_Bp (in module jax_dna.utils.types) Arr_Bp_Pseq (in module jax_dna.utils.types) Arr_N (in module jax_dna.utils.types) Arr_Nucleotide (in module jax_dna.utils.types) Arr_Nucleotide_15 (in module jax_dna.utils.types) Arr_Nucleotide_2 (in module jax_dna.utils.types) Arr_Nucleotide_2_Int (in module jax_dna.utils.types) Arr_Nucleotide_3 (in module jax_dna.utils.types) Arr_Nucleotide_4 (in module jax_dna.utils.types) Arr_Nucleotide_Int (in module jax_dna.utils.types) ARR_OR_SCALAR (in module jax_dna.utils.types) Arr_States (in module jax_dna.utils.types) Arr_States_3 (in module jax_dna.utils.types) Arr_Unbonded_Neighbors (in module jax_dna.utils.types) Arr_Unbonded_Neighbors_2 (in module jax_dna.utils.types) Arr_Unpaired (in module jax_dna.utils.types) Arr_Unpaired_Pseq (in module jax_dna.utils.types) array (jax_dna.input.trajectory.NucleotideState attribute)

B

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

b_low_hb (jax_dna.energy.dna1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (jax_dna.energy.dna1.HydrogenBondingConfiguration attribute) (jax_dna.energy.dna2.HydrogenBondingConfiguration attribute) b_low_stack (jax_dna.energy.dna1.stacking.StackingConfiguration attribute) (jax_dna.energy.dna1.StackingConfiguration attribute) (jax_dna.energy.dna2.StackingConfiguration attribute) (jax_dna.energy.rna2.stacking.StackingConfiguration attribute) (jax_dna.energy.rna2.StackingConfiguration attribute) b_neg_cos_phi1_stack (jax_dna.energy.dna1.stacking.StackingConfiguration attribute) (jax_dna.energy.dna1.StackingConfiguration attribute) (jax_dna.energy.dna2.StackingConfiguration attribute) (jax_dna.energy.rna2.stacking.StackingConfiguration attribute) (jax_dna.energy.rna2.StackingConfiguration attribute) b_neg_cos_phi2_stack (jax_dna.energy.dna1.stacking.StackingConfiguration attribute) (jax_dna.energy.dna1.StackingConfiguration attribute) (jax_dna.energy.dna2.StackingConfiguration attribute) (jax_dna.energy.rna2.stacking.StackingConfiguration attribute) (jax_dna.energy.rna2.StackingConfiguration attribute) b_stack_10 (jax_dna.energy.rna2.stacking.StackingConfiguration attribute) (jax_dna.energy.rna2.StackingConfiguration attribute) b_stack_4 (jax_dna.energy.dna1.stacking.StackingConfiguration attribute) (jax_dna.energy.dna1.StackingConfiguration attribute) (jax_dna.energy.dna2.StackingConfiguration attribute) b_stack_5 (jax_dna.energy.dna1.stacking.StackingConfiguration attribute) (jax_dna.energy.dna1.StackingConfiguration attribute) (jax_dna.energy.dna2.StackingConfiguration attribute) (jax_dna.energy.rna2.stacking.StackingConfiguration attribute) (jax_dna.energy.rna2.StackingConfiguration attribute) b_stack_6 (jax_dna.energy.dna1.stacking.StackingConfiguration attribute) (jax_dna.energy.dna1.StackingConfiguration attribute) (jax_dna.energy.dna2.StackingConfiguration attribute) (jax_dna.energy.rna2.stacking.StackingConfiguration attribute) (jax_dna.energy.rna2.StackingConfiguration attribute) b_stack_9 (jax_dna.energy.rna2.stacking.StackingConfiguration attribute) (jax_dna.energy.rna2.StackingConfiguration attribute) back_base_vector (jax_dna.input.trajectory.NucleotideState property) back_base_vectors (jax_dna.energy.base.BaseNucleotide attribute) (jax_dna.energy.dna1.Nucleotide attribute) (jax_dna.energy.dna1.nucleotide.Nucleotide attribute) (jax_dna.energy.dna2.Nucleotide attribute) (jax_dna.energy.dna2.nucleotide.Nucleotide attribute) (jax_dna.energy.rna2.Nucleotide attribute) (jax_dna.energy.rna2.nucleotide.Nucleotide attribute) back_sites (jax_dna.energy.base.BaseNucleotide attribute) (jax_dna.energy.dna1.Nucleotide attribute) (jax_dna.energy.dna1.nucleotide.Nucleotide attribute) (jax_dna.energy.dna2.Nucleotide attribute) (jax_dna.energy.dna2.nucleotide.Nucleotide attribute) (jax_dna.energy.rna2.Nucleotide attribute) (jax_dna.energy.rna2.nucleotide.Nucleotide attribute) back_sites_dna1 (jax_dna.energy.dna2.Nucleotide attribute) (jax_dna.energy.dna2.nucleotide.Nucleotide attribute) base_normal (jax_dna.input.trajectory.NucleotideState property) base_normals (jax_dna.energy.base.BaseNucleotide attribute) (jax_dna.energy.dna1.Nucleotide attribute) (jax_dna.energy.dna1.nucleotide.Nucleotide attribute) (jax_dna.energy.dna2.Nucleotide attribute) (jax_dna.energy.dna2.nucleotide.Nucleotide attribute) (jax_dna.energy.rna2.Nucleotide attribute) (jax_dna.energy.rna2.nucleotide.Nucleotide attribute) base_sites (jax_dna.energy.base.BaseNucleotide attribute) (jax_dna.energy.dna1.Nucleotide attribute) (jax_dna.energy.dna1.nucleotide.Nucleotide attribute) (jax_dna.energy.dna2.Nucleotide attribute) (jax_dna.energy.dna2.nucleotide.Nucleotide attribute) (jax_dna.energy.rna2.Nucleotide attribute) (jax_dna.energy.rna2.nucleotide.Nucleotide attribute) BaseConfiguration (class in jax_dna.energy.configuration) BaseEnergyFunction (class in jax_dna.energy.base) BaseNucleotide (class in jax_dna.energy.base) BaseObservable (class in jax_dna.observables.base) BaseSimulation (class in jax_dna.simulators.base) BaseSimulator (class in jax_dna.optimization.simulator) batched() (in module jax_dna.utils.helpers) bb_p3_sites (jax_dna.energy.rna2.Nucleotide attribute) (jax_dna.energy.rna2.nucleotide.Nucleotide attribute) bb_p5_sites (jax_dna.energy.rna2.Nucleotide attribute) (jax_dna.energy.rna2.nucleotide.Nucleotide attribute) beta (jax_dna.gradient_estimators.difftre.DiffTRe attribute) BIN_PATH_ENV_VAR (in module jax_dna.simulators.oxdna) (in module jax_dna.simulators.oxdna.oxdna) bonded_neighbors (jax_dna.input.topology.Topology attribute) (jax_dna.simulators.jax_md.StaticSimulatorParams attribute) (jax_dna.simulators.jax_md.utils.StaticSimulatorParams attribute) BondedExcludedVolume (class in jax_dna.energy.dna1) (class in jax_dna.energy.dna1.bonded_excluded_volume) (class in jax_dna.energy.dna2) (class in jax_dna.energy.na1) (class in jax_dna.energy.na1.bonded_excluded_volume) BondedExcludedVolumeConfiguration (class in jax_dna.energy.dna1) (class in jax_dna.energy.dna1.bonded_excluded_volume) (class in jax_dna.energy.dna2) (class in jax_dna.energy.na1) (class in jax_dna.energy.na1.bonded_excluded_volume) box_size (jax_dna.simulators.jax_md.NeighborList attribute) (jax_dna.simulators.jax_md.utils.NeighborList attribute) bp1 (jax_dna.observables.stretch_torsion.ExtensionZ attribute) bp2 (jax_dna.observables.stretch_torsion.ExtensionZ attribute) BP_IDX_MAP (in module jax_dna.utils.constants) BP_IDXS (in module jax_dna.utils.constants) BP_TYPES (in module jax_dna.utils.constants) bps (jax_dna.input.sequence_constraints.SequenceConstraints attribute) build_energy_function() (in module jax_dna.gradient_estimators.difftre) BUILD_PATH_ENV_VAR (in module jax_dna.simulators.oxdna) (in module jax_dna.simulators.oxdna.oxdna) build_run_fn() (in module jax_dna.simulators.jax_md.jaxmd) build_wait_interval (jax_dna.simulators.oxdna.oxdna.oxDNASimulator attribute) (jax_dna.simulators.oxdna.oxDNASimulator attribute)

C

calc_rows_and_columns() (in module jax_dna.ui.loggers.jupyter) calculate() (jax_dna.optimization.objective.DiffTReObjective method) (jax_dna.optimization.objective.Objective method) calculate_extension() (in module jax_dna.observables.wlc) center (jax_dna.energy.base.BaseNucleotide attribute) (jax_dna.energy.dna1.Nucleotide attribute) (jax_dna.energy.dna1.nucleotide.Nucleotide attribute) (jax_dna.energy.dna2.Nucleotide attribute) (jax_dna.energy.dna2.nucleotide.Nucleotide attribute) (jax_dna.energy.rna2.Nucleotide attribute) (jax_dna.energy.rna2.nucleotide.Nucleotide attribute) change_size() (jax_dna.ui.loggers.jupyter.PlotlyLogger method) check() (jax_dna.simulators.oxdna.oxdna.oxDNABinarySemaphore method) (jax_dna.simulators.oxdna.oxDNABinarySemaphore method) check_build_ready (jax_dna.simulators.oxdna.oxdna.oxDNASimulator attribute) (jax_dna.simulators.oxdna.oxDNASimulator attribute) check_consistent_constraints() (in module jax_dna.input.sequence_constraints) check_cover() (in module jax_dna.input.sequence_constraints) check_valid_seq() (in module jax_dna.input.topology) checkpoint_every (jax_dna.simulators.jax_md.StaticSimulatorParams attribute) (jax_dna.simulators.jax_md.utils.StaticSimulatorParams attribute) checkpoint_scan() (in module jax_dna.simulators.jax_md.utils) clamp() (in module jax_dna.utils.math) CLASSIC (jax_dna.utils.types.oxDNAFormat attribute) CMAKE_BIN_ENV_VAR (in module jax_dna.simulators.oxdna) (in module jax_dna.simulators.oxdna.oxdna) CMAKE_MAKE_BIN_LOC_GUESSES (in module jax_dna.simulators.oxdna.oxdna) coaxial_stacking() (in module jax_dna.energy.dna1.interactions) (in module jax_dna.energy.dna2.interactions) CoaxialStacking (class in jax_dna.energy.dna1) (class in jax_dna.energy.dna1.coaxial_stacking) (class in jax_dna.energy.dna2) (class in jax_dna.energy.dna2.coaxial_stacking) (class in jax_dna.energy.na1) (class in jax_dna.energy.na1.coaxial_stacking) CoaxialStackingConfiguration (class in jax_dna.energy.dna1) (class in jax_dna.energy.dna1.coaxial_stacking) (class in jax_dna.energy.dna2) (class in jax_dna.energy.dna2.coaxial_stacking) (class in jax_dna.energy.na1) (class in jax_dna.energy.na1.coaxial_stacking) com (jax_dna.input.trajectory.NucleotideState property) COMPLETE (jax_dna.ui.loggers.logger.Status attribute) ComposedEnergyFunction (class in jax_dna.energy.base) compute_l_vector() (in module jax_dna.observables.persistence_length) compute_loss() (in module jax_dna.optimization.objective)

