mythos.energy.dna1.interactions
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
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Smoothed version of the FENE potential. |
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Excluded volume energy for bonded interactions. |
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Excluded volume energy for unbonded interactions. |
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Stacking energy. |
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Cross-stacking energy. |
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Coaxial stacking energy. |
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Hydrogen bonding energy. |
Module Contents
- mythos.energy.dna1.interactions.v_fene_smooth(r: mythos.utils.types.ARR_OR_SCALAR, eps_backbone: mythos.utils.types.Scalar, r0_backbone: mythos.utils.types.Scalar, delta_backbone: mythos.utils.types.Scalar, fmax: mythos.utils.types.Scalar = 500, finf: mythos.utils.types.Scalar = 4.0) mythos.utils.types.ARR_OR_SCALAR[source]
Smoothed version of the FENE potential.
- mythos.energy.dna1.interactions.exc_vol_bonded(dr_base: mythos.utils.types.ARR_OR_SCALAR, dr_back_base: mythos.utils.types.ARR_OR_SCALAR, dr_base_back: mythos.utils.types.ARR_OR_SCALAR, eps_exc: mythos.utils.types.Scalar, dr_star_base: mythos.utils.types.Scalar, sigma_base: mythos.utils.types.Scalar, b_base: mythos.utils.types.Scalar, dr_c_base: mythos.utils.types.Scalar, dr_star_back_base: mythos.utils.types.Scalar, sigma_back_base: mythos.utils.types.Scalar, b_back_base: mythos.utils.types.Scalar, dr_c_back_base: mythos.utils.types.Scalar, dr_star_base_back: mythos.utils.types.Scalar, sigma_base_back: mythos.utils.types.Scalar, b_base_back: mythos.utils.types.Scalar, dr_c_base_back: mythos.utils.types.Scalar) mythos.utils.types.Scalar[source]
Excluded volume energy for bonded interactions.
- mythos.energy.dna1.interactions.exc_vol_unbonded(dr_base: mythos.utils.types.ARR_OR_SCALAR, dr_backbone: mythos.utils.types.ARR_OR_SCALAR, dr_back_base: mythos.utils.types.ARR_OR_SCALAR, dr_base_back: mythos.utils.types.ARR_OR_SCALAR, eps_exc: mythos.utils.types.Scalar, dr_star_base: mythos.utils.types.Scalar, sigma_base: mythos.utils.types.Scalar, b_base: mythos.utils.types.Scalar, dr_c_base: mythos.utils.types.Scalar, dr_star_back_base: mythos.utils.types.Scalar, sigma_back_base: mythos.utils.types.Scalar, b_back_base: mythos.utils.types.Scalar, dr_c_back_base: mythos.utils.types.Scalar, dr_star_base_back: mythos.utils.types.Scalar, sigma_base_back: mythos.utils.types.Scalar, b_base_back: mythos.utils.types.Scalar, dr_c_base_back: mythos.utils.types.Scalar, dr_star_backbone: mythos.utils.types.Scalar, sigma_backbone: mythos.utils.types.Scalar, b_backbone: mythos.utils.types.Scalar, dr_c_backbone: mythos.utils.types.Scalar) mythos.utