mythos.energy.dna2

Implementation of the oxDNA2 energy model in mythos.

Submodules

Classes

`BondedExcludedVolume`	Bonded excluded volume energy function for DNA1 model.
`BondedExcludedVolumeConfiguration`	Configuration for the bonded excluded volume energy function.
`CrossStacking`	Cross-stacking energy function for DNA1 model.
`CrossStackingConfiguration`	Configuration for the cross-stacking energy function.
`Fene`	FENE energy function for DNA1 model.
`FeneConfiguration`	Configuration for the FENE energy function.
`HydrogenBonding`	Hydrogen bonding energy function for DNA1 model.
`HydrogenBondingConfiguration`	Configuration for the hydrogen bonding energy function.
`StackingConfiguration`	Configuration for the stacking energy function.
`UnbondedExcludedVolume`	Unbonded excluded volume energy function for DNA1 model.
`UnbondedExcludedVolumeConfiguration`	Configuration for the unbonded excluded volume energy function.
`CoaxialStacking`	Coaxial stacking energy function for DNA1 model.
`CoaxialStackingConfiguration`	Configuration for the coaxial stacking energy function.
`Debye`	Debye-huckel energy function for DNA2 model.
`DebyeConfiguration`	Configuration for the debye-huckel energy function.
`Nucleotide`	Nucleotide rigid body with additional sites for DNA2.
`Stacking`	Stacking energy function for DNA2 model.

Functions

`default_configs`(→ tuple[mythos.utils.types.PyTree, ...)	Return the default simulation and energy configurations for dna2.
`default_energy_configs`(, opts)	Return the default configurations for the energy functions for dna2.
`default_energy_fns`(...)	Return the default energy functions for dna2.
`default_transform_fn`(→ callable)	Return the default transform function for dna2 simulations.
`create_default_energy_fn`(...)	Create the default oxDNA2 energy function.

Package Contents

class mythos.energy.dna2.BondedExcludedVolume[source]

Bases: mythos.energy.base.BaseEnergyFunction

Bonded excluded volume energy function for DNA1 model.

params: BondedExcludedVolumeConfiguration

pairwise_energies(body: mythos.energy.base.BaseNucleotide, bonded_neighbors: mythos.utils.types.Arr_Bonded_Neighbors_2) → mythos.utils.types.Arr_Bonded_Neighbors[source]: Computes the excluded volume energy for each bonded pair.

compute_energy(nucleotide: mythos.energy.base.BaseNucleotide) → mythos.utils.types.Scalar[source]: Compute the energy of the system given the nucleotide.

class mythos.energy.dna2.BondedExcludedVolumeConfiguration[source]

Bases: mythos.energy.configuration.BaseConfiguration

Configuration for the bonded excluded volume energy function.

eps_exc: float | None = None

dr_star_base: float | None = None

sigma_base: float | None = None

sigma_back_base: float | None = None

sigma_base_back: float | None = None

dr_star_back_base: float | None = None

dr_star_base_back: float | None = None

b_base: float | None = None

dr_c_base: float | None = None

b_back_base: float | None = None

dr_c_back_base: float | None = None

b_base_back: float | None = None

dr_c_base_back: float | None = None

required_params: tuple[str] = ('eps_exc', 'dr_star_base', 'sigma_base', 'sigma_back_base', 'sigma_base_back',...

dependent_params: tuple[str] = ('b_base', 'dr_c_base', 'b_back_base', 'dr_c_back_base', 'b_base_back', 'dr_c_base_back')

init_params() → BondedExcludedVolumeConfiguration[source]

Initializes the dependent parameters in configuration.

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

class mythos.energy.dna2.CrossStacking[source]

Bases: mythos.energy.base.BaseEnergyFunction

Cross-stacking energy function for DNA1 model.

params: CrossStackingConfiguration

pairwise_energies(body_i: mythos.energy.base.BaseNucleotide, body_j: mythos.energy.base.BaseNucleotide, unbonded_neighbors: mythos.utils.types.Arr_Unbonded_Neighbors_2) → mythos.utils.types.Arr_Unbonded_Neighbors[source]: Computes the cross stacking energy for each unbonded pair.

compute_energy(nucleotide: mythos.energy.base.BaseNucleotide) → mythos.utils.types.Scalar[source]: Compute the energy of the system given the nucleotide.

class mythos.energy.dna2.CrossStackingConfiguration[source]

Bases: mythos.energy.configuration.BaseConfiguration

Configuration for the cross-stacking energy function.