compute_loss_and_grad (in module jax_dna.optimization.objective) compute_metadata() (in module jax_dna.observables.persistence_length) compute_pitch() (in module jax_dna.observables.pitch) compute_seq_dep_weight() (in module jax_dna.energy.utils) compute_terms() (jax_dna.energy.base.ComposedEnergyFunction method) compute_v_hb() (jax_dna.energy.dna1.hydrogen_bonding.HydrogenBonding method) (jax_dna.energy.dna1.HydrogenBonding method) (jax_dna.energy.dna2.HydrogenBonding method) compute_v_stack() (jax_dna.energy.dna1.Stacking method) (jax_dna.energy.dna1.stacking.Stacking method) (jax_dna.energy.rna2.Stacking method) (jax_dna.energy.rna2.stacking.Stacking method) compute_weights_and_neff() (in module jax_dna.optimization.objective) ConsoleLogger (class in jax_dna.ui.loggers.console) convert_to_fname() (in module jax_dna.ui.loggers.logger) cos_phi3_c_coax (jax_dna.energy.dna1.coaxial_stacking.CoaxialStackingConfiguration attribute) (jax_dna.energy.dna1.CoaxialStackingConfiguration attribute) cos_phi3_star_coax (jax_dna.energy.dna1.coaxial_stacking.CoaxialStackingConfiguration attribute) (jax_dna.energy.dna1.CoaxialStackingConfiguration attribute) cos_phi4_c_coax (jax_dna.energy.dna1.coaxial_stacking.CoaxialStackingConfiguration attribute) (jax_dna.energy.dna1.CoaxialStackingConfiguration attribute) cos_phi4_star_coax (jax_dna.energy.dna1.coaxial_stacking.CoaxialStackingConfiguration attribute) (jax_dna.energy.dna1.CoaxialStackingConfiguration attribute) coth() (in module jax_dna.observables.wlc) cross_prods (jax_dna.energy.base.BaseNucleotide attribute) (jax_dna.energy.dna1.Nucleotide attribute) (jax_dna.energy.dna1.nucleotide.Nucleotide attribute) (jax_dna.energy.dna2.Nucleotide attribute) (jax_dna.energy.dna2.nucleotide.Nucleotide attribute) (jax_dna.energy.rna2.Nucleotide attribute) (jax_dna.energy.rna2.nucleotide.Nucleotide attribute) cross_stacking() (in module jax_dna.energy.dna1.interactions) (in module jax_dna.energy.rna2.interactions) CrossStacking (class in jax_dna.energy.dna1) (class in jax_dna.energy.dna1.cross_stacking) (class in jax_dna.energy.dna2) (class in jax_dna.energy.na1) (class in jax_dna.energy.na1.cross_stacking) (class in jax_dna.energy.rna2) (class in jax_dna.energy.rna2.cross_stacking) CrossStackingConfiguration (class in jax_dna.energy.dna1) (class in jax_dna.energy.dna1.cross_stacking) (class in jax_dna.energy.dna2) (class in jax_dna.energy.na1) (class in jax_dna.energy.na1.cross_stacking) (class in jax_dna.energy.rna2) (class in jax_dna.energy.rna2.cross_stacking)

D

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

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

E

empty_dict (in module jax_dna.optimization.objective) energies (jax_dna.input.trajectory.Trajectory attribute) energy_configs (jax_dna.gradient_estimators.difftre.DiffTRe attribute) (jax_dna.simulators.jax_md.jaxmd.JaxMDSimulator attribute) (jax_dna.simulators.jax_md.JaxMDSimulator attribute) (jax_dna.simulators.oxdna.oxdna.oxDNASimulator attribute) (jax_dna.simulators.oxdna.oxDNASimulator attribute) energy_fn_builder (jax_dna.gradient_estimators.difftre.DiffTRe attribute) energy_fn_builder() (in module jax_dna.energy) energy_fns (jax_dna.energy.base.ComposedEnergyFunction attribute) (jax_dna.gradient_estimators.difftre.DiffTRe attribute) (jax_dna.simulators.jax_md.jaxmd.JaxMDSimulator attribute) (jax_dna.simulators.jax_md.JaxMDSimulator attribute) EnergyFn (in module jax_dna.optimization.objective) eps_backbone (jax_dna.energy.dna1.fene.FeneConfiguration attribute) (jax_dna.energy.dna1.FeneConfiguration attribute) (jax_dna.energy.dna2.FeneConfiguration attribute) eps_exc (jax_dna.energy.dna1.bonded_excluded_volume.BondedExcludedVolumeConfiguration attribute) (jax_dna.energy.dna1.BondedExcludedVolumeConfiguration attribute) (jax_dna.energy.dna1.unbonded_excluded_volume.UnbondedExcludedVolumeConfiguration attribute) (jax_dna.energy.dna1.UnbondedExcludedVolumeConfiguration attribute) (jax_dna.energy.dna2.BondedExcludedVolumeConfiguration attribute) (jax_dna.energy.dna2.UnbondedExcludedVolumeConfiguration attribute) eps_hb (jax_dna.energy.dna1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (jax_dna.energy.dna1.HydrogenBondingConfiguration attribute) (jax_dna.energy.dna2.HydrogenBondingConfiguration attribute) eps_stack (jax_dna.energy.dna1.stacking.StackingConfiguration attribute) (jax_dna.energy.dna1.StackingConfiguration attribute) (jax_dna.energy.dna2.StackingConfiguration attribute) (jax_dna.energy.rna2.stacking.StackingConfiguration attribute) (jax_dna.energy.rna2.StackingConfiguration attribute) eps_stack_base (jax_dna.energy.dna1.stacking.StackingConfiguration attribute) (jax_dna.energy.dna1.StackingConfiguration attribute) (jax_dna.energy.dna2.StackingConfiguration attribute) (jax_dna.energy.rna2.stacking.StackingConfiguration attribute) (jax_dna.energy.rna2.StackingConfiguration attribute) eps_stack_kt_coeff (jax_dna.energy.dna1.stacking.StackingConfiguration attribute) (jax_dna.energy.dna1.StackingConfiguration attribute) (jax_dna.energy.dna2.StackingConfiguration attribute) (jax_dna.energy.rna2.stacking.StackingConfiguration attribute) (jax_dna.energy.rna2.StackingConfiguration attribute) ERR_BATCHED_N (in module jax_dna.utils.helpers) ERR_BIN_PATH_NOT_SET (in module jax_dna.simulators.oxdna) (in module jax_dna.simulators.oxdna.oxdna) ERR_BP_ARR_CONTAINS_DUPLICATES (in module jax_dna.input.sequence_constraints) ERR_BUILD_PATH_NOT_SET (in module jax_dna.simulators.oxdna) (in module jax_dna.simulators.oxdna.oxdna) ERR_BUILD_SETUP_FAILED (in module jax_dna.simulators.oxdna) (in module jax_dna.simulators.oxdna.oxdna) ERR_CALL_NOT_IMPLEMENTED (in module jax_dna.energy.base) ERR_CANNOT_PROCESS_SRC_H (in module jax_dna.simulators.oxdna.utils) ERR_CHKPNT_SCN (in module jax_dna.simulators.jax_md.utils) ERR_COMPOSED_ENERGY_FN_LEN_MISMATCH (in module jax_dna.energy.base) ERR_COMPOSED_ENERGY_FN_TYPE_ENERGY_FNS (in module jax_dna.energy.base) ERR_DIFFTRE_MISSING_KWARGS (in module jax_dna.optimization.objective) ERR_DISPLACEMENT_FN_REQUIRED (in module jax_dna.observables.diameter) ERR_DSEQ_TO_PSEQ_INVALID_BP (in module jax_dna.input.sequence_constraints) ERR_FILE_NOT_FOUND (in module jax_dna.input.topology) ERR_FIXED_BOX_SIZE (in module jax_dna.input.trajectory) ERR_INPUT_FILE_NOT_FOUND (in module jax_dna.simulators.oxdna) (in module jax_dna.simulators.oxdna.oxdna) ERR_INVALID_BP_INDICES (in module jax_dna.input.sequence_constraints) ERR_INVALID_BP_SHAPE (in module jax_dna.input.sequence_constraints) ERR_INVALID_HEADER_TYPE (in module jax_dna.simulators.oxdna.utils) ERR_INVALID_OXDNA_FORMAT (in module jax_dna.input.topology) ERR_MISSING_AGG_GRAD_FN (in module jax_dna.optimization.optimization) ERR_MISSING_ARG (in module jax_dna.optimization.objective) ERR_MISSING_OBJECTIVES (in module jax_dna.optimization.optimization) ERR_MISSING_OPTIMIZER (in module jax_dna.optimization.optimization)

