mythos.energy.na1

Implementation of the oxNA energy model in mythos.

Submodules

• mythos.energy.na1.bonded_excluded_volume
• mythos.energy.na1.coaxial_stacking
• mythos.energy.na1.cross_stacking
• mythos.energy.na1.debye
• mythos.energy.na1.fene
• mythos.energy.na1.hydrogen_bonding
• mythos.energy.na1.nucleotide
• mythos.energy.na1.stacking
• mythos.energy.na1.unbonded_excluded_volume
• mythos.energy.na1.utils

Classes

BondedExcludedVolume	Bonded excluded volume energy function for NA1 model.
BondedExcludedVolumeConfiguration	Configuration for the bonded excluded volume energy function.
CoaxialStacking	Coaxial stacking energy function for NA1 model.
CoaxialStackingConfiguration	Configuration for the cross-stacking energy function.
CrossStacking	Cross-stacking energy function for NA1 model.
CrossStackingConfiguration	Configuration for the cross-stacking energy function.
Debye	Debye-huckel energy function for NA1 model.
DebyeConfiguration	Configuration for the debye-huckel energy function.
Fene	FENE energy function for NA1 model.
FeneConfiguration	Configuration for the FENE energy function.
HydrogenBonding	Hydrogen bonding energy function for NA1 model.
HydrogenBondingConfiguration	Configuration for the cross-stacking energy function.
HybridNucleotide	Nucleotide rigid body with additional sites for NA1.
Stacking	Stacking energy function for DNA1 model.
StackingConfiguration	Configuration for the stacking energy function.
UnbondedExcludedVolume	Unbonded excluded volume energy function for NA1 model.
UnbondedExcludedVolumeConfiguration	Configuration for the unbonded excluded volume energy function.

Package Contents

class mythos.energy.na1.BondedExcludedVolume

Bases: mythos.energy.base.BaseEnergyFunction

Bonded excluded volume energy function for NA1 model.

params: BondedExcludedVolumeConfiguration

compute_energy(nucleotide: mythos.energy.na1.nucleotide.HybridNucleotide) → mythos.utils.types.Scalar

Compute the energy of the system given the nucleotide.

class mythos.energy.na1.BondedExcludedVolumeConfiguration

Bases: mythos.energy.configuration.BaseConfiguration

Configuration for the bonded excluded volume energy function.

nt_type: mythos.utils.types.Arr_Nucleotide | None = None

dna_eps_exc: float | None = None

dna_dr_star_base: float | None = None

dna_sigma_base: float | None = None

dna_sigma_back_base: float | None = None

dna_sigma_base_back: float | None = None

dna_dr_star_back_base: float | None = None

dna_dr_star_base_back: float | None = None

rna_eps_exc: float | None = None

rna_dr_star_base: float | None = None

rna_sigma_base: float | None = None

rna_sigma_back_base: float | None = None

rna_sigma_base_back: float | None = None

rna_dr_star_back_base: float | None = None

rna_dr_star_base_back: float | None = None

dna_config: mythos.energy.dna1.BondedExcludedVolumeConfiguration | None = None

rna_config: mythos.energy.dna1.BondedExcludedVolumeConfiguration | None = None

required_params: tuple[str] = ('nt_type', 'dna_eps_exc', 'dna_dr_star_base', 'dna_sigma_base', 'dna_sigma_back_base',...

init_params() → BondedExcludedVolumeConfiguration

Initializes the dependent parameters in configuration.

Should be implemented in the subclass if dependent parameters are present.

class mythos.energy.na1.CoaxialStacking

Bases: mythos.energy.base.BaseEnergyFunction

Coaxial stacking energy function for NA1 model.

params: CoaxialStackingConfiguration

compute_energy(nucleotide: mythos.energy.na1.nucleotide.HybridNucleotide) → mythos.utils.types.Scalar

Compute the energy of the system given the nucleotide.

class mythos.energy.na1.CoaxialStackingConfiguration

Bases: mythos.energy.configuration.BaseConfiguration

Configuration for the cross-stacking energy function.

