jax_dna.energy.dna1.interactions ================================ .. py:module:: jax_dna.energy.dna1.interactions .. autoapi-nested-parse:: DNA1 interactions. These functions are based on the oxDNA1 model paper found here: https://ora.ox.ac.uk/objects/uuid:b2415bb2-7975-4f59-b5e2-8c022b4a3719/files/mdcac62bc9133143fc05070ed20048c50 Functions --------- .. autoapisummary:: jax_dna.energy.dna1.interactions.v_fene_smooth jax_dna.energy.dna1.interactions.exc_vol_bonded jax_dna.energy.dna1.interactions.exc_vol_unbonded jax_dna.energy.dna1.interactions.stacking jax_dna.energy.dna1.interactions.cross_stacking jax_dna.energy.dna1.interactions.coaxial_stacking jax_dna.energy.dna1.interactions.hydrogen_bonding Module Contents --------------- .. py:function:: v_fene_smooth(r: jax_dna.utils.types.ARR_OR_SCALAR, eps_backbone: jax_dna.utils.types.Scalar, r0_backbone: jax_dna.utils.types.Scalar, delta_backbone: jax_dna.utils.types.Scalar, fmax: jax_dna.utils.types.Scalar = 500, finf: jax_dna.utils.types.Scalar = 4.0) -> jax_dna.utils.types.ARR_OR_SCALAR Smoothed version of the FENE potential. .. py:function:: exc_vol_bonded(dr_base: jax_dna.utils.types.ARR_OR_SCALAR, dr_back_base: jax_dna.utils.types.ARR_OR_SCALAR, dr_base_back: jax_dna.utils.types.ARR_OR_SCALAR, eps_exc: jax_dna.utils.types.Scalar, dr_star_base: jax_dna.utils.types.Scalar, sigma_base: jax_dna.utils.types.Scalar, b_base: jax_dna.utils.types.Scalar, dr_c_base: jax_dna.utils.types.Scalar, dr_star_back_base: jax_dna.utils.types.Scalar, sigma_back_base: jax_dna.utils.types.Scalar, b_back_base: jax_dna.utils.types.Scalar, dr_c_back_base: jax_dna.utils.types.Scalar, dr_star_base_back: jax_dna.utils.types.Scalar, sigma_base_back: jax_dna.utils.types.Scalar, b_base_back: jax_dna.utils.types.Scalar, dr_c_base_back: jax_dna.utils.types.Scalar) -> jax_dna.utils.types.Scalar Excluded volume energy for bonded interactions. .. py:function:: exc_vol_unbonded(dr_base: jax_dna.utils.types.ARR_OR_SCALAR, dr_backbone: jax_dna.utils.types.ARR_OR_SCALAR, dr_back_base: jax_dna.utils.types.ARR_OR_SCALAR, dr_base_back: jax_dna.utils.types.ARR_OR_SCALAR, eps_exc: jax_dna.utils.types.Scalar, dr_star_base: jax_dna.utils.types.Scalar, sigma_base: jax_dna.utils.types.Scalar, b_base: jax_dna.utils.types.Scalar, dr_c_base: jax_dna.utils.types.Scalar, dr_star_back_base: jax_dna.utils.types.Scalar, sigma_back_base: jax_dna.utils.types.Scalar, b_back_base: jax_dna.utils.types.Scalar, dr_c_back_base: jax_dna.utils.types.Scalar, dr_star_base_back: jax_dna.utils.types.Scalar, sigma_base_back: jax_dna.utils.types.Scalar, b_base_back: jax_dna.utils.types.Scalar, dr_c_base_back: jax_dna.utils.types.Scalar, dr_star_backbone: jax_dna.utils.types.Scalar, sigma_backbone: jax_dna.utils.types.Scalar, b_backbone: jax_dna.utils.types.Scalar, dr_c_backbone: jax_dna.utils.types.Scalar) -> jax_dna.utils.types.Scalar Excluded volume energy for unbonded interactions. .. py:function:: stacking(r_stack: jax_dna.utils.types.ARR_OR_SCALAR, theta4: jax_dna.utils.types.ARR_OR_SCALAR, theta5: jax_dna.utils.types.ARR_OR_SCALAR, theta6: 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_4: jax_dna.utils.types.Scalar, delta_theta_star_stack_4: jax_dna.utils.types.Scalar, a_stack_4: jax_dna.utils.types.Scalar, delta_theta_stack_4_c: jax_dna.utils.types.Scalar, b_stack_4: 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, 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 Stacking energy. .. py:function:: 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, theta4: 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_4: jax_dna.utils.types.Scalar, delta_theta_star_cross_4: jax_dna.utils.types.Scalar, delta_theta_cross_4_c: jax_dna.utils.types.Scalar, a_cross_4: jax_dna.utils.types.Scalar, b_cross_4: 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 Cross-stacking energy. .. py:function:: coaxial_stacking(dr_stack: jax_dna.utils.types.ARR_OR_SCALAR, theta4: jax_dna.utils.types.ARR_OR_SCALAR, theta1: jax_dna.utils.types.ARR_OR_SCALAR, theta5: jax_dna.utils.types.ARR_OR_SCALAR, theta6: jax_dna.utils.types.ARR_OR_SCALAR, cosphi3: jax_dna.utils.types.ARR_OR_SCALAR, cosphi4: jax_dna.utils.types.ARR_OR_SCALAR, dr_low_coax: jax_dna.utils.types.Scalar, dr_high_coax: jax_dna.utils.types.Scalar, dr_c_low_coax: jax_dna.utils.types.Scalar, dr_c_high_coax: jax_dna.utils.types.Scalar, k_coax: jax_dna.utils.types.Scalar, dr0_coax: jax_dna.utils.types.Scalar, dr_c_coax: jax_dna.utils.types.Scalar, b_low_coax: jax_dna.utils.types.Scalar, b_high_coax: jax_dna.utils.types.Scalar, theta0_coax_4: jax_dna.utils.types.Scalar, delta_theta_star_coax_4: jax_dna.utils.types.Scalar, delta_theta_coax_4_c: jax_dna.utils.types.Scalar, a_coax_4: jax_dna.utils.types.Scalar, b_coax_4: jax_dna.utils.types.Scalar, theta0_coax_1: jax_dna.utils.types.Scalar, delta_theta_star_coax_1: jax_dna.utils.types.Scalar, delta_theta_coax_1_c: jax_dna.utils.types.Scalar, a_coax_1: jax_dna.utils.types.Scalar, b_coax_1: jax_dna.utils.types.Scalar, theta0_coax_5: jax_dna.utils.types.Scalar, delta_theta_star_coax_5: jax_dna.utils.types.Scalar, delta_theta_coax_5_c: jax_dna.utils.types.Scalar, a_coax_5: jax_dna.utils.types.Scalar, b_coax_5: jax_dna.utils.types.Scalar, theta0_coax_6: jax_dna.utils.types.Scalar, delta_theta_star_coax_6: jax_dna.utils.types.Scalar, delta_theta_coax_6_c: jax_dna.utils.types.Scalar, a_coax_6: jax_dna.utils.types.Scalar, b_coax_6: jax_dna.utils.types.Scalar, cos_phi3_star_coax: jax_dna.utils.types.Scalar, cos_phi3_c_coax: jax_dna.utils.types.Scalar, a_coax_3p: jax_dna.utils.types.Scalar, b_cos_phi3_coax: jax_dna.utils.types.Scalar, cos_phi4_star_coax: jax_dna.utils.types.Scalar, cos_phi4_c_coax: jax_dna.utils.types.Scalar, a_coax_4p: jax_dna.utils.types.Scalar, b_cos_phi4_coax: jax_dna.utils.types.Scalar) -> jax_dna.utils.types.Scalar Coaxial stacking energy. .. py:function:: hydrogen_bonding(dr_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, theta4: 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_hb: jax_dna.utils.types.Scalar, dr_high_hb: jax_dna.utils.types.Scalar, dr_c_low_hb: jax_dna.utils.types.Scalar, dr_c_high_hb: jax_dna.utils.types.Scalar, eps_hb: jax_dna.utils.types.Scalar, a_hb: jax_dna.utils.types.Scalar, dr0_hb: jax_dna.utils.types.Scalar, dr_c_hb: jax_dna.utils.types.Scalar, b_low_hb: jax_dna.utils.types.Scalar, b_high_hb: jax_dna.utils.types.Scalar, theta0_hb_1: jax_dna.utils.types.Scalar, delta_theta_star_hb_1: jax_dna.utils.types.Scalar, a_hb_1: jax_dna.utils.types.Scalar, delta_theta_hb_1_c: jax_dna.utils.types.Scalar, b_hb_1: jax_dna.utils.types.Scalar, theta0_hb_2: jax_dna.utils.types.Scalar, delta_theta_star_hb_2: jax_dna.utils.types.Scalar, a_hb_2: jax_dna.utils.types.Scalar, delta_theta_hb_2_c: jax_dna.utils.types.Scalar, b_hb_2: jax_dna.utils.types.Scalar, theta0_hb_3: jax_dna.utils.types.Scalar, delta_theta_star_hb_3: jax_dna.utils.types.Scalar, a_hb_3: jax_dna.utils.types.Scalar, delta_theta_hb_3_c: jax_dna.utils.types.Scalar, b_hb_3: jax_dna.utils.types.Scalar, theta0_hb_4: jax_dna.utils.types.Scalar, delta_theta_star_hb_4: jax_dna.utils.types.Scalar, a_hb_4: jax_dna.utils.types.Scalar, delta_theta_hb_4_c: jax_dna.utils.types.Scalar, b_hb_4: jax_dna.utils.types.Scalar, theta0_hb_7: jax_dna.utils.types.Scalar, delta_theta_star_hb_7: jax_dna.utils.types.Scalar, a_hb_7: jax_dna.utils.types.Scalar, delta_theta_hb_7_c: jax_dna.utils.types.Scalar, b_hb_7: jax_dna.utils.types.Scalar, theta0_hb_8: jax_dna.utils.types.Scalar, delta_theta_star_hb_8: jax_dna.utils.types.Scalar, a_hb_8: jax_dna.utils.types.Scalar, delta_theta_hb_8_c: jax_dna.utils.types.Scalar, b_hb_8: jax_dna.utils.types.Scalar) -> jax_dna.utils.types.Scalar Hydrogen bonding energy.