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

F

f1() (in module jax_dna.energy.dna1.base_functions) (in module jax_dna.energy.dna2.base_functions) f2() (in module jax_dna.energy.dna1.base_functions) (in module jax_dna.energy.dna2.base_functions) f3() (in module jax_dna.energy.dna1.base_functions) (in module jax_dna.energy.dna2.base_functions) f4() (in module jax_dna.energy.dna1.base_functions) (in module jax_dna.energy.dna2.base_functions) f5() (in module jax_dna.energy.dna1.base_functions) (in module jax_dna.energy.dna2.base_functions) f6() (in module jax_dna.energy.dna2.base_functions) Fene (class in jax_dna.energy.dna1) (class in jax_dna.energy.dna1.fene) (class in jax_dna.energy.dna2) (class in jax_dna.energy.na1) (class in jax_dna.energy.na1.fene) FeneConfiguration (class in jax_dna.energy.dna1) (class in jax_dna.energy.dna1.fene) (class in jax_dna.energy.dna2) (class in jax_dna.energy.na1) (class in jax_dna.energy.na1.fene) fig (jax_dna.ui.loggers.jupyter.PlotlyLogger attribute)

figure_widget_f (in module jax_dna.ui.loggers.jupyter) finf (jax_dna.energy.dna1.fene.FeneConfiguration attribute) (jax_dna.energy.dna1.FeneConfiguration attribute) (jax_dna.energy.dna2.FeneConfiguration attribute) fit_wlc() (in module jax_dna.observables.wlc) flatten_n() (in module jax_dna.simulators.jax_md.utils) FLOAT (jax_dna.utils.types.oxDNAModelHType attribute) fmax (jax_dna.energy.dna1.fene.FeneConfiguration attribute) (jax_dna.energy.dna1.FeneConfiguration attribute) (jax_dna.energy.dna2.FeneConfiguration attribute) from_bps() (in module jax_dna.input.sequence_constraints) from_dict() (jax_dna.energy.configuration.BaseConfiguration class method) from_file() (in module jax_dna.input.trajectory) from_oxdna_file() (in module jax_dna.input.topology) from_rigid_body() (jax_dna.energy.base.BaseNucleotide static method) (jax_dna.energy.dna1.Nucleotide static method) (jax_dna.energy.dna1.nucleotide.Nucleotide static method) (jax_dna.energy.dna2.Nucleotide static method) (jax_dna.energy.dna2.nucleotide.Nucleotide static method) (jax_dna.energy.na1.HybridNucleotide static method) (jax_dna.energy.na1.nucleotide.HybridNucleotide static method) (jax_dna.energy.rna2.Nucleotide static method) (jax_dna.energy.rna2.nucleotide.Nucleotide static method)

G

gamma (jax_dna.simulators.jax_md.StaticSimulatorParams attribute) (jax_dna.simulators.jax_md.utils.StaticSimulatorParams attribute) get_all_l_vectors (in module jax_dna.observables.persistence_length) get_duplex_quartets() (in module jax_dna.observables.base) get_f1_smoothing_params() (in module jax_dna.energy.dna1.base_smoothing_functions) get_f2_smoothing_params() (in module jax_dna.energy.dna1.base_smoothing_functions) get_f3_smoothing_params() (in module jax_dna.energy.dna1.base_smoothing_functions)

get_f4_smoothing_params() (in module jax_dna.energy.dna1.base_smoothing_functions) get_f5_smoothing_params() (in module jax_dna.energy.dna1.base_smoothing_functions) get_fn (in module jax_dna.optimization.optimization) get_kt() (in module jax_dna.utils.units) get_neighbor_list_fn() (in module jax_dna.utils.neighbors) get_pair_probs() (in module jax_dna.energy.utils) grad_update_fn (in module jax_dna.optimization.optimization) Grads (in module jax_dna.utils.types)

H

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

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

I

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

init_positions (jax_dna.simulators.jax_md.NeighborList attribute) (jax_dna.simulators.jax_md.utils.NeighborList attribute) init_state (jax_dna.gradient_estimators.difftre.DiffTRe attribute) initialize() (jax_dna.gradient_estimators.difftre.DiffTRe method) input_dir (jax_dna.simulators.oxdna.oxdna.oxDNASimulator attribute) (jax_dna.simulators.oxdna.oxDNASimulator attribute) INTEGER (jax_dna.utils.types.oxDNAModelHType attribute) INVALID_DICT_LINE (in module jax_dna.input.oxdna_input) is_dna_rna_pair() (in module jax_dna.energy.na1.utils) is_end (jax_dna.energy.dna2.debye.DebyeConfiguration attribute) (jax_dna.energy.dna2.DebyeConfiguration attribute) (jax_dna.energy.na1.debye.DebyeConfiguration attribute) (jax_dna.energy.na1.DebyeConfiguration attribute) (jax_dna.input.topology.Topology attribute) is_ready() (jax_dna.optimization.objective.DiffTReObjective method) (jax_dna.optimization.objective.Objective method) is_rna_pair() (in module jax_dna.energy.na1.utils) is_unpaired (jax_dna.input.sequence_constraints.SequenceConstraints attribute)

J

jax_dna module jax_dna._version module jax_dna.energy module jax_dna.energy.base module jax_dna.energy.configuration module jax_dna.energy.dna1 module jax_dna.energy.dna1.base_functions module jax_dna.energy.dna1.base_smoothing_functions module jax_dna.energy.dna1.bonded_excluded_volume module jax_dna.energy.dna1.coaxial_stacking module jax_dna.energy.dna1.cross_stacking module jax_dna.energy.dna1.expected_hydrogen_bonding module jax_dna.energy.dna1.expected_stacking module jax_dna.energy.dna1.fene module jax_dna.energy.dna1.hydrogen_bonding module jax_dna.energy.dna1.interactions module jax_dna.energy.dna1.nucleotide module jax_dna.energy.dna1.stacking module jax_dna.energy.dna1.unbonded_excluded_volume module jax_dna.energy.dna2 module jax_dna.energy.dna2.base_functions module jax_dna.energy.dna2.coaxial_stacking module jax_dna.energy.dna2.debye module jax_dna.energy.dna2.interactions module jax_dna.energy.dna2.nucleotide module jax_dna.energy.dna2.stacking module jax_dna.energy.na1 module jax_dna.energy.na1.bonded_excluded_volume module jax_dna.energy.na1.coaxial_stacking module jax_dna.energy.na1.cross_stacking module jax_dna.energy.na1.debye module jax_dna.energy.na1.fene module jax_dna.energy.na1.hydrogen_bonding module jax_dna.energy.na1.nucleotide module jax_dna.energy.na1.stacking module jax_dna.energy.na1.unbonded_excluded_volume module jax_dna.energy.na1.utils module jax_dna.energy.potentials module jax_dna.energy.rna2 module jax_dna.energy.rna2.cross_stacking module jax_dna.energy.rna2.interactions module jax_dna.energy.rna2.nucleotide module jax_dna.energy.rna2.stacking module jax_dna.energy.utils module jax_dna.gradient_estimators module jax_dna.gradient_estimators.difftre module jax_dna.input module

jax_dna.input.dna1 module jax_dna.input.oxdna_input module jax_dna.input.sequence_constraints module jax_dna.input.toml module jax_dna.input.topology module jax_dna.input.trajectory module jax_dna.input.tree module jax_dna.losses module jax_dna.losses.observable_wrappers module jax_dna.observables module jax_dna.observables.base module jax_dna.observables.diameter module jax_dna.observables.persistence_length module jax_dna.observables.pitch module jax_dna.observables.propeller module jax_dna.observables.rise module jax_dna.observables.rmse module jax_dna.observables.stretch_torsion module jax_dna.observables.wlc module jax_dna.optimization module jax_dna.optimization.objective module jax_dna.optimization.optimization module jax_dna.optimization.simulator module jax_dna.simulators module jax_dna.simulators.base module jax_dna.simulators.io module jax_dna.simulators.jax_md module jax_dna.simulators.jax_md.jaxmd module jax_dna.simulators.jax_md.utils module jax_dna.simulators.oxdna module jax_dna.simulators.oxdna.oxdna module jax_dna.simulators.oxdna.utils module jax_dna.ui module jax_dna.ui.loggers module jax_dna.ui.loggers.console module jax_dna.ui.loggers.jupyter module jax_dna.ui.loggers.logger module jax_dna.utils module jax_dna.utils.constants module jax_dna.utils.helpers module jax_dna.utils.math module jax_dna.utils.neighbors module jax_dna.utils.types module jax_dna.utils.units module JaxMDSimulator (class in jax_dna.simulators.jax_md) (class in jax_dna.simulators.jax_md.jaxmd) JOULES_PER_OXDNA_ENERGY (in module jax_dna.utils.units) JupyterLogger (class in jax_dna.ui.loggers.jupyter)

K

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

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

L

l2_loss() (in module jax_dna.losses.observable_wrappers) lambda_ (jax_dna.energy.dna2.debye.DebyeConfiguration attribute) (jax_dna.energy.dna2.DebyeConfiguration attribute) lambda_factor (jax_dna.energy.dna2.debye.DebyeConfiguration attribute) (jax_dna.energy.dna2.DebyeConfiguration attribute) LBL_OBJ_HEADER (in module jax_dna.ui.loggers.jupyter) LBL_OBS_HEADER (in module jax_dna.ui.loggers.jupyter) LBL_PROG_BAR (in module jax_dna.ui.loggers.jupyter) LBL_SIM_HEADER (in module jax_dna.ui.loggers.jupyter) LBL_TOP_HEADER (in module jax_dna.ui.loggers.jupyter) length() (jax_dna.simulators.io.SimulatorTrajectory method) load_pytree() (in module jax_dna.input.tree) local_helical_axis() (in module jax_dna.observables.base) log_dir (jax_dna.ui.loggers.logger.Logger attribute) log_metric() (jax_dna.ui.loggers.console.ConsoleLogger method) (jax_dna.ui.loggers.jupyter.JupyterLogger method) (jax_dna.ui.loggers.jupyter.PlotlyLogger method) (jax_dna.ui.loggers.logger.Logger method)

Logger (class in jax_dna.ui.loggers.logger) logger (in module jax_dna.simulators.oxdna.oxdna) (jax_dna.optimization.optimization.Optimization attribute) (jax_dna.optimization.optimization.SimpleOptimizer attribute) logger_config (jax_dna.simulators.oxdna.oxdna.oxDNASimulator attribute) (jax_dna.simulators.oxdna.oxDNASimulator attribute) logging_observables() (jax_dna.optimization.objective.Objective method) loss() (in module jax_dna.observables.wlc) loss_fn (jax_dna.losses.observable_wrappers.ObservableLossFn attribute) loss_fns (jax_dna.gradient_estimators.difftre.DiffTRe attribute) loss_input (in module jax_dna.losses.observable_wrappers) losses_reduce_fn (jax_dna.gradient_estimators.difftre.DiffTRe attribute) LossFn (class in jax_dna.losses.observable_wrappers) LpMetadata (class in jax_dna.observables.persistence_length)