nt_type: mythos.utils.types.Arr_Nucleotide | None = None

dna_dr_low_coax: float | None = None

dna_dr_high_coax: float | None = None

dna_k_coax: float | None = None

dna_dr0_coax: float | None = None

dna_dr_c_coax: float | None = None

dna_theta0_coax_4: float | None = None

dna_delta_theta_star_coax_4: float | None = None

dna_a_coax_4: float | None = None

dna_theta0_coax_1: float | None = None

dna_delta_theta_star_coax_1: float | None = None

dna_a_coax_1: float | None = None

dna_theta0_coax_5: float | None = None

dna_delta_theta_star_coax_5: float | None = None

dna_a_coax_5: float | None = None

dna_theta0_coax_6: float | None = None

dna_delta_theta_star_coax_6: float | None = None

dna_a_coax_6: float | None = None

dna_a_coax_1_f6: float | None = None

dna_b_coax_1_f6: float | None = None

rna_dr_low_coax: float | None = None

rna_dr_high_coax: float | None = None

rna_k_coax: float | None = None

rna_dr0_coax: float | None = None

rna_dr_c_coax: float | None = None

rna_theta0_coax_4: float | None = None

rna_delta_theta_star_coax_4: float | None = None

rna_a_coax_4: float | None = None

rna_theta0_coax_1: float | None = None

rna_delta_theta_star_coax_1: float | None = None

rna_a_coax_1: float | None = None

rna_theta0_coax_5: float | None = None

rna_delta_theta_star_coax_5: float | None = None

rna_a_coax_5: float | None = None

rna_theta0_coax_6: float | None = None

rna_delta_theta_star_coax_6: float | None = None

rna_a_coax_6: float | None = None

rna_cos_phi3_star_coax: float | None = None

rna_a_coax_3p: float | None = None

rna_cos_phi4_star_coax: float | None = None

rna_a_coax_4p: float | None = None

drh_dr_low_coax: float | None = None

drh_dr_high_coax: float | None = None

drh_k_coax: float | None = None

drh_dr0_coax: float | None = None

drh_dr_c_coax: float | None = None

drh_theta0_coax_4: float | None = None

drh_delta_theta_star_coax_4: float | None = None

drh_a_coax_4: float | None = None

drh_theta0_coax_1: float | None = None

drh_delta_theta_star_coax_1: float | None = None

drh_a_coax_1: float | None = None

drh_theta0_coax_5: float | None = None

drh_delta_theta_star_coax_5: float | None = None

drh_a_coax_5: float | None = None

drh_theta0_coax_6: float | None = None

drh_delta_theta_star_coax_6: float | None = None

drh_a_coax_6: float | None = None

drh_cos_phi3_star_coax: float | None = None

drh_a_coax_3p: float | None = None

drh_cos_phi4_star_coax: float | None = None

drh_a_coax_4p: float | None = None

dna_config: mythos.energy.dna2.CoaxialStackingConfiguration | None = None

rna_config: mythos.energy.dna1.CoaxialStackingConfiguration | None = None

drh_config: mythos.energy.dna1.CoaxialStackingConfiguration | None = None

required_params: tuple[str] = ('nt_type', 'dna_dr_low_coax', 'dna_dr_high_coax', 'dna_k_coax', 'dna_dr0_coax',...

init_params() → CoaxialStackingConfiguration

Initializes the dependent parameters in configuration.

Should be implemented in the subclass if dependent parameters are present.

class mythos.energy.na1.CrossStacking

Bases: mythos.energy.base.BaseEnergyFunction

Cross-stacking energy function for NA1 model.

params: CrossStackingConfiguration

compute_energy(nucleotide: mythos.energy.na1.nucleotide.HybridNucleotide) → mythos.utils.types.Scalar

Compute the energy of the system given the nucleotide.

class mythos.energy.na1.CrossStackingConfiguration

Bases: mythos.energy.configuration.BaseConfiguration

Configuration for the cross-stacking energy function.