dr_low_cross: float | None = None

dr_high_cross: float | None = None

k_cross: float | None = None

r0_cross: float | None = None

dr_c_cross: float | None = None

theta0_cross_1: float | None = None

delta_theta_star_cross_1: float | None = None

a_cross_1: float | None = None

theta0_cross_2: float | None = None

delta_theta_star_cross_2: float | None = None

a_cross_2: float | None = None

theta0_cross_3: float | None = None

delta_theta_star_cross_3: float | None = None

a_cross_3: float | None = None

theta0_cross_4: float | None = None

delta_theta_star_cross_4: float | None = None

a_cross_4: float | None = None

theta0_cross_7: float | None = None

delta_theta_star_cross_7: float | None = None

a_cross_7: float | None = None

theta0_cross_8: float | None = None

delta_theta_star_cross_8: float | None = None

a_cross_8: float | None = None

b_low_cross: float | None = None

dr_c_low_cross: float | None = None

b_high_cross: float | None = None

dr_c_high_cross: float | None = None

b_cross_1: float | None = None

delta_theta_cross_1_c: float | None = None

b_cross_2: float | None = None

delta_theta_cross_2_c: float | None = None

b_cross_3: float | None = None

delta_theta_cross_3_c: float | None = None

b_cross_4: float | None = None

delta_theta_cross_4_c: float | None = None

b_cross_7: float | None = None

delta_theta_cross_7_c: float | None = None

b_cross_8: float | None = None

delta_theta_cross_8_c: float | None = None

required_params: tuple[str] = ('dr_low_cross', 'dr_high_cross', 'k_cross', 'r0_cross', 'dr_c_cross', 'theta0_cross_1',...

dependent_params: tuple[str] = ('b_low_cross', 'dr_c_low_cross', 'b_high_cross', 'dr_c_high_cross', 'b_cross_1',...

init_params() → CrossStackingConfiguration[source]

Initializes the dependent parameters in configuration.

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

class mythos.energy.dna2.Fene[source]

Bases: mythos.energy.base.BaseEnergyFunction

FENE energy function for DNA1 model.

params: FeneConfiguration

pairwise_energies(body: mythos.energy.base.BaseNucleotide, bonded_neighbors: mythos.utils.types.Arr_Bonded_Neighbors_2) → mythos.utils.types.Arr_Bonded_Neighbors[source]: Computes the FENE energy for each bonded pair.

compute_energy(nucleotide: mythos.energy.base.BaseNucleotide) → mythos.utils.types.Scalar[source]: Compute the energy of the system given the nucleotide.

class mythos.energy.dna2.FeneConfiguration[source]

Bases: mythos.energy.configuration.BaseConfiguration

Configuration for the FENE energy function.

eps_backbone: float | None = None

r0_backbone: float | None = None

delta_backbone: float | None = None

fmax: float | None = None

finf: float | None = None

required_params: tuple[str] = ('eps_backbone', 'r0_backbone', 'delta_backbone', 'fmax', 'finf')

init_params() → FeneConfiguration[source]

Initializes the dependent parameters in configuration.

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

class mythos.energy.dna2.HydrogenBonding[source]

Bases: mythos.energy.base.BaseEnergyFunction

Hydrogen bonding energy function for DNA1 model.

params: HydrogenBondingConfiguration

compute_v_hb(body_i: mythos.energy.base.BaseNucleotide, body_j: mythos.energy.base.BaseNucleotide, unbonded_neighbors: mythos.utils.types.Arr_Unbonded_Neighbors) → mythos.utils.types.Arr_Unbonded_Neighbors[source]: Computes the sequence-independent energy for each unbonded pair.

weight(i: int, j: int, seq: mythos.utils.types.Probabilistic_Sequence) → float[source]: Computes the sequence-dependent weight for an unbonded pair.

pairwise_energies(body_i: mythos.energy.base.BaseNucleotide, body_j: mythos.energy.base.BaseNucleotide, seq: mythos.utils.types.Discrete_Sequence, unbonded_neighbors: mythos.utils.types.Arr_Unbonded_Neighbors_2) → mythos.utils.types.Arr_Unbonded_Neighbors[source]: Computes the hydrogen bonding energy for each unbonded pair.

compute_energy(nucleotide: mythos.energy.base.BaseNucleotide) → mythos.utils.types.Scalar[source]: Compute the energy of the system given the nucleotide.

class mythos.energy.dna2.HydrogenBondingConfiguration[source]

Bases: mythos.energy.configuration.BaseConfiguration

Configuration for the hydrogen bonding energy function.