M

MAKE_BIN_ENV_VAR (in module jax_dna.simulators.oxdna) (in module jax_dna.simulators.oxdna.oxdna) make_subplots_f (in module jax_dna.ui.loggers.jupyter) mass (jax_dna.simulators.jax_md.SimulationState attribute) (jax_dna.simulators.jax_md.StaticSimulatorParams attribute) (jax_dna.simulators.jax_md.utils.SimulationState attribute) (jax_dna.simulators.jax_md.utils.StaticSimulatorParams attribute) meta_data() (jax_dna.optimization.simulator.BaseSimulator method) MetaData (in module jax_dna.utils.types) min_n_eff (jax_dna.gradient_estimators.difftre.DiffTRe attribute) MIN_VALID_HEADER_TOKEN_COUNT (in module jax_dna.simulators.oxdna.utils) MISSING_LOGDIR_WANING (in module jax_dna.ui.loggers.logger) module jax_dna jax_dna._version jax_dna.energy jax_dna.energy.base jax_dna.energy.configuration jax_dna.energy.dna1 jax_dna.energy.dna1.base_functions jax_dna.energy.dna1.base_smoothing_functions jax_dna.energy.dna1.bonded_excluded_volume jax_dna.energy.dna1.coaxial_stacking jax_dna.energy.dna1.cross_stacking jax_dna.energy.dna1.expected_hydrogen_bonding jax_dna.energy.dna1.expected_stacking jax_dna.energy.dna1.fene jax_dna.energy.dna1.hydrogen_bonding jax_dna.energy.dna1.interactions jax_dna.energy.dna1.nucleotide jax_dna.energy.dna1.stacking jax_dna.energy.dna1.unbonded_excluded_volume jax_dna.energy.dna2 jax_dna.energy.dna2.base_functions jax_dna.energy.dna2.coaxial_stacking jax_dna.energy.dna2.debye jax_dna.energy.dna2.interactions jax_dna.energy.dna2.nucleotide jax_dna.energy.dna2.stacking jax_dna.energy.na1 jax_dna.energy.na1.bonded_excluded_volume jax_dna.energy.na1.coaxial_stacking jax_dna.energy.na1.cross_stacking jax_dna.energy.na1.debye jax_dna.energy.na1.fene jax_dna.energy.na1.hydrogen_bonding jax_dna.energy.na1.nucleotide jax_dna.energy.na1.stacking jax_dna.energy.na1.unbonded_excluded_volume jax_dna.energy.na1.utils jax_dna.energy.potentials jax_dna.energy.rna2 jax_dna.energy.rna2.cross_stacking jax_dna.energy.rna2.interactions jax_dna.energy.rna2.nucleotide jax_dna.energy.rna2.stacking jax_dna.energy.utils jax_dna.gradient_estimators jax_dna.gradient_estimators.difftre jax_dna.input jax_dna.input.dna1 jax_dna.input.oxdna_input jax_dna.input.sequence_constraints jax_dna.input.toml jax_dna.input.topology jax_dna.input.trajectory jax_dna.input.tree jax_dna.losses jax_dna.losses.observable_wrappers jax_dna.observables jax_dna.observables.base jax_dna.observables.diameter jax_dna.observables.persistence_length jax_dna.observables.pitch jax_dna.observables.propeller jax_dna.observables.rise jax_dna.observables.rmse jax_dna.observables.stretch_torsion jax_dna.observables.wlc jax_dna.optimization jax_dna.optimization.objective jax_dna.optimization.optimization jax_dna.optimization.simulator jax_dna.simulators jax_dna.simulators.base jax_dna.simulators.io jax_dna.simulators.jax_md jax_dna.simulators.jax_md.jaxmd jax_dna.simulators.jax_md.utils jax_dna.simulators.oxdna jax_dna.simulators.oxdna.oxdna jax_dna.simulators.oxdna.utils jax_dna.ui jax_dna.ui.loggers jax_dna.ui.loggers.console jax_dna.ui.loggers.jupyter jax_dna.ui.loggers.logger jax_dna.utils jax_dna.utils.constants jax_dna.utils.helpers jax_dna.utils.math jax_dna.utils.neighbors jax_dna.utils.types jax_dna.utils.units

mult() (in module jax_dna.utils.math)

N

N_1ST_LINE_OXDNA_CLASSIC (in module jax_dna.input.topology) N_1ST_LINE_OXDNA_NEW (in module jax_dna.input.topology) n_bp (jax_dna.input.sequence_constraints.SequenceConstraints attribute) N_BP_TYPES (in module jax_dna.utils.constants) n_build_threads (jax_dna.simulators.oxdna.oxdna.oxDNASimulator attribute) (jax_dna.simulators.oxdna.oxDNASimulator attribute) N_DIMS_NUCLEOTIDES_POSITION (in module jax_dna.observables.rmse) n_eq_steps (jax_dna.gradient_estimators.difftre.DiffTRe attribute) N_NT (in module jax_dna.utils.constants) N_NT_PER_BP (in module jax_dna.utils.constants) n_nucleotides (jax_dna.input.sequence_constraints.SequenceConstraints attribute) (jax_dna.input.topology.Topology attribute) (jax_dna.input.trajectory.Trajectory attribute) n_steps (jax_dna.gradient_estimators.difftre.DiffTRe attribute) n_unpaired (jax_dna.input.sequence_constraints.SequenceConstraints attribute) name() (jax_dna.optimization.objective.Objective method) (jax_dna.optimization.simulator.BaseSimulator method) needed_observables() (jax_dna.optimization.objective.Objective method) neg_cos_phi1_c_stack (jax_dna.energy.dna1.stacking.StackingConfiguration attribute) (jax_dna.energy.dna1.StackingConfiguration attribute) (jax_dna.energy.dna2.StackingConfiguration attribute) (jax_dna.energy.rna2.stacking.StackingConfiguration attribute) (jax_dna.energy.rna2.StackingConfiguration attribute) neg_cos_phi1_star_stack (jax_dna.energy.dna1.stacking.StackingConfiguration attribute) (jax_dna.energy.dna1.StackingConfiguration attribute) (jax_dna.energy.dna2.StackingConfiguration attribute) (jax_dna.energy.rna2.stacking.StackingConfiguration attribute) (jax_dna.energy.rna2.StackingConfiguration attribute) neg_cos_phi2_c_stack (jax_dna.energy.dna1.stacking.StackingConfiguration attribute) (jax_dna.energy.dna1.StackingConfiguration attribute) (jax_dna.energy.dna2.StackingConfiguration attribute) (jax_dna.energy.rna2.stacking.StackingConfiguration attribute) (jax_dna.energy.rna2.StackingConfiguration attribute) neg_cos_phi2_star_stack (jax_dna.energy.dna1.stacking.StackingConfiguration attribute) (jax_dna.energy.dna1.StackingConfiguration attribute) (jax_dna.energy.dna2.StackingConfiguration attribute) (jax_dna.energy.rna2.stacking.StackingConfiguration attribute) (jax_dna.energy.rna2.StackingConfiguration attribute)

NeighborHelper (class in jax_dna.simulators.jax_md.utils) NeighborList (class in jax_dna.simulators.jax_md) (class in jax_dna.simulators.jax_md.utils) neighbors (jax_dna.simulators.jax_md.jaxmd.JaxMDSimulator attribute) (jax_dna.simulators.jax_md.JaxMDSimulator attribute) NEW (jax_dna.utils.types.oxDNAFormat attribute) NM_PER_OXDNA_LENGTH (in module jax_dna.utils.units) non_optimizable_required_params (jax_dna.energy.configuration.BaseConfiguration attribute) NoNeighborList (class in jax_dna.simulators.jax_md) (class in jax_dna.simulators.jax_md.utils) nt_type (jax_dna.energy.na1.bonded_excluded_volume.BondedExcludedVolumeConfiguration attribute) (jax_dna.energy.na1.BondedExcludedVolumeConfiguration attribute) (jax_dna.energy.na1.coaxial_stacking.CoaxialStackingConfiguration attribute) (jax_dna.energy.na1.CoaxialStackingConfiguration attribute) (jax_dna.energy.na1.cross_stacking.CrossStackingConfiguration attribute) (jax_dna.energy.na1.CrossStackingConfiguration attribute) (jax_dna.energy.na1.debye.DebyeConfiguration attribute) (jax_dna.energy.na1.DebyeConfiguration attribute) (jax_dna.energy.na1.fene.FeneConfiguration attribute) (jax_dna.energy.na1.FeneConfiguration attribute) (jax_dna.energy.na1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (jax_dna.energy.na1.HydrogenBondingConfiguration attribute) (jax_dna.energy.na1.stacking.StackingConfiguration attribute) (jax_dna.energy.na1.StackingConfiguration attribute) (jax_dna.energy.na1.unbonded_excluded_volume.UnbondedExcludedVolumeConfiguration attribute) (jax_dna.energy.na1.UnbondedExcludedVolumeConfiguration attribute) (jax_dna.input.topology.Topology attribute) Nucleotide (class in jax_dna.energy.dna1) (class in jax_dna.energy.dna1.nucleotide) (class in jax_dna.energy.dna2) (class in jax_dna.energy.dna2.nucleotide) (class in jax_dna.energy.rna2) (class in jax_dna.energy.rna2.nucleotide) NUCLEOTIDE_STATE_SHAPE (in module jax_dna.input.trajectory) NUCLEOTIDES_IDX (in module jax_dna.utils.constants) NucleotideState (class in jax_dna.input.trajectory) NucleotideType (class in jax_dna.input.topology)

O

obj_btns (jax_dna.ui.loggers.jupyter.JupyterLogger attribute) Objective (class in jax_dna.optimization.objective) objective (jax_dna.optimization.optimization.SimpleOptimizer attribute) objectives (jax_dna.optimization.optimization.Optimization attribute) obs_btns (jax_dna.ui.loggers.jupyter.JupyterLogger attribute) observable (jax_dna.losses.observable_wrappers.ObservableLossFn attribute) observable_plots (jax_dna.ui.loggers.jupyter.PlotlyLogger attribute) ObservableLossFn (class in jax_dna.losses.observable_wrappers) obtained_observables() (jax_dna.optimization.objective.Objective method) OPT_ALL (jax_dna.energy.configuration.BaseConfiguration attribute) opt_params (jax_dna.energy.configuration.BaseConfiguration property) Optimization (class in jax_dna.optimization.optimization) optimizer (jax_dna.optimization.optimization.Optimization attribute) (jax_dna.optimization.optimization.SimpleOptimizer attribute) optimizer_state (jax_dna.optimization.optimization.Optimization attribute) (jax_dna.optimization.optimization.SimpleOptimizer attribute) orientation (jax_dna.energy.base.BaseNucleotide attribute) (jax_dna.energy.dna1.Nucleotide attribute) (jax_dna.energy.dna1.nucleotide.Nucleotide attribute) (jax_dna.energy.dna2.Nucleotide attribute) (jax_dna.energy.dna2.nucleotide.Nucleotide attribute) (jax_dna.energy.rna2.Nucleotide attribute) (jax_dna.energy.rna2.nucleotide.Nucleotide attribute)