nt_type: mythos.utils.types.Arr_Nucleotide | None = None

dna_dr_low_cross: float | None = None

dna_dr_high_cross: float | None = None

dna_k_cross: float | None = None

dna_r0_cross: float | None = None

dna_dr_c_cross: float | None = None

dna_theta0_cross_1: float | None = None

dna_delta_theta_star_cross_1: float | None = None

dna_a_cross_1: float | None = None

dna_theta0_cross_2: float | None = None

dna_delta_theta_star_cross_2: float | None = None

dna_a_cross_2: float | None = None

dna_theta0_cross_3: float | None = None

dna_delta_theta_star_cross_3: float | None = None

dna_a_cross_3: float | None = None

dna_theta0_cross_4: float | None = None

dna_delta_theta_star_cross_4: float | None = None

dna_a_cross_4: float | None = None

dna_theta0_cross_7: float | None = None

dna_delta_theta_star_cross_7: float | None = None

dna_a_cross_7: float | None = None

dna_theta0_cross_8: float | None = None

dna_delta_theta_star_cross_8: float | None = None

dna_a_cross_8: float | None = None

rna_dr_low_cross: float | None = None

rna_dr_high_cross: float | None = None

rna_k_cross: float | None = None

rna_r0_cross: float | None = None

rna_dr_c_cross: float | None = None

rna_theta0_cross_1: float | None = None

rna_delta_theta_star_cross_1: float | None = None

rna_a_cross_1: float | None = None

rna_theta0_cross_2: float | None = None

rna_delta_theta_star_cross_2: float | None = None

rna_a_cross_2: float | None = None

rna_theta0_cross_3: float | None = None

rna_delta_theta_star_cross_3: float | None = None

rna_a_cross_3: float | None = None

rna_theta0_cross_7: float | None = None

rna_delta_theta_star_cross_7: float | None = None

rna_a_cross_7: float | None = None

rna_theta0_cross_8: float | None = None

rna_delta_theta_star_cross_8: float | None = None

rna_a_cross_8: float | None = None

drh_dr_low_cross: float | None = None

drh_dr_high_cross: float | None = None

drh_k_cross: float | None = None

drh_r0_cross: float | None = None

drh_dr_c_cross: float | None = None

drh_theta0_cross_1: float | None = None

drh_delta_theta_star_cross_1: float | None = None

drh_a_cross_1: float | None = None

drh_theta0_cross_2: float | None = None

drh_delta_theta_star_cross_2: float | None = None

drh_a_cross_2: float | None = None

drh_theta0_cross_3: float | None = None

drh_delta_theta_star_cross_3: float | None = None

drh_a_cross_3: float | None = None

drh_theta0_cross_4: float | None = None

drh_delta_theta_star_cross_4: float | None = None

drh_a_cross_4: float | None = None

drh_theta0_cross_7: float | None = None

drh_delta_theta_star_cross_7: float | None = None

drh_a_cross_7: float | None = None

drh_theta0_cross_8: float | None = None

drh_delta_theta_star_cross_8: float | None = None

drh_a_cross_8: float | None = None

dna_config: mythos.energy.dna1.CrossStackingConfiguration | None = None

rna_config: mythos.energy.rna2.CrossStackingConfiguration | None = None

drh_config: mythos.energy.dna1.CrossStackingConfiguration | None = None

required_params: tuple[str] = ('nt_type', 'dna_dr_low_cross', 'dna_dr_high_cross', 'dna_k_cross', 'dna_r0_cross',...

init_params() → CrossStackingConfiguration

Initializes the dependent parameters in configuration.

Should be implemented in the subclass if dependent parameters are present.

class mythos.energy.na1.Debye

Bases: mythos.energy.dna2.Debye

Debye-huckel energy function for NA1 model.

params: DebyeConfiguration

compute_energy(nucleotide: mythos.energy.na1.nucleotide.HybridNucleotide) → mythos.utils.types.Scalar

Compute the energy of the system given the nucleotide.

class mythos.energy.na1.DebyeConfiguration

Bases: mythos.energy.configuration.BaseConfiguration

Configuration for the debye-huckel energy function.

nt_type: mythos.utils.types.Arr_Nucleotide | None = None

half_charged_ends: bool | None = None

kt: float | None = None

salt_conc: float | None = None

dna_q_eff: float | None = None

dna_lambda_factor: float | None = None

dna_prefactor_coeff: float | None = None

rna_q_eff: float | None = None

rna_lambda_factor: float | None = None

rna_prefactor_coeff: float | None = None

drh_q_eff: float | None = None

drh_lambda_factor: float | None = None

drh_prefactor_coeff: float | None = None

dna_config: mythos.energy.dna2.DebyeConfiguration | None = None

rna_config: mythos.energy.dna2.DebyeConfiguration | None = None

drh_config: mythos.energy.dna2.DebyeConfiguration | None = None

required_params: tuple[str] = ('nt_type', 'half_charged_ends', 'kt', 'salt_conc', 'dna_q_eff', 'dna_lambda_factor',...

init_params() → DebyeConfiguration

Initializes the dependent parameters in configuration.