eps_hb: float | None = None

a_hb: float | None = None

dr0_hb: float | None = None

dr_c_hb: float | None = None

dr_low_hb: float | None = None

dr_high_hb: float | None = None

a_hb_1: float | None = None

theta0_hb_1: float | None = None

delta_theta_star_hb_1: float | None = None

a_hb_2: float | None = None

theta0_hb_2: float | None = None

delta_theta_star_hb_2: float | None = None

a_hb_3: float | None = None

theta0_hb_3: float | None = None

delta_theta_star_hb_3: float | None = None

a_hb_4: float | None = None

theta0_hb_4: float | None = None

delta_theta_star_hb_4: float | None = None

a_hb_7: float | None = None

theta0_hb_7: float | None = None

delta_theta_star_hb_7: float | None = None

a_hb_8: float | None = None

theta0_hb_8: float | None = None

delta_theta_star_hb_8: float | None = None

ss_hb_weights: numpy.ndarray | None = None

b_low_hb: float | None = None

dr_c_low_hb: float | None = None

b_high_hb: float | None = None

dr_c_high_hb: float | None = None

b_hb_1: float | None = None

delta_theta_hb_1_c: float | None = None

b_hb_2: float | None = None

delta_theta_hb_2_c: float | None = None

b_hb_3: float | None = None

delta_theta_hb_3_c: float | None = None

b_hb_4: float | None = None

delta_theta_hb_4_c: float | None = None

b_hb_7: float | None = None

delta_theta_hb_7_c: float | None = None

b_hb_8: float | None = None

delta_theta_hb_8_c: float | None = None

eps_hb_weights: numpy.ndarray | None = None

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

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

required_params: tuple[str] = ('eps_hb', 'a_hb', 'dr0_hb', 'dr_c_hb', 'dr_low_hb', 'dr_high_hb', 'a_hb_1', 'theta0_hb_1',...

dependent_params: tuple[str] = ('b_low_hb', 'dr_c_low_hb', 'b_high_hb', 'dr_c_high_hb', 'b_hb_1', 'delta_theta_hb_1_c',...

init_params() → HydrogenBondingConfiguration[source]

Initializes the dependent parameters in configuration.

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

class mythos.energy.dna2.StackingConfiguration[source]

Bases: mythos.energy.configuration.BaseConfiguration

Configuration for the stacking energy function.

eps_stack_base: float | None = None

eps_stack_kt_coeff: float | None = None

dr_low_stack: float | None = None

dr_high_stack: float | None = None

a_stack: float | None = None

dr0_stack: float | None = None

dr_c_stack: float | None = None

theta0_stack_4: float | None = None

delta_theta_star_stack_4: float | None = None

a_stack_4: float | None = None

theta0_stack_5: float | None = None

delta_theta_star_stack_5: float | None = None

a_stack_5: float | None = None

theta0_stack_6: float | None = None

delta_theta_star_stack_6: float | None = None

a_stack_6: float | None = None

neg_cos_phi1_star_stack: float | None = None

a_stack_1: float | None = None

neg_cos_phi2_star_stack: float | None = None

a_stack_2: float | None = None

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

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

kt: float | None = None

ss_stack_weights: numpy.ndarray | None = None

b_low_stack: float | None = None

dr_c_low_stack: float | None = None

b_high_stack: float | None = None

dr_c_high_stack: float | None = None

b_stack_4: float | None = None

delta_theta_stack_4_c: float | None = None

b_stack_5: float | None = None

delta_theta_stack_5_c: float | None = None

b_stack_6: float | None = None

delta_theta_stack_6_c: float | None = None

b_neg_cos_phi1_stack: float | None = None

neg_cos_phi1_c_stack: float | None = None

b_neg_cos_phi2_stack: float | None = None

neg_cos_phi2_c_stack: float | None = None

eps_stack: float | None = None

required_params: tuple[str] = ('eps_stack_base', 'eps_stack_kt_coeff', 'dr_low_stack', 'dr_high_stack', 'a_stack',...

dependent_params: tuple[str] = ('b_low_stack', 'dr_c_low_stack', 'b_high_stack', 'dr_c_high_stack', 'b_stack_4',...

init_params() → StackingConfiguration[source]

Initializes the dependent parameters in configuration.