OXDNA_TOPOLOGY_FILE_KEY (in module jax_dna.simulators.oxdna.oxdna) OXDNA_TRAJECTORY_FILE_KEY (in module jax_dna.simulators.oxdna.oxdna) oxDNABinarySemaphore (class in jax_dna.simulators.oxdna) (class in jax_dna.simulators.oxdna.oxdna) oxDNABinarySemaphoreActor (class in jax_dna.simulators.oxdna) (class in jax_dna.simulators.oxdna.oxdna) oxDNAFormat (class in jax_dna.utils.types) oxDNAModelHType (class in jax_dna.utils.types) oxDNASimulator (class in jax_dna.simulators.oxdna) (class in jax_dna.simulators.oxdna.oxdna) oxDNASimulatorType (class in jax_dna.utils.types)

P

pairwise_energies() (jax_dna.energy.dna1.bonded_excluded_volume.BondedExcludedVolume method) (jax_dna.energy.dna1.BondedExcludedVolume method) (jax_dna.energy.dna1.coaxial_stacking.CoaxialStacking method) (jax_dna.energy.dna1.CoaxialStacking method) (jax_dna.energy.dna1.cross_stacking.CrossStacking method) (jax_dna.energy.dna1.CrossStacking method) (jax_dna.energy.dna1.Fene method) (jax_dna.energy.dna1.fene.Fene method) (jax_dna.energy.dna1.hydrogen_bonding.HydrogenBonding method) (jax_dna.energy.dna1.HydrogenBonding method) (jax_dna.energy.dna1.Stacking method) (jax_dna.energy.dna1.stacking.Stacking method) (jax_dna.energy.dna1.unbonded_excluded_volume.UnbondedExcludedVolume method) (jax_dna.energy.dna1.UnbondedExcludedVolume method) (jax_dna.energy.dna2.BondedExcludedVolume method) (jax_dna.energy.dna2.coaxial_stacking.CoaxialStacking method) (jax_dna.energy.dna2.CoaxialStacking method) (jax_dna.energy.dna2.CrossStacking method) (jax_dna.energy.dna2.Debye method) (jax_dna.energy.dna2.debye.Debye method) (jax_dna.energy.dna2.Fene method) (jax_dna.energy.dna2.HydrogenBonding method) (jax_dna.energy.dna2.Stacking method) (jax_dna.energy.dna2.stacking.Stacking method) (jax_dna.energy.dna2.UnbondedExcludedVolume method) (jax_dna.energy.rna2.cross_stacking.CrossStacking method) (jax_dna.energy.rna2.CrossStacking method) (jax_dna.energy.rna2.Stacking method) (jax_dna.energy.rna2.stacking.Stacking method) Params (in module jax_dna.utils.types) params (jax_dna.energy.dna1.bonded_excluded_volume.BondedExcludedVolume attribute) (jax_dna.energy.dna1.BondedExcludedVolume attribute) (jax_dna.energy.dna1.coaxial_stacking.CoaxialStacking attribute) (jax_dna.energy.dna1.CoaxialStacking attribute) (jax_dna.energy.dna1.cross_stacking.CrossStacking attribute) (jax_dna.energy.dna1.CrossStacking attribute) (jax_dna.energy.dna1.expected_hydrogen_bonding.ExpectedHydrogenBonding attribute) (jax_dna.energy.dna1.expected_stacking.ExpectedStacking attribute) (jax_dna.energy.dna1.ExpectedHydrogenBonding attribute) (jax_dna.energy.dna1.ExpectedStacking attribute) (jax_dna.energy.dna1.Fene attribute) (jax_dna.energy.dna1.fene.Fene attribute) (jax_dna.energy.dna1.hydrogen_bonding.HydrogenBonding attribute) (jax_dna.energy.dna1.HydrogenBonding attribute) (jax_dna.energy.dna1.Stacking attribute) (jax_dna.energy.dna1.stacking.Stacking attribute) (jax_dna.energy.dna1.unbonded_excluded_volume.UnbondedExcludedVolume attribute) (jax_dna.energy.dna1.UnbondedExcludedVolume attribute) (jax_dna.energy.dna2.BondedExcludedVolume attribute) (jax_dna.energy.dna2.coaxial_stacking.CoaxialStacking attribute) (jax_dna.energy.dna2.CoaxialStacking attribute) (jax_dna.energy.dna2.CrossStacking attribute) (jax_dna.energy.dna2.Debye attribute) (jax_dna.energy.dna2.debye.Debye attribute) (jax_dna.energy.dna2.Fene attribute) (jax_dna.energy.dna2.HydrogenBonding attribute) (jax_dna.energy.dna2.Stacking attribute) (jax_dna.energy.dna2.stacking.Stacking attribute) (jax_dna.energy.dna2.UnbondedExcludedVolume attribute) (jax_dna.energy.na1.bonded_excluded_volume.BondedExcludedVolume attribute) (jax_dna.energy.na1.BondedExcludedVolume attribute) (jax_dna.energy.na1.coaxial_stacking.CoaxialStacking attribute) (jax_dna.energy.na1.CoaxialStacking attribute) (jax_dna.energy.na1.cross_stacking.CrossStacking attribute) (jax_dna.energy.na1.CrossStacking attribute) (jax_dna.energy.na1.Debye attribute) (jax_dna.energy.na1.debye.Debye attribute) (jax_dna.energy.na1.Fene attribute) (jax_dna.energy.na1.fene.Fene attribute) (jax_dna.energy.na1.hydrogen_bonding.HydrogenBonding attribute) (jax_dna.energy.na1.HydrogenBonding attribute) (jax_dna.energy.na1.Stacking attribute) (jax_dna.energy.na1.stacking.Stacking attribute) (jax_dna.energy.na1.unbonded_excluded_volume.UnbondedExcludedVolume attribute) (jax_dna.energy.na1.UnbondedExcludedVolume attribute) (jax_dna.energy.rna2.cross_stacking.CrossStacking attribute) (jax_dna.energy.rna2.CrossStacking attribute) (jax_dna.energy.rna2.Stacking attribute) (jax_dna.energy.rna2.stacking.Stacking attribute)

params_to_optimize (jax_dna.energy.configuration.BaseConfiguration attribute) parse_str() (in module jax_dna.input.toml) parse_toml() (in module jax_dna.input.toml) parse_value() (in module jax_dna.input.toml) PathOrStr (in module jax_dna.utils.types) percent_complete (jax_dna.ui.loggers.jupyter.JupyterLogger attribute) persistence_length_fit() (in module jax_dna.observables.persistence_length) PitchAngle (class in jax_dna.observables.pitch) PlotlyLogger (class in jax_dna.ui.loggers.jupyter) plots (jax_dna.ui.loggers.jupyter.JupyterLogger attribute) PN_PER_OXDNA_FORCE (in module jax_dna.utils.units) position (jax_dna.simulators.jax_md.SimulationState attribute) (jax_dna.simulators.jax_md.utils.SimulationState attribute) post_step() (jax_dna.optimization.objective.DiffTReObjective method) (jax_dna.optimization.objective.Objective method) (jax_dna.optimization.optimization.Optimization method) (jax_dna.optimization.optimization.SimpleOptimizer method) prefactor (jax_dna.energy.dna2.debye.DebyeConfiguration attribute) (jax_dna.energy.dna2.DebyeConfiguration attribute) prefactor_coeff (jax_dna.energy.dna2.debye.DebyeConfiguration attribute) (jax_dna.energy.dna2.DebyeConfiguration attribute) principal_axes_to_euler_angles() (in module jax_dna.utils.math) Probabilistic_Sequence (in module jax_dna.utils.types) prog_bar (jax_dna.ui.loggers.jupyter.JupyterLogger attribute) propeller_twist_rad (in module jax_dna.observables.propeller) PropellerTwist (class in jax_dna.observables.propeller) PyTree (in module jax_dna.utils.types)

Q

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

quartets (jax_dna.observables.persistence_length.LpMetadata attribute) (jax_dna.observables.pitch.PitchAngle attribute) (jax_dna.observables.rise.Rise attribute) (jax_dna.observables.stretch_torsion.TwistXY attribute) quaternions (jax_dna.input.trajectory.NucleotideState property)

R

r0_backbone (jax_dna.energy.dna1.fene.FeneConfiguration attribute) (jax_dna.energy.dna1.FeneConfiguration attribute) (jax_dna.energy.dna2.FeneConfiguration attribute) r0_cross (jax_dna.energy.dna1.cross_stacking.CrossStackingConfiguration attribute) (jax_dna.energy.dna1.CrossStackingConfiguration attribute) (jax_dna.energy.dna2.CrossStackingConfiguration attribute) (jax_dna.energy.rna2.cross_stacking.CrossStackingConfiguration attribute) (jax_dna.energy.rna2.CrossStackingConfiguration attribute) r_cut (jax_dna.energy.dna2.debye.DebyeConfiguration attribute) (jax_dna.energy.dna2.DebyeConfiguration attribute) r_cutoff (jax_dna.simulators.jax_md.NeighborList attribute) (jax_dna.simulators.jax_md.utils.NeighborList attribute) r_high (jax_dna.energy.dna2.debye.DebyeConfiguration attribute) (jax_dna.energy.dna2.DebyeConfiguration attribute) read() (in module jax_dna.input.oxdna_input) read_src_h() (in module jax_dna.simulators.oxdna.utils) REQUIRED_KEYS (in module jax_dna.simulators.jax_md.jaxmd) (in module jax_dna.simulators.oxdna.oxdna) required_observables() (jax_dna.optimization.objective.Objective method) required_params (jax_dna.energy.configuration.BaseConfiguration attribute) (jax_dna.energy.dna1.bonded_excluded_volume.BondedExcludedVolumeConfiguration attribute) (jax_dna.energy.dna1.BondedExcludedVolumeConfiguration attribute) (jax_dna.energy.dna1.coaxial_stacking.CoaxialStackingConfiguration attribute) (jax_dna.energy.dna1.CoaxialStackingConfiguration attribute) (jax_dna.energy.dna1.cross_stacking.CrossStackingConfiguration attribute) (jax_dna.energy.dna1.CrossStackingConfiguration attribute) (jax_dna.energy.dna1.expected_hydrogen_bonding.ExpectedHydrogenBondingConfiguration attribute) (jax_dna.energy.dna1.expected_stacking.ExpectedStackingConfiguration attribute) (jax_dna.energy.dna1.ExpectedHydrogenBondingConfiguration attribute) (jax_dna.energy.dna1.ExpectedStackingConfiguration attribute) (jax_dna.energy.dna1.fene.FeneConfiguration attribute) (jax_dna.energy.dna1.FeneConfiguration attribute) (jax_dna.energy.dna1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (jax_dna.energy.dna1.HydrogenBondingConfiguration attribute) (jax_dna.energy.dna1.stacking.StackingConfiguration attribute) (jax_dna.energy.dna1.StackingConfiguration attribute) (jax_dna.energy.dna1.unbonded_excluded_volume.UnbondedExcludedVolumeConfiguration attribute) (jax_dna.energy.dna1.UnbondedExcludedVolumeConfiguration attribute) (jax_dna.energy.dna2.BondedExcludedVolumeConfiguration attribute) (jax_dna.energy.dna2.coaxial_stacking.CoaxialStackingConfiguration attribute) (jax_dna.energy.dna2.CoaxialStackingConfiguration attribute) (jax_dna.energy.dna2.CrossStackingConfiguration attribute) (jax_dna.energy.dna2.debye.DebyeConfiguration attribute) (jax_dna.energy.dna2.DebyeConfiguration attribute) (jax_dna.energy.dna2.FeneConfiguration attribute) (jax_dna.energy.dna2.HydrogenBondingConfiguration attribute) (jax_dna.energy.dna2.StackingConfiguration attribute) (jax_dna.energy.dna2.UnbondedExcludedVolumeConfiguration attribute) (jax_dna.energy.na1.bonded_excluded_volume.BondedExcludedVolumeConfiguration attribute) (jax_dna.energy.na1.BondedExcludedVolumeConfiguration attribute) (jax_dna.energy.na1.coaxial_stacking.CoaxialStackingConfiguration attribute) (jax_dna.energy.na1.CoaxialStackingConfiguration attribute) (jax_dna.energy.na1.cross_stacking.CrossStackingConfiguration attribute) (jax_dna.energy.na1.CrossStackingConfiguration attribute) (jax_dna.energy.na1.debye.DebyeConfiguration attribute) (jax_dna.energy.na1.DebyeConfiguration attribute) (jax_dna.energy.na1.fene.FeneConfiguration attribute) (jax_dna.energy.na1.FeneConfiguration attribute) (jax_dna.energy.na1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (jax_dna.energy.na1.HydrogenBondingConfiguration attribute) (jax_dna.energy.na1.stacking.StackingConfiguration attribute) (jax_dna.energy.na1.StackingConfiguration attribute) (jax_dna.energy.na1.unbonded_excluded_volume.UnbondedExcludedVolumeConfiguration attribute) (jax_dna.energy.na1.UnbondedExcludedVolumeConfiguration attribute) (jax_dna.energy.rna2.cross_stacking.CrossStackingConfiguration attribute) (jax_dna.energy.rna2.CrossStackingConfiguration attribute) (jax_dna.energy.rna2.stacking.StackingConfiguration attribute) (jax_dna.energy.rna2.StackingConfiguration attribute) return_observable (jax_dna.losses.observable_wrappers.ObservableLossFn attribute) rigid_body (jax_dna.simulators.io.SimulatorTrajectory attribute) rigid_body_transform_fn (jax_dna.energy.base.ComposedEnergyFunction attribute) (jax_dna.observables.base.BaseObservable attribute) Rise (class in jax_dna.observables.rise) RMSE (class in jax_dna.observables.rmse) rna (jax_dna.energy.na1.HybridNucleotide attribute) (jax_dna.energy.na1.nucleotide.HybridNucleotide attribute) RNA (jax_dna.input.topology.NucleotideType attribute) rna_a_coax_1 (jax_dna.energy.na1.coaxial_stacking.CoaxialStackingConfiguration attribute) (jax_dna.energy.na1.CoaxialStackingConfiguration attribute) rna_a_coax_3p (jax_dna.energy.na1.coaxial_stacking.CoaxialStackingConfiguration attribute) (jax_dna.energy.na1.CoaxialStackingConfiguration attribute) rna_a_coax_4 (jax_dna.energy.na1.coaxial_stacking.CoaxialStackingConfiguration attribute) (jax_dna.energy.na1.CoaxialStackingConfiguration attribute) rna_a_coax_4p (jax_dna.energy.na1.coaxial_stacking.CoaxialStackingConfiguration attribute) (jax_dna.energy.na1.CoaxialStackingConfiguration attribute) rna_a_coax_5 (jax_dna.energy.na1.coaxial_stacking.CoaxialStackingConfiguration attribute) (jax_dna.energy.na1.CoaxialStackingConfiguration attribute) rna_a_coax_6 (jax_dna.energy.na1.coaxial_stacking.CoaxialStackingConfiguration attribute) (jax_dna.energy.na1.CoaxialStackingConfiguration attribute) rna_a_cross_1 (jax_dna.energy.na1.cross_stacking.CrossStackingConfiguration attribute) (jax_dna.energy.na1.CrossStackingConfiguration attribute) rna_a_cross_2 (jax_dna.energy.na1.cross_stacking.CrossStackingConfiguration attribute) (jax_dna.energy.na1.CrossStackingConfiguration attribute) rna_a_cross_3 (jax_dna.energy.na1.cross_stacking.CrossStackingConfiguration attribute) (jax_dna.energy.na1.CrossStackingConfiguration attribute) rna_a_cross_7 (jax_dna.energy.na1.cross_stacking.CrossStackingConfiguration attribute) (jax_dna.energy.na1.CrossStackingConfiguration attribute) rna_a_cross_8 (jax_dna.energy.na1.cross_stacking.CrossStackingConfiguration attribute) (jax_dna.energy.na1.CrossStackingConfiguration attribute) rna_a_hb (jax_dna.energy.na1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (jax_dna.energy.na1.HydrogenBondingConfiguration attribute) rna_a_hb_1 (jax_dna.energy.na1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (jax_dna.energy.na1.HydrogenBondingConfiguration attribute) rna_a_hb_2 (jax_dna.energy.na1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (jax_dna.energy.na1.HydrogenBondingConfiguration attribute) rna_a_hb_3 (jax_dna.energy.na1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (jax_dna.energy.na1.HydrogenBondingConfiguration attribute) rna_a_hb_4 (jax_dna.energy.na1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (jax_dna.energy.na1.HydrogenBondingConfiguration attribute) rna_a_hb_7 (jax_dna.energy.na1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (jax_dna.energy.na1.HydrogenBondingConfiguration attribute) rna_a_hb_8 (jax_dna.energy.na1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (jax_dna.energy.na1.HydrogenBondingConfiguration attribute) rna_a_stack (jax_dna.energy.na1.stacking.StackingConfiguration attribute) (jax_dna.energy.na1.StackingConfiguration attribute) rna_a_stack_1 (jax_dna.energy.na1.stacking.StackingConfiguration attribute) (jax_dna.energy.na1.StackingConfiguration attribute) rna_a_stack_10 (jax_dna.energy.na1.stacking.StackingConfiguration attribute) (jax_dna.energy.na1.StackingConfiguration attribute) rna_a_stack_2 (jax_dna.energy.na1.stacking.StackingConfiguration attribute) (jax_dna.energy.na1.StackingConfiguration attribute) rna_a_stack_5 (jax_dna.energy.na1.stacking.StackingConfiguration attribute) (jax_dna.energy.na1.StackingConfiguration attribute) rna_a_stack_6 (jax_dna.energy.na1.stacking.StackingConfiguration attribute) (jax_dna.energy.na1.StackingConfiguration attribute) rna_a_stack_9 (jax_dna.energy.na1.stacking.StackingConfiguration attribute) (jax_dna.energy.na1.StackingConfiguration attribute) RNA_ALPHA (in module jax_dna.utils.constants) rna_config (jax_dna.energy.na1.bonded_excluded_volume.BondedExcludedVolumeConfiguration attribute) (jax_dna.energy.na1.BondedExcludedVolumeConfiguration attribute) (jax_dna.energy.na1.coaxial_stacking.CoaxialStackingConfiguration attribute) (jax_dna.energy.na1.CoaxialStackingConfiguration attribute) (jax_dna.energy.na1.cross_stacking.CrossStackingConfiguration attribute) (jax_dna.energy.na1.CrossStackingConfiguration attribute) (jax_dna.energy.na1.debye.DebyeConfiguration attribute) (jax_dna.energy.na1.DebyeConfiguration attribute) (jax_dna.energy.na1.fene.FeneConfiguration attribute) (jax_dna.energy.na1.FeneConfiguration attribute) (jax_dna.energy.na1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (jax_dna.energy.na1.HydrogenBondingConfiguration attribute) (jax_dna.energy.na1.stacking.StackingConfiguration attribute) (jax_dna.energy.na1.StackingConfiguration attribute) (jax_dna.energy.na1.unbonded_excluded_volume.UnbondedExcludedVolumeConfiguration attribute) (jax_dna.energy.na1.UnbondedExcludedVolumeConfiguration attribute) rna_cos_phi3_star_coax (jax_dna.energy.na1.coaxial_stacking.CoaxialStackingConfiguration attribute) (jax_dna.energy.na1.CoaxialStackingConfiguration attribute) rna_cos_phi4_star_coax (jax_dna.energy.na1.coaxial_stacking.CoaxialStackingConfiguration attribute) (jax_dna.energy.na1.CoaxialStackingConfiguration attribute) rna_delta_backbone (jax_dna.energy.na1.fene.FeneConfiguration attribute) (jax_dna.energy.na1.FeneConfiguration attribute) rna_delta_theta_star_coax_1 (jax_dna.energy.na1.coaxial_stacking.CoaxialStackingConfiguration attribute) (jax_dna.energy.na1.CoaxialStackingConfiguration attribute) rna_delta_theta_star_coax_4 (jax_dna.energy.na1.coaxial_stacking.CoaxialStackingConfiguration attribute) (jax_dna.energy.na1.CoaxialStackingConfiguration attribute) rna_delta_theta_star_coax_5 (jax_dna.energy.na1.coaxial_stacking.CoaxialStackingConfiguration attribute) (jax_dna.energy.na1.CoaxialStackingConfiguration attribute) rna_delta_theta_star_coax_6 (jax_dna.energy.na1.coaxial_stacking.CoaxialStackingConfiguration attribute) (jax_dna.energy.na1.CoaxialStackingConfiguration attribute) rna_delta_theta_star_cross_1 (jax_dna.energy.na1.cross_stacking.CrossStackingConfiguration attribute) (jax_dna.energy.na1.CrossStackingConfiguration attribute) rna_delta_theta_star_cross_2 (jax_dna.energy.na1.cross_stacking.CrossStackingConfiguration attribute) (jax_dna.energy.na1.CrossStackingConfiguration attribute) rna_delta_theta_star_cross_3 (jax_dna.energy.na1.cross_stacking.CrossStackingConfiguration attribute) (jax_dna.energy.na1.CrossStackingConfiguration attribute)

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

S

salt_conc (jax_dna.energy.dna2.debye.DebyeConfiguration attribute) (jax_dna.energy.dna2.DebyeConfiguration attribute) (jax_dna.energy.na1.debye.DebyeConfiguration attribute) (jax_dna.energy.na1.DebyeConfiguration attribute) sample_every (jax_dna.gradient_estimators.difftre.DiffTRe attribute) save_pytree() (in module jax_dna.input.tree) Scalar (in module jax_dna.utils.types) scatter_f (in module jax_dna.ui.loggers.jupyter) seq (jax_dna.input.topology.Topology attribute) (jax_dna.simulators.jax_md.StaticSimulatorParams attribute) (jax_dna.simulators.jax_md.utils.StaticSimulatorParams attribute) Sequence (in module jax_dna.utils.types) sequence_constraints (jax_dna.energy.dna1.expected_hydrogen_bonding.ExpectedHydrogenBondingConfiguration attribute) (jax_dna.energy.dna1.expected_stacking.ExpectedStackingConfiguration attribute) (jax_dna.energy.dna1.ExpectedHydrogenBondingConfiguration attribute) (jax_dna.energy.dna1.ExpectedStackingConfiguration attribute) SequenceConstraints (class in jax_dna.input.sequence_constraints) set() (jax_dna.simulators.oxdna.oxdna.oxDNABinarySemaphore method) (jax_dna.simulators.oxdna.oxDNABinarySemaphore method) set_build_ready (jax_dna.simulators.oxdna.oxdna.oxDNASimulator attribute) (jax_dna.simulators.oxdna.oxDNASimulator attribute) set_objective_complete() (jax_dna.ui.loggers.console.ConsoleLogger method) (jax_dna.ui.loggers.jupyter.JupyterLogger method) (jax_dna.ui.loggers.logger.Logger method) set_objective_error() (jax_dna.ui.loggers.console.ConsoleLogger method) (jax_dna.ui.loggers.jupyter.JupyterLogger method) (jax_dna.ui.loggers.logger.Logger method) set_objective_running() (jax_dna.ui.loggers.console.ConsoleLogger method) (jax_dna.ui.loggers.jupyter.JupyterLogger method) (jax_dna.ui.loggers.logger.Logger method) set_objective_started() (jax_dna.ui.loggers.console.ConsoleLogger method) (jax_dna.ui.loggers.jupyter.JupyterLogger method) (jax_dna.ui.loggers.logger.Logger method) set_observable_complete() (jax_dna.ui.loggers.console.ConsoleLogger method) (jax_dna.ui.loggers.jupyter.JupyterLogger method) (jax_dna.ui.loggers.logger.Logger method) set_observable_error() (jax_dna.ui.loggers.console.ConsoleLogger method) (jax_dna.ui.loggers.jupyter.JupyterLogger method) (jax_dna.ui.loggers.logger.Logger method) set_observable_running() (jax_dna.ui.loggers.console.ConsoleLogger method) (jax_dna.ui.loggers.jupyter.JupyterLogger method) (jax_dna.ui.loggers.logger.Logger method) set_observable_started() (jax_dna.ui.loggers.console.ConsoleLogger method) (jax_dna.ui.loggers.jupyter.JupyterLogger method) (jax_dna.ui.loggers.logger.Logger method) set_simulator_complete() (jax_dna.ui.loggers.console.ConsoleLogger method) (jax_dna.ui.loggers.jupyter.JupyterLogger method) (jax_dna.ui.loggers.logger.Logger method) set_simulator_error() (jax_dna.ui.loggers.console.ConsoleLogger method) (jax_dna.ui.loggers.jupyter.JupyterLogger method) (jax_dna.ui.loggers.logger.Logger method) set_simulator_running() (jax_dna.ui.loggers.console.ConsoleLogger method) (jax_dna.ui.loggers.jupyter.JupyterLogger method) (jax_dna.ui.loggers.logger.Logger method) set_simulator_started() (jax_dna.ui.loggers.console.ConsoleLogger method) (jax_dna.ui.loggers.jupyter.JupyterLogger method) (jax_dna.ui.loggers.logger.Logger method) setup_figure_layout() (in module jax_dna.ui.loggers.jupyter) show() (jax_dna.ui.loggers.jupyter.JupyterLogger method) (jax_dna.ui.loggers.jupyter.PlotlyLogger method) sigma_back_base (jax_dna.energy.dna1.bonded_excluded_volume.BondedExcludedVolumeConfiguration attribute) (jax_dna.energy.dna1.BondedExcludedVolumeConfiguration attribute) (jax_dna.energy.dna1.unbonded_excluded_volume.UnbondedExcludedVolumeConfiguration attribute) (jax_dna.energy.dna1.UnbondedExcludedVolumeConfiguration attribute) (jax_dna.energy.dna2.BondedExcludedVolumeConfiguration attribute) (jax_dna.energy.dna2.UnbondedExcludedVolumeConfiguration attribute) sigma_backbone (jax_dna.energy.dna1.unbonded_excluded_volume.UnbondedExcludedVolumeConfiguration attribute) (jax_dna.energy.dna1.UnbondedExcludedVolumeConfiguration attribute) (jax_dna.energy.dna2.UnbondedExcludedVolumeConfiguration attribute) sigma_base (jax_dna.energy.dna1.bonded_excluded_volume.BondedExcludedVolumeConfiguration attribute) (jax_dna.energy.dna1.BondedExcludedVolumeConfiguration attribute) (jax_dna.energy.dna1.unbonded_excluded_volume.UnbondedExcludedVolumeConfiguration attribute) (jax_dna.energy.dna1.UnbondedExcludedVolumeConfiguration attribute) (jax_dna.energy.dna2.BondedExcludedVolumeConfiguration attribute) (jax_dna.energy.dna2.UnbondedExcludedVolumeConfiguration attribute) sigma_base_back (jax_dna.energy.dna1.bonded_excluded_volume.BondedExcludedVolumeConfiguration attribute) (jax_dna.energy.dna1.BondedExcludedVolumeConfiguration attribute) (jax_dna.energy.dna1.unbonded_excluded_volume.UnbondedExcludedVolumeConfiguration attribute) (jax_dna.energy.dna1.UnbondedExcludedVolumeConfiguration attribute) (jax_dna.energy.dna2.BondedExcludedVolumeConfiguration attribute) (jax_dna.energy.dna2.UnbondedExcludedVolumeConfiguration attribute) sim_btns (jax_dna.ui.loggers.jupyter.JupyterLogger attribute) sim_init_fn (jax_dna.gradient_estimators.difftre.DiffTRe attribute) (jax_dna.simulators.jax_md.StaticSimulatorParams property) (jax_dna.simulators.jax_md.utils.StaticSimulatorParams property) SIM_STATE (in module jax_dna.simulators.jax_md.jaxmd) sim_type (jax_dna.simulators.oxdna.oxdna.oxDNASimulator attribute) (jax_dna.simulators.oxdna.oxDNASimulator attribute) SimGradObjectiveActor (class in jax_dna.optimization.objective)

SimpleOptimizer (class in jax_dna.optimization.optimization) SimulationState (class in jax_dna.simulators.jax_md) (class in jax_dna.simulators.jax_md.utils) simulator (jax_dna.optimization.optimization.SimpleOptimizer attribute) simulator_init (jax_dna.simulators.jax_md.jaxmd.JaxMDSimulator attribute) (jax_dna.simulators.jax_md.JaxMDSimulator attribute) simulator_params (jax_dna.simulators.jax_md.jaxmd.JaxMDSimulator attribute) (jax_dna.simulators.jax_md.JaxMDSimulator attribute) SimulatorActor (class in jax_dna.optimization.simulator) SimulatorActorOutput (in module jax_dna.utils.types) simulators (jax_dna.optimization.optimization.Optimization attribute) SimulatorTrajectory (class in jax_dna.simulators.io) single_angle_xy() (in module jax_dna.observables.stretch_torsion) single_diameter() (in module jax_dna.observables.diameter) single_diameter_mapped (in module jax_dna.observables.diameter) single_extension_z() (in module jax_dna.observables.stretch_torsion) single_pitch_angle() (in module jax_dna.observables.pitch) single_pitch_angle_mapped (in module jax_dna.observables.pitch) single_propeller_twist_rad() (in module jax_dna.observables.propeller) single_rise() (in module jax_dna.observables.rise) single_rise_mapped (in module jax_dna.observables.rise) single_rmse() (in module jax_dna.observables.rmse) slice() (jax_dna.input.trajectory.Trajectory method) (jax_dna.simulators.io.SimulatorTrajectory method) smooth_abs() (in module jax_dna.utils.math) smoothing_coeff (jax_dna.energy.dna2.debye.DebyeConfiguration attribute) (jax_dna.energy.dna2.DebyeConfiguration attribute) space (jax_dna.simulators.jax_md.jaxmd.JaxMDSimulator attribute) (jax_dna.simulators.jax_md.JaxMDSimulator attribute) split_and_stack() (in module jax_dna.simulators.jax_md.utils) split_by_ready() (in module jax_dna.optimization.optimization) SquaredError (class in jax_dna.losses.observable_wrappers) ss_hb_weights (jax_dna.energy.dna1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (jax_dna.energy.dna1.HydrogenBondingConfiguration attribute) (jax_dna.energy.dna2.HydrogenBondingConfiguration attribute) ss_stack_weights (jax_dna.energy.dna1.stacking.StackingConfiguration attribute) (jax_dna.energy.dna1.StackingConfiguration attribute) (jax_dna.energy.dna2.StackingConfiguration attribute) (jax_dna.energy.rna2.stacking.StackingConfiguration attribute) (jax_dna.energy.rna2.StackingConfiguration attribute) stack3_sites (jax_dna.energy.rna2.Nucleotide attribute) (jax_dna.energy.rna2.nucleotide.Nucleotide attribute) stack5_sites (jax_dna.energy.rna2.Nucleotide attribute) (jax_dna.energy.rna2.nucleotide.Nucleotide attribute) stack_sites (jax_dna.energy.base.BaseNucleotide attribute) (jax_dna.energy.dna1.Nucleotide attribute) (jax_dna.energy.dna1.nucleotide.Nucleotide attribute) (jax_dna.energy.dna2.Nucleotide attribute) (jax_dna.energy.dna2.nucleotide.Nucleotide attribute) (jax_dna.energy.rna2.Nucleotide attribute) (jax_dna.energy.rna2.nucleotide.Nucleotide attribute) STACK_WEIGHTS_SA (in module jax_dna.energy.dna1.stacking) Stacking (class in jax_dna.energy.dna1) (class in jax_dna.energy.dna1.stacking) (class in jax_dna.energy.dna2) (class in jax_dna.energy.dna2.stacking) (class in jax_dna.energy.na1) (class in jax_dna.energy.na1.stacking) (class in jax_dna.energy.rna2) (class in jax_dna.energy.rna2.stacking) stacking() (in module jax_dna.energy.dna1.interactions) (in module jax_dna.energy.rna2.interactions) StackingConfiguration (class in jax_dna.energy.dna1) (class in jax_dna.energy.dna1.stacking) (class in jax_dna.energy.dna2) (class in jax_dna.energy.na1) (class in jax_dna.energy.na1.stacking) (class in jax_dna.energy.rna2) (class in jax_dna.energy.rna2.stacking) STARTED (jax_dna.ui.loggers.logger.Status attribute) state_rigid_bodies (jax_dna.input.trajectory.Trajectory property) state_rigid_body (jax_dna.input.trajectory.Trajectory property) states (jax_dna.input.trajectory.Trajectory attribute) StaticSimulatorParams (class in jax_dna.simulators.jax_md) (class in jax_dna.simulators.jax_md.utils) Status (class in jax_dna.ui.loggers.logger) STATUS_STYLE (jax_dna.ui.loggers.jupyter.JupyterLogger attribute) step() (jax_dna.optimization.optimization.Optimization method) (jax_dna.optimization.optimization.SimpleOptimizer method) step_fn (jax_dna.simulators.jax_md.StaticSimulatorParams property) (jax_dna.simulators.jax_md.utils.StaticSimulatorParams property) strand_counts (jax_dna.input.topology.Topology attribute) strand_lengths (jax_dna.input.trajectory.Trajectory attribute) stretch() (in module jax_dna.observables.stretch_torsion) stretch_torsion() (in module jax_dna.observables.stretch_torsion) STRING (jax_dna.utils.types.oxDNAModelHType attribute) svd_align() (in module jax_dna.observables.rmse) SYMPY_EVAL_N (in module jax_dna.input.toml) (in module jax_dna.simulators.oxdna.utils)

T

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

theta0_hb_2 (jax_dna.energy.dna1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (jax_dna.energy.dna1.HydrogenBondingConfiguration attribute) (jax_dna.energy.dna2.HydrogenBondingConfiguration attribute) theta0_hb_3 (jax_dna.energy.dna1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (jax_dna.energy.dna1.HydrogenBondingConfiguration attribute) (jax_dna.energy.dna2.HydrogenBondingConfiguration attribute) theta0_hb_4 (jax_dna.energy.dna1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (jax_dna.energy.dna1.HydrogenBondingConfiguration attribute) (jax_dna.energy.dna2.HydrogenBondingConfiguration attribute) theta0_hb_7 (jax_dna.energy.dna1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (jax_dna.energy.dna1.HydrogenBondingConfiguration attribute) (jax_dna.energy.dna2.HydrogenBondingConfiguration attribute) theta0_hb_8 (jax_dna.energy.dna1.hydrogen_bonding.HydrogenBondingConfiguration attribute) (jax_dna.energy.dna1.HydrogenBondingConfiguration attribute) (jax_dna.energy.dna2.HydrogenBondingConfiguration attribute) theta0_stack_10 (jax_dna.energy.rna2.stacking.StackingConfiguration attribute) (jax_dna.energy.rna2.StackingConfiguration attribute) theta0_stack_4 (jax_dna.energy.dna1.stacking.StackingConfiguration attribute) (jax_dna.energy.dna1.StackingConfiguration attribute) (jax_dna.energy.dna2.StackingConfiguration attribute) theta0_stack_5 (jax_dna.energy.dna1.stacking.StackingConfiguration attribute) (jax_dna.energy.dna1.StackingConfiguration attribute) (jax_dna.energy.dna2.StackingConfiguration attribute) (jax_dna.energy.rna2.stacking.StackingConfiguration attribute) (jax_dna.energy.rna2.StackingConfiguration attribute) theta0_stack_6 (jax_dna.energy.dna1.stacking.StackingConfiguration attribute) (jax_dna.energy.dna1.StackingConfiguration attribute) (jax_dna.energy.dna2.StackingConfiguration attribute) (jax_dna.energy.rna2.stacking.StackingConfiguration attribute) (jax_dna.energy.rna2.StackingConfiguration attribute) theta0_stack_9 (jax_dna.energy.rna2.stacking.StackingConfiguration attribute) (jax_dna.energy.rna2.StackingConfiguration attribute) THREE_DIMENSIONS (in module jax_dna.observables.rmse) times (jax_dna.input.trajectory.Trajectory attribute) to_dictionary() (jax_dna.energy.configuration.BaseConfiguration method) to_rigid_body() (jax_dna.input.trajectory.NucleotideState method) Topology (class in jax_dna.input.topology) topology (jax_dna.simulators.jax_md.jaxmd.JaxMDSimulator attribute) (jax_dna.simulators.jax_md.JaxMDSimulator attribute) (jax_dna.simulators.jax_md.NeighborList attribute) (jax_dna.simulators.jax_md.utils.NeighborList attribute) torsion() (in module jax_dna.observables.stretch_torsion) Trajectory (class in jax_dna.input.trajectory) TRAJECTORY_ENERGIES_SHAPE (in module jax_dna.input.trajectory) TRAJECTORY_TIMES_DIMS (in module jax_dna.input.trajectory) transform_fn (jax_dna.simulators.jax_md.jaxmd.JaxMDSimulator attribute) (jax_dna.simulators.jax_md.JaxMDSimulator attribute) tree_concatenate() (in module jax_dna.utils.helpers) tree_stack() (in module jax_dna.utils.helpers) TwistXY (class in jax_dna.observables.stretch_torsion) TWO_DIMENSIONS (in module jax_dna.utils.constants)

U

unbonded_nbrs (jax_dna.simulators.jax_md.NoNeighborList attribute) (jax_dna.simulators.jax_md.utils.NoNeighborList attribute) unbonded_neighbors (jax_dna.input.topology.Topology attribute) UnbondedExcludedVolume (class in jax_dna.energy.dna1) (class in jax_dna.energy.dna1.unbonded_excluded_volume) (class in jax_dna.energy.dna2) (class in jax_dna.energy.na1) (class in jax_dna.energy.na1.unbonded_excluded_volume) UnbondedExcludedVolumeConfiguration (class in jax_dna.energy.dna1) (class in jax_dna.energy.dna1.unbonded_excluded_volume) (class in jax_dna.energy.dna2) (class in jax_dna.energy.na1) (class in jax_dna.energy.na1.unbonded_excluded_volume) unpaired (jax_dna.input.sequence_constraints.SequenceConstraints attribute) UNSPECIFIED (jax_dna.input.topology.NucleotideType attribute) update() (jax_dna.optimization.objective.Objective method) (jax_dna.simulators.base.BaseSimulation method) (jax_dna.simulators.jax_md.NeighborList method) (jax_dna.simulators.jax_md.NoNeighborList method) (jax_dna.simulators.jax_md.utils.NeighborHelper method) (jax_dna.simulators.jax_md.utils.NeighborList method) (jax_dna.simulators.jax_md.utils.NoNeighborList method)

update_objective_status() (jax_dna.ui.loggers.console.ConsoleLogger method) (jax_dna.ui.loggers.jupyter.JupyterLogger method) (jax_dna.ui.loggers.logger.Logger method) update_observable_status() (jax_dna.ui.loggers.console.ConsoleLogger method) (jax_dna.ui.loggers.jupyter.JupyterLogger method) (jax_dna.ui.loggers.logger.Logger method) update_params() (in module jax_dna.simulators.oxdna.utils) update_simulator_status() (jax_dna.ui.loggers.console.ConsoleLogger method) (jax_dna.ui.loggers.jupyter.JupyterLogger method) (jax_dna.ui.loggers.logger.Logger method)

V

v_fene() (in module jax_dna.energy.potentials) v_fene_smooth() (in module jax_dna.energy.dna1.interactions) v_harmonic() (in module jax_dna.energy.potentials) v_lj() (in module jax_dna.energy.potentials) v_mod() (in module jax_dna.energy.potentials) v_morse() (in module jax_dna.energy.potentials) v_smooth() (in module jax_dna.energy.potentials)

VALID_NEIGHBOR_SECOND_DIM (in module jax_dna.input.topology) validate_box_size() (in module jax_dna.input.trajectory) Vector3D (in module jax_dna.utils.types) Vector4D (in module jax_dna.utils.types) vector_autocorrelate() (in module jax_dna.observables.persistence_length) velocity (jax_dna.input.trajectory.NucleotideState property) version (in module jax_dna._version) version_tuple (in module jax_dna._version)

W

wait_fn (in module jax_dna.optimization.optimization) WARN_CANT_GUESS_BIN_LOC (in module jax_dna.simulators.oxdna.oxdna) WARN_CLASSIC_UNSPECIFIED_NT_TYPE (in module jax_dna.input.topology) WARN_DEPENDENT_PARAMS_NOT_INITIALIZED (in module jax_dna.energy.configuration) WARN_INIT_PARAMS_NOT_IMPLEMENTED (in module jax_dna.energy.configuration) WARN_INVALID_NCOLS_NROWS (in module jax_dna.ui.loggers.jupyter) WARN_NEW_UNSPECIFIED_NT_TYPE (in module jax_dna.input.topology)

weight() (jax_dna.energy.dna1.expected_hydrogen_bonding.ExpectedHydrogenBonding method) (jax_dna.energy.dna1.expected_stacking.ExpectedStacking method) (jax_dna.energy.dna1.ExpectedHydrogenBonding method) (jax_dna.energy.dna1.ExpectedStacking method) weights (jax_dna.energy.base.ComposedEnergyFunction attribute) write() (in module jax_dna.input.oxdna_input) write_src_h() (in module jax_dna.simulators.oxdna.utils) write_to() (in module jax_dna.input.oxdna_input)