Should be implemented in the subclass if dependent parameters are present.

class mythos.energy.na1.Fene

Bases: mythos.energy.base.BaseEnergyFunction

FENE energy function for NA1 model.

params: FeneConfiguration

compute_energy(nucleotide: mythos.energy.na1.nucleotide.HybridNucleotide) → mythos.utils.types.Scalar

Compute the energy of the system given the nucleotide.

class mythos.energy.na1.FeneConfiguration

Bases: mythos.energy.configuration.BaseConfiguration

Configuration for the FENE energy function.

nt_type: mythos.utils.types.Arr_Nucleotide | None = None

dna_eps_backbone: float | None = None

dna_r0_backbone: float | None = None

dna_delta_backbone: float | None = None

dna_fmax: float | None = None

dna_finf: float | None = None

rna_eps_backbone: float | None = None

rna_r0_backbone: float | None = None

rna_delta_backbone: float | None = None

rna_fmax: float | None = None

rna_finf: float | None = None

dna_config: mythos.energy.dna1.FeneConfiguration | None = None

rna_config: mythos.energy.dna1.FeneConfiguration | None = None

required_params: tuple[str] = ('nt_type', 'dna_eps_backbone', 'dna_r0_backbone', 'dna_delta_backbone', 'dna_fmax', 'dna_finf',...

init_params() → FeneConfiguration

Initializes the dependent parameters in configuration.

Should be implemented in the subclass if dependent parameters are present.

class mythos.energy.na1.HydrogenBonding

Bases: mythos.energy.base.BaseEnergyFunction

Hydrogen bonding energy function for NA1 model.

params: HydrogenBondingConfiguration

compute_energy(nucleotide: mythos.energy.na1.nucleotide.HybridNucleotide) → mythos.utils.types.Scalar

Compute the energy of the system given the nucleotide.

class mythos.energy.na1.HydrogenBondingConfiguration

Bases: mythos.energy.configuration.BaseConfiguration

Configuration for the cross-stacking energy function.

