jax_dna.energy.rna2.interactions
RNA2 interactions.
These functions are based on the RNA2 model paper found here: https://arxiv.org/abs/1403.4180
Functions
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Stacking energy. |
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Cross-stacking energy. |
Module Contents
- jax_dna.energy.rna2.interactions.stacking(r_stack: jax_dna.utils.types.ARR_OR_SCALAR, theta5: jax_dna.utils.types.ARR_OR_SCALAR, theta6: jax_dna.utils.types.ARR_OR_SCALAR, theta9: jax_dna.utils.types.ARR_OR_SCALAR, theta10: jax_dna.utils.types.ARR_OR_SCALAR, cosphi1: jax_dna.utils.types.ARR_OR_SCALAR, cosphi2: jax_dna.utils.types.ARR_OR_SCALAR, dr_low_stack: jax_dna.utils.types.Scalar, dr_high_stack: jax_dna.utils.types.Scalar, eps_stack: jax_dna.utils.types.Scalar, a_stack: jax_dna.utils.types.Scalar, dr0_stack: jax_dna.utils.types.Scalar, dr_c_stack: jax_dna.utils.types.Scalar, dr_c_low_stack: jax_dna.utils.types.Scalar, dr_c_high_stack: jax_dna.utils.types.Scalar, b_low_stack: jax_dna.utils.types.Scalar, b_high_stack: jax_dna.utils.types.Scalar, theta0_stack_5: jax_dna.utils.types.Scalar, delta_theta_star_stack_5: jax_dna.utils.types.Scalar, a_stack_5: jax_dna.utils.types.Scalar, delta_theta_stack_5_c: jax_dna.utils.types.Scalar, b_stack_5: jax_dna.utils.types.Scalar, theta0_stack_6: jax_dna.utils.types.Scalar, delta_theta_star_stack_6: jax_dna.utils.types.Scalar, a_stack_6: jax_dna.utils.types.Scalar, delta_theta_stack_6_c: jax_dna.utils.types.Scalar, b_stack_6: jax_dna.utils.types.Scalar, theta0_stack_9: jax_dna.utils.types.Scalar, delta_theta_star_stack_9: jax_dna.utils.types.Scalar, a_stack_9: jax_dna.utils.types.Scalar, delta_theta_stack_9_c: jax_dna.utils.types.Scalar, b_stack_9: jax_dna.utils.types.Scalar, theta0_stack_10: jax_dna.utils.types.Scalar, delta_theta_star_stack_10: jax_dna.utils.types.Scalar, a_stack_10: jax_dna.utils.types.Scalar, delta_theta_stack_10_c: jax_dna.utils.types.Scalar, b_stack_10: jax_dna.utils.types.Scalar, neg_cos_phi1_star_stack: jax_dna.utils.types.Scalar, a_stack_1: jax_dna.utils.types.Scalar, neg_cos_phi1_c_stack: jax_dna.utils.types.Scalar, b_neg_cos_phi1_stack: jax_dna.utils.types.Scalar, neg_cos_phi2_star_stack: jax_dna.utils.types.Scalar, a_stack_2: jax_dna.utils.types.Scalar, neg_cos_phi2_c_stack: jax_dna.utils.types.Scalar, b_neg_cos_phi2_stack: jax_dna.utils.types.Scalar) jax_dna.utils.types.Scalar[source]
Stacking energy.
- jax_dna.energy.rna2.interactions.cross_stacking(r_hb: jax_dna.utils.types.ARR_OR_SCALAR, theta1: jax_dna.utils.types.ARR_OR_SCALAR, theta2: jax_dna.utils.types.ARR_OR_SCALAR, theta3: jax_dna.utils.types.ARR_OR_SCALAR, theta7: jax_dna.utils.types.ARR_OR_SCALAR, theta8: jax_dna.utils.types.ARR_OR_SCALAR, dr_low_cross: jax_dna.utils.types.Scalar, dr_high_cross: jax_dna.utils.types.Scalar, dr_c_low_cross: jax_dna.utils.types.Scalar, dr_c_high_cross: jax_dna.utils.types.Scalar, k_cross: jax_dna.utils.types.Scalar, r0_cross: jax_dna.utils.types.Scalar, dr_c_cross: jax_dna.utils.types.Scalar, b_low_cross: jax_dna.utils.types.Scalar, b_high_cross: jax_dna.utils.types.Scalar, theta0_cross_1: jax_dna.utils.types.Scalar, delta_theta_star_cross_1: jax_dna.utils.types.Scalar, delta_theta_cross_1_c: jax_dna.utils.types.Scalar, a_cross_1: jax_dna.utils.types.Scalar, b_cross_1: jax_dna.utils.types.Scalar, theta0_cross_2: jax_dna.utils.types.Scalar, delta_theta_star_cross_2: jax_dna.utils.types.Scalar, delta_theta_cross_2_c: jax_dna.utils.types.Scalar, a_cross_2: jax_dna.utils.types.Scalar, b_cross_2: jax_dna.utils.types.Scalar, theta0_cross_3: jax_dna.utils.types.Scalar, delta_theta_star_cross_3: jax_dna.utils.types.Scalar, delta_theta_cross_3_c: jax_dna.utils.types.Scalar, a_cross_3: jax_dna.utils.types.Scalar, b_cross_3: jax_dna.utils.types.Scalar, theta0_cross_7: jax_dna.utils.types.Scalar, delta_theta_star_cross_7: jax_dna.utils.types.Scalar, delta_theta_cross_7_c: jax_dna.utils.types.Scalar, a_cross_7: jax_dna.utils.types.Scalar, b_cross_7: jax_dna.utils.types.Scalar, theta0_cross_8: jax_dna.utils.types.Scalar, delta_theta_star_cross_8: jax_dna.utils.types.Scalar, delta_theta_cross_8_c: jax_dna.utils.types.Scalar, a_cross_8: jax_dna.utils.types.Scalar, b_cross_8: jax_dna.utils.types.Scalar) jax_dna.utils.types.Scalar[source]
Cross-stacking energy.