"""Cross-stacking energy term for NA1 model."""
import chex
import jax
import jax.numpy as jnp
from typing_extensions import override
import mythos.energy.base as je_base
import mythos.energy.configuration as config
import mythos.energy.dna1 as dna1_energy
import mythos.energy.na1.nucleotide as na1_nucleotide
import mythos.energy.na1.utils as je_utils
import mythos.energy.rna2 as rna2_energy
import mythos.utils.types as typ
[docs]
@chex.dataclass(frozen=True)
class CrossStackingConfiguration(config.BaseConfiguration):
"""Configuration for the cross-stacking energy function."""
# independent parameters
nt_type: typ.Arr_Nucleotide | None = None
## DNA2-specific
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
## RNA2-specific
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
## DNA/RNA-hybrid-specific
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
# dependent parameters
dna_config: dna1_energy.CrossStackingConfiguration | None = None
rna_config: rna2_energy.CrossStackingConfiguration | None = None
drh_config: dna1_energy.CrossStackingConfiguration | None = None
# override
required_params: tuple[str] = (
"nt_type",
# DNA2-specific
"dna_dr_low_cross",
"dna_dr_high_cross",
"dna_k_cross",
"dna_r0_cross",
"dna_dr_c_cross",
"dna_theta0_cross_1",
"dna_delta_theta_star_cross_1",
"dna_a_cross_1",
"dna_theta0_cross_2",
"dna_delta_theta_star_cross_2",
"dna_a_cross_2",
"dna_theta0_cross_3",
"dna_delta_theta_star_cross_3",
"dna_a_cross_3",
"dna_theta0_cross_4",
"dna_delta_theta_star_cross_4",
"dna_a_cross_4",
"dna_theta0_cross_7",
"dna_delta_theta_star_cross_7",
"dna_a_cross_7",
"dna_theta0_cross_8",
"dna_delta_theta_star_cross_8",
"dna_a_cross_8",
# RNA2-specific
"rna_dr_low_cross",
"rna_dr_high_cross",
"rna_k_cross",
"rna_r0_cross",
"rna_dr_c_cross",
"rna_theta0_cross_1",
"rna_delta_theta_star_cross_1",
"rna_a_cross_1",
"rna_theta0_cross_2",
"rna_delta_theta_star_cross_2",
"rna_a_cross_2",
"rna_theta0_cross_3",
"rna_delta_theta_star_cross_3",
"rna_a_cross_3",
"rna_theta0_cross_7",
"rna_delta_theta_star_cross_7",
"rna_a_cross_7",
"rna_theta0_cross_8",
"rna_delta_theta_star_cross_8",
"rna_a_cross_8",
# DNA/RNA-hybrid-specific
"drh_dr_low_cross",
"drh_dr_high_cross",
"drh_k_cross",
"drh_r0_cross",
"drh_dr_c_cross",
"drh_theta0_cross_1",
"drh_delta_theta_star_cross_1",
"drh_a_cross_1",
"drh_theta0_cross_2",
"drh_delta_theta_star_cross_2",
"drh_a_cross_2",
"drh_theta0_cross_3",
"drh_delta_theta_star_cross_3",
"drh_a_cross_3",
"drh_theta0_cross_4",
"drh_delta_theta_star_cross_4",
"drh_a_cross_4",
"drh_theta0_cross_7",
"drh_delta_theta_star_cross_7",
"drh_a_cross_7",
"drh_theta0_cross_8",
"drh_delta_theta_star_cross_8",
"drh_a_cross_8",
)
[docs]
@override
def init_params(self) -> "CrossStackingConfiguration":
dna_config = dna1_energy.CrossStackingConfiguration(
dr_low_cross=self.dna_dr_low_cross,
dr_high_cross=self.dna_dr_high_cross,
k_cross=self.dna_k_cross,
r0_cross=self.dna_r0_cross,
dr_c_cross=self.dna_dr_c_cross,
theta0_cross_1=self.dna_theta0_cross_1,
delta_theta_star_cross_1=self.dna_delta_theta_star_cross_1,
a_cross_1=self.dna_a_cross_1,
theta0_cross_2=self.dna_theta0_cross_2,
delta_theta_star_cross_2=self.dna_delta_theta_star_cross_2,
a_cross_2=self.dna_a_cross_2,
theta0_cross_3=self.dna_theta0_cross_3,
delta_theta_star_cross_3=self.dna_delta_theta_star_cross_3,
a_cross_3=self.dna_a_cross_3,
theta0_cross_4=self.dna_theta0_cross_4,
delta_theta_star_cross_4=self.dna_delta_theta_star_cross_4,
a_cross_4=self.dna_a_cross_4,
theta0_cross_7=self.dna_theta0_cross_7,
delta_theta_star_cross_7=self.dna_delta_theta_star_cross_7,
a_cross_7=self.dna_a_cross_7,