nt_type: mythos.utils.types.Arr_Nucleotide | None = None

dna_eps_hb: float | None = None

dna_a_hb: float | None = None

dna_dr0_hb: float | None = None

dna_dr_c_hb: float | None = None

dna_dr_low_hb: float | None = None

dna_dr_high_hb: float | None = None

dna_a_hb_1: float | None = None

dna_theta0_hb_1: float | None = None

dna_delta_theta_star_hb_1: float | None = None

dna_a_hb_2: float | None = None

dna_theta0_hb_2: float | None = None

dna_delta_theta_star_hb_2: float | None = None

dna_a_hb_3: float | None = None

dna_theta0_hb_3: float | None = None

dna_delta_theta_star_hb_3: float | None = None

dna_a_hb_4: float | None = None

dna_theta0_hb_4: float | None = None

dna_delta_theta_star_hb_4: float | None = None

dna_a_hb_7: float | None = None

dna_theta0_hb_7: float | None = None

dna_delta_theta_star_hb_7: float | None = None

dna_a_hb_8: float | None = None

dna_theta0_hb_8: float | None = None

dna_delta_theta_star_hb_8: float | None = None

dna_ss_hb_weights: numpy.ndarray | None = None

rna_eps_hb: float | None = None

rna_a_hb: float | None = None

rna_dr0_hb: float | None = None

rna_dr_c_hb: float | None = None

rna_dr_low_hb: float | None = None

rna_dr_high_hb: float | None = None

rna_a_hb_1: float | None = None

rna_theta0_hb_1: float | None = None

rna_delta_theta_star_hb_1: float | None = None

rna_a_hb_2: float | None = None

rna_theta0_hb_2: float | None = None

rna_delta_theta_star_hb_2: float | None = None

rna_a_hb_3: float | None = None

rna_theta0_hb_3: float | None = None

rna_delta_theta_star_hb_3: float | None = None

rna_a_hb_4: float | None = None

rna_theta0_hb_4: float | None = None

rna_delta_theta_star_hb_4: float | None = None

rna_a_hb_7: float | None = None

rna_theta0_hb_7: float | None = None

rna_delta_theta_star_hb_7: float | None = None

rna_a_hb_8: float | None = None

rna_theta0_hb_8: float | None = None

rna_delta_theta_star_hb_8: float | None = None

rna_ss_hb_weights: numpy.ndarray | None = None

drh_eps_hb: float | None = None

drh_a_hb: float | None = None

drh_dr0_hb: float | None = None

drh_dr_c_hb: float | None = None

drh_dr_low_hb: float | None = None

drh_dr_high_hb: float | None = None

drh_a_hb_1: float | None = None

drh_theta0_hb_1: float | None = None

drh_delta_theta_star_hb_1: float | None = None

drh_a_hb_2: float | None = None

drh_theta0_hb_2: float | None = None

drh_delta_theta_star_hb_2: float | None = None

drh_a_hb_3: float | None = None

drh_theta0_hb_3: float | None = None

drh_delta_theta_star_hb_3: float | None = None

drh_a_hb_4: float | None = None

drh_theta0_hb_4: float | None = None

drh_delta_theta_star_hb_4: float | None = None

drh_a_hb_7: float | None = None

drh_theta0_hb_7: float | None = None

drh_delta_theta_star_hb_7: float | None = None

drh_a_hb_8: float | None = None

drh_theta0_hb_8: float | None = None

drh_delta_theta_star_hb_8: float | None = None

drh_ss_hb_weights: numpy.ndarray | None = None

pseq: mythos.utils.types.Probabilistic_Sequence | None = None

pseq_constraints: mythos.input.sequence_constraints.SequenceConstraints | None = None

dna_config: mythos.energy.dna1.HydrogenBondingConfiguration | None = None

rna_config: mythos.energy.dna1.HydrogenBondingConfiguration | None = None

drh_config: mythos.energy.dna1.HydrogenBondingConfiguration | None = None

required_params: tuple[str] = ('nt_type', 'dna_eps_hb', 'dna_a_hb', 'dna_dr0_hb', 'dna_dr_c_hb', 'dna_dr_low_hb',...

init_params() → HydrogenBondingConfiguration

Initializes the dependent parameters in configuration.

Should be implemented in the subclass if dependent parameters are present.

class mythos.energy.na1.HybridNucleotide

Nucleotide rigid body with additional sites for NA1.

This class is inteneded to be used as a dataclass for a nucleotide rigid body as a rigid_body_transform_fn in jax_md.energy.ComposedEnergyFunction.

dna: mythos.energy.dna2.nucleotide.Nucleotide

rna: mythos.energy.rna2.nucleotide.Nucleotide

static from_rigid_body(rigid_body: jax_md.rigid_body.RigidBody, dna_com_to_backbone_x: mythos.utils.types.Scalar, dna_com_to_backbone_y: mythos.utils.types.Scalar, dna_com_to_backbone_dna1: mythos.utils.types.Scalar, dna_com_to_hb: mythos.utils.types.Scalar, dna_com_to_stacking: mythos.utils.types.Scalar, rna_com_to_backbone_x: mythos.utils.types.Scalar, rna_com_to_backbone_y: mythos.utils.types.Scalar, rna_com_to_stacking: mythos.utils.types.Scalar, rna_com_to_hb: mythos.utils.types.Scalar, rna_p3_x: mythos.utils.types.Scalar, rna_p3_y: mythos.utils.types.Scalar, rna_p3_z: mythos.utils.types.Scalar, rna_p5_x: mythos.utils.types.Scalar, rna_p5_y: mythos.utils.types.Scalar, rna_p5_z: mythos.utils.types.Scalar, rna_pos_stack_3_a1: mythos.utils.types.Scalar, rna_pos_stack_3_a2: mythos.utils.types.Scalar, rna_pos_stack_5_a1: mythos.utils.types.Scalar, rna_pos_stack_5_a2: mythos.utils.types.Scalar) → HybridNucleotide

Class method to precompute nucleotide sites from a rigid body.

class mythos.energy.na1.Stacking

Bases: mythos.energy.base.BaseEnergyFunction

Stacking energy function for DNA1 model.

params: StackingConfiguration

compute_energy(nucleotide: mythos.energy.na1.nucleotide.HybridNucleotide) → mythos.utils.types.Scalar

Compute the energy of the system given the nucleotide.

class mythos.energy.na1.StackingConfiguration

Bases: mythos.energy.configuration.BaseConfiguration

Configuration for the stacking energy function.

nt_type: mythos.utils.types.Arr_Nucleotide | None = None

kt: float | None = None

dna_eps_stack_base: float | None = None

dna_eps_stack_kt_coeff: float | None = None

dna_dr_low_stack: float | None = None

dna_dr_high_stack: float | None = None

dna_a_stack: float | None = None

dna_dr0_stack: float | None = None

dna_dr_c_stack: float | None = None

dna_theta0_stack_4: float | None = None

dna_delta_theta_star_stack_4: float | None = None

dna_a_stack_4: float | None = None

dna_theta0_stack_5: float | None = None

dna_delta_theta_star_stack_5: float | None = None

dna_a_stack_5: float | None = None

dna_theta0_stack_6: float | None = None

dna_delta_theta_star_stack_6: float | None = None

dna_a_stack_6: float | None = None

dna_neg_cos_phi1_star_stack: float | None = None

dna_a_stack_1: float | None = None

dna_neg_cos_phi2_star_stack: float | None = None

dna_a_stack_2: float | None = None

dna_ss_stack_weights: numpy.ndarray | None = None

rna_eps_stack_base: float | None = None

rna_eps_stack_kt_coeff: float | None = None

rna_dr_low_stack: float | None = None

rna_dr_high_stack: float | None = None

rna_a_stack: float | None = None

rna_dr0_stack: float | None = None

rna_dr_c_stack: float | None = None

rna_theta0_stack_5: float | None = None

rna_delta_theta_star_stack_5: float | None = None

rna_a_stack_5: float | None = None

rna_theta0_stack_6: float | None = None

rna_delta_theta_star_stack_6: float | None = None

rna_a_stack_6: float | None = None

rna_theta0_stack_9: float | None = None

rna_delta_theta_star_stack_9: float | None = None

rna_a_stack_9: float | None = None

rna_theta0_stack_10: float | None = None

rna_delta_theta_star_stack_10: float | None = None

rna_a_stack_10: float | None = None

rna_neg_cos_phi1_star_stack: float | None = None

rna_a_stack_1: float | None = None

rna_neg_cos_phi2_star_stack: float | None = None

rna_a_stack_2: float | None = None

rna_ss_stack_weights: numpy.ndarray | None = None

dna_config: mythos.energy.dna1.StackingConfiguration | None = None

rna_config: mythos.energy.rna2.StackingConfiguration | None = None

required_params: tuple[str] = ('nt_type', 'kt', 'dna_eps_stack_base', 'dna_eps_stack_kt_coeff', 'dna_dr_low_stack',...

init_params() → StackingConfiguration

Initializes the dependent parameters in configuration.

Should be implemented in the subclass if dependent parameters are present.

class mythos.energy.na1.UnbondedExcludedVolume

Bases: mythos.energy.base.BaseEnergyFunction

Unbonded excluded volume energy function for NA1 model.

params: UnbondedExcludedVolumeConfiguration

compute_energy(nucleotide: mythos.energy.na1.nucleotide.HybridNucleotide) → mythos.utils.types.Scalar

Compute the energy of the system given the nucleotide.

class mythos.energy.na1.UnbondedExcludedVolumeConfiguration

Bases: mythos.energy.configuration.BaseConfiguration

Configuration for the unbonded excluded volume energy function.

nt_type: mythos.utils.types.Arr_Nucleotide | None = None

dna_eps_exc: float | None = None

dna_dr_star_base: float | None = None

dna_sigma_base: float | None = None

dna_dr_star_back_base: float | None = None

dna_sigma_back_base: float | None = None

dna_dr_star_base_back: float | None = None

dna_sigma_base_back: float | None = None

dna_dr_star_backbone: float | None = None

dna_sigma_backbone: float | None = None

rna_eps_exc: float | None = None

rna_dr_star_base: float | None = None

rna_sigma_base: float | None = None

rna_dr_star_back_base: float | None = None

rna_sigma_back_base: float | None = None

rna_dr_star_base_back: float | None = None

rna_sigma_base_back: float | None = None

rna_dr_star_backbone: float | None = None

rna_sigma_backbone: float | None = None

drh_eps_exc: float | None = None

drh_dr_star_base: float | None = None

drh_sigma_base: float | None = None

drh_dr_star_back_base: float | None = None

drh_sigma_back_base: float | None = None

drh_dr_star_base_back: float | None = None

drh_sigma_base_back: float | None = None

drh_dr_star_backbone: float | None = None

drh_sigma_backbone: float | None = None

dna_config: mythos.energy.dna1.UnbondedExcludedVolumeConfiguration | None = None

rna_config: mythos.energy.dna1.UnbondedExcludedVolumeConfiguration | None = None

drh_config: mythos.energy.dna1.UnbondedExcludedVolumeConfiguration | None = None

required_params: tuple[str] = ('nt_type', 'dna_eps_exc', 'dna_dr_star_base', 'dna_sigma_base', 'dna_dr_star_back_base',...

init_params() → UnbondedExcludedVolumeConfiguration

Initializes the dependent parameters in configuration.

Should be implemented in the subclass if dependent parameters are present.