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

class mythos.energy.dna2.UnbondedExcludedVolume[source]

Bases: mythos.energy.base.BaseEnergyFunction

Unbonded excluded volume energy function for DNA1 model.

params: UnbondedExcludedVolumeConfiguration

pairwise_energies(body_i: mythos.energy.base.BaseNucleotide, body_j: mythos.energy.base.BaseNucleotide, unbonded_neighbors: mythos.utils.types.Arr_Unbonded_Neighbors_2) → mythos.utils.types.Arr_Bonded_Neighbors[source]: Computes the excluded volume energy for each unbonded pair.

compute_energy(nucleotide: mythos.energy.base.BaseNucleotide) → mythos.utils.types.Scalar[source]: Compute the energy of the system given the nucleotide.

class mythos.energy.dna2.UnbondedExcludedVolumeConfiguration[source]

Bases: mythos.energy.configuration.BaseConfiguration

Configuration for the unbonded excluded volume energy function.

eps_exc: float | None = None

dr_star_base: float | None = None

sigma_base: float | None = None

dr_star_back_base: float | None = None

sigma_back_base: float | None = None

dr_star_base_back: float | None = None

sigma_base_back: float | None = None

dr_star_backbone: float | None = None

sigma_backbone: float | None = None

b_base: float | None = None

dr_c_base: float | None = None

b_back_base: float | None = None

dr_c_back_base: float | None = None

b_base_back: float | None = None

dr_c_base_back: float | None = None

b_backbone: float | None = None

dr_c_backbone: float | None = None

required_params: tuple[str] = ('eps_exc', 'dr_star_base', 'sigma_base', 'dr_star_back_base', 'sigma_back_base',...

dependent_params: tuple[str] = ('b_base', 'dr_c_base', 'b_back_base', 'dr_c_back_base', 'b_base_back', 'dr_c_base_back',...

init_params() → UnbondedExcludedVolumeConfiguration[source]

Initializes the dependent parameters in configuration.

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

class mythos.energy.dna2.CoaxialStacking[source]

Bases: mythos.energy.base.BaseEnergyFunction

Coaxial stacking energy function for DNA1 model.

params: CoaxialStackingConfiguration

pairwise_energies(body_i: mythos.energy.dna2.nucleotide.Nucleotide, body_j: mythos.energy.dna2.nucleotide.Nucleotide, unbonded_neighbors: mythos.utils.types.Arr_Unbonded_Neighbors_2) → mythos.utils.types.Arr_Unbonded_Neighbors[source]: Computes the coaxial stacking energy for each unbonded pair.

compute_energy(nucleotide: mythos.energy.dna2.nucleotide.Nucleotide) → mythos.utils.types.Scalar[source]: Compute the energy of the system given the nucleotide.

class mythos.energy.dna2.CoaxialStackingConfiguration[source]

Bases: mythos.energy.configuration.BaseConfiguration

Configuration for the coaxial stacking energy function.

dr_low_coax: float | None = None

dr_high_coax: float | None = None

k_coax: float | None = None

dr0_coax: float | None = None

dr_c_coax: float | None = None

theta0_coax_4: float | None = None

delta_theta_star_coax_4: float | None = None

a_coax_4: float | None = None

theta0_coax_1: float | None = None

delta_theta_star_coax_1: float | None = None

a_coax_1: float | None = None

theta0_coax_5: float | None = None

delta_theta_star_coax_5: float | None = None

a_coax_5: float | None = None

theta0_coax_6: float | None = None

delta_theta_star_coax_6: float | None = None

a_coax_6: float | None = None

a_coax_1_f6: float | None = None

b_coax_1_f6: float | None = None

b_low_coax: float | None = None

dr_c_low_coax: float | None = None

b_high_coax: float | None = None

dr_c_high_coax: float | None = None

b_coax_4: float | None = None

delta_theta_coax_4_c: float | None = None

b_coax_1: float | None = None

delta_theta_coax_1_c: float | None = None

b_coax_5: float | None = None

delta_theta_coax_5_c: float | None = None

b_coax_6: float | None = None

delta_theta_coax_6_c: float | None = None

required_params: tuple[str] = ('dr_low_coax', 'dr_high_coax', 'k_coax', 'dr0_coax', 'dr_c_coax', 'theta0_coax_4',...

init_params() → CoaxialStackingConfiguration[source]

Initializes the dependent parameters in configuration.

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

class mythos.energy.dna2.Debye[source]

Bases: mythos.energy.base.BaseEnergyFunction

Debye-huckel energy function for DNA2 model.

params: DebyeConfiguration

is_end: mythos.utils.types.Arr_Nucleotide_Int | None = None

__post_init__(topology: mythos.input.topology.Topology | None) → None[source]

pairwise_energies(body_i: mythos.energy.base.BaseNucleotide, body_j: mythos.energy.base.BaseNucleotide, unbonded_neighbors: mythos.utils.types.Arr_Unbonded_Neighbors_2) → mythos.utils.types.Arr_Bonded_Neighbors[source]: Computes the debye-huckel energy for each unbonded pair.

compute_energy(nucleotide: mythos.energy.base.BaseNucleotide) → mythos.utils.types.Scalar[source]: Compute the energy of the system given the nucleotide.

class mythos.energy.dna2.DebyeConfiguration[source]

Bases: mythos.energy.configuration.BaseConfiguration

Configuration for the debye-huckel energy function.

q_eff: float | None = None

lambda_factor: float | None = None

prefactor_coeff: float | None = None

kt: float | None = None

salt_conc: float | None = None

half_charged_ends: bool | None = None

lambda_: float | None = None

kappa: float | None = None

r_high: float | None = None

prefactor: float | None = None

smoothing_coeff: float | None = None

r_cut: float | None = None

required_params: tuple[str] = ('q_eff', 'lambda_factor', 'prefactor_coeff', 'kt', 'salt_conc', 'half_charged_ends')

init_params() → DebyeConfiguration[source]

Initializes the dependent parameters in configuration.

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

class mythos.energy.dna2.Nucleotide[source]

Bases: mythos.energy.base.BaseNucleotide

Nucleotide rigid body with additional sites for DNA2.

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.

center: mythos.utils.types.Arr_Nucleotide_3

orientation: mythos.utils.types.Arr_Nucleotide_3 | jax_md.rigid_body.Quaternion

stack_sites: mythos.utils.types.Arr_Nucleotide_3

back_sites: mythos.utils.types.Arr_Nucleotide_3

back_sites_dna1: mythos.utils.types.Arr_Nucleotide_3

base_sites: mythos.utils.types.Arr_Nucleotide_3

back_base_vectors: mythos.utils.types.Arr_Nucleotide_3

base_normals: mythos.utils.types.Arr_Nucleotide_3

cross_prods: mythos.utils.types.Arr_Nucleotide_3

static from_rigid_body(rigid_body: jax_md.rigid_body.RigidBody, com_to_backbone_x: mythos.utils.types.Scalar, com_to_backbone_y: mythos.utils.types.Scalar, com_to_backbone_dna1: mythos.utils.types.Scalar, com_to_hb: mythos.utils.types.Scalar, com_to_stacking: mythos.utils.types.Scalar) → Nucleotide[source]: Class method to precompute nucleotide sites from a rigid body.

class mythos.energy.dna2.Stacking[source]

Bases: mythos.energy.dna1.Stacking

Stacking energy function for DNA2 model.

params: mythos.energy.dna1.StackingConfiguration

pairwise_energies(body: mythos.energy.dna2.nucleotide.Nucleotide, seq: mythos.utils.types.Discrete_Sequence, bonded_neighbors: mythos.utils.types.Arr_Bonded_Neighbors_2) → mythos.utils.types.Arr_Bonded_Neighbors[source]: Computes the stacking energy for each bonded pair.

compute_energy(nucleotide: mythos.energy.dna2.nucleotide.Nucleotide) → mythos.utils.types.Scalar[source]: Compute the energy of the system given the nucleotide.

mythos.energy.dna2.default_configs() → tuple[mythos.utils.types.PyTree, mythos.utils.types.PyTree][source]: Return the default simulation and energy configurations for dna2.

mythos.energy.dna2.default_energy_configs(overrides: dict = MappingProxyType({}), opts: dict = MappingProxyType({})) → list[mythos.energy.configuration.BaseConfiguration][source]: Return the default configurations for the energy functions for dna2.

mythos.energy.dna2.default_energy_fns() → list[mythos.energy.base.BaseEnergyFunction][source]: Return the default energy functions for dna2.

mythos.energy.dna2.default_transform_fn() → callable[source]: Return the default transform function for dna2 simulations.

mythos.energy.dna2.create_default_energy_fn(topology: mythos.input.topology.Topology, displacement_fn: callable = DEFAULT_DISPLACEMENT) → mythos.energy.base.EnergyFunction[source]

Create the default oxDNA2 energy function.

This creates the composed energy function from the default set of function classes, associated configs, and the default transform function - built for the provided topology and displacement function.

Parameters:

topology – The topology of the system.
displacement_fn – The displacement function to use. defaults to DEFAULT_DISPLACEMENT.