theta0_cross_8=self.dna_theta0_cross_8,
delta_theta_star_cross_8=self.dna_delta_theta_star_cross_8,
a_cross_8=self.dna_a_cross_8,
).init_params()
rna_config = rna2_energy.CrossStackingConfiguration(
dr_low_cross=self.rna_dr_low_cross,
dr_high_cross=self.rna_dr_high_cross,
k_cross=self.rna_k_cross,
r0_cross=self.rna_r0_cross,
dr_c_cross=self.rna_dr_c_cross,
theta0_cross_1=self.rna_theta0_cross_1,
delta_theta_star_cross_1=self.rna_delta_theta_star_cross_1,
a_cross_1=self.rna_a_cross_1,
theta0_cross_2=self.rna_theta0_cross_2,
delta_theta_star_cross_2=self.rna_delta_theta_star_cross_2,
a_cross_2=self.rna_a_cross_2,
theta0_cross_3=self.rna_theta0_cross_3,
delta_theta_star_cross_3=self.rna_delta_theta_star_cross_3,
a_cross_3=self.rna_a_cross_3,
theta0_cross_7=self.rna_theta0_cross_7,
delta_theta_star_cross_7=self.rna_delta_theta_star_cross_7,
a_cross_7=self.rna_a_cross_7,
theta0_cross_8=self.rna_theta0_cross_8,
delta_theta_star_cross_8=self.rna_delta_theta_star_cross_8,
a_cross_8=self.rna_a_cross_8,
).init_params()
drh_config = dna1_energy.CrossStackingConfiguration(
dr_low_cross=self.drh_dr_low_cross,
dr_high_cross=self.drh_dr_high_cross,
k_cross=self.drh_k_cross,
r0_cross=self.drh_r0_cross,
dr_c_cross=self.drh_dr_c_cross,
theta0_cross_1=self.drh_theta0_cross_1,
delta_theta_star_cross_1=self.drh_delta_theta_star_cross_1,
a_cross_1=self.drh_a_cross_1,
theta0_cross_2=self.drh_theta0_cross_2,
delta_theta_star_cross_2=self.drh_delta_theta_star_cross_2,
a_cross_2=self.drh_a_cross_2,
theta0_cross_3=self.drh_theta0_cross_3,
delta_theta_star_cross_3=self.drh_delta_theta_star_cross_3,
a_cross_3=self.drh_a_cross_3,
theta0_cross_4=self.drh_theta0_cross_4,
delta_theta_star_cross_4=self.drh_delta_theta_star_cross_4,
a_cross_4=self.drh_a_cross_4,
theta0_cross_7=self.drh_theta0_cross_7,
delta_theta_star_cross_7=self.drh_delta_theta_star_cross_7,
a_cross_7=self.drh_a_cross_7,
theta0_cross_8=self.drh_theta0_cross_8,
delta_theta_star_cross_8=self.drh_delta_theta_star_cross_8,
a_cross_8=self.drh_a_cross_8,
).init_params()
return self.replace(
dna_config=dna_config,
rna_config=rna_config,
drh_config=drh_config,
)
[docs]
@chex.dataclass(frozen=True)
class CrossStacking(je_base.BaseEnergyFunction):
"""Cross-stacking energy function for NA1 model."""
params: CrossStackingConfiguration
[docs]
@override
def compute_energy(self, nucleotide: na1_nucleotide.HybridNucleotide) -> typ.Scalar:
op_i = self.unbonded_neighbors[0]
op_j = self.unbonded_neighbors[1]
is_rna_bond = jax.vmap(je_utils.is_rna_pair, (0, 0, None))(op_i, op_j, self.params.nt_type)
is_drh_bond = jax.vmap(je_utils.is_dna_rna_pair, (0, 0, None))(op_i, op_j, self.params.nt_type)
is_rdh_bond = jax.vmap(je_utils.is_dna_rna_pair, (0, 0, None))(op_j, op_i, self.params.nt_type)
mask = jnp.array(op_i < nucleotide.dna.center.shape[0], dtype=jnp.float32)
dna_dgs = dna1_energy.CrossStacking.create_from(self, params=self.params.dna_config).pairwise_energies(
nucleotide.dna,
nucleotide.dna,
self.unbonded_neighbors,
)
rna_dgs = rna2_energy.CrossStacking.create_from(self, params=self.params.rna_config).pairwise_energies(
nucleotide.rna,
nucleotide.rna,
self.unbonded_neighbors,
)
drh_dgs = dna1_energy.CrossStacking.create_from(self, params=self.params.drh_config).pairwise_energies(
nucleotide.dna,
nucleotide.rna,
self.unbonded_neighbors,
)
rdh_dgs = dna1_energy.CrossStacking.create_from(self, params=self.params.drh_config).pairwise_energies(
nucleotide.rna,
nucleotide.dna,
self.unbonded_neighbors,
)
dgs = jnp.where(is_rna_bond, rna_dgs, jnp.where(is_drh_bond, drh_dgs, jnp.where(is_rdh_bond, rdh_dgs, dna_dgs)))
dgs = jnp.where(mask, dgs, 0.0)
return dgs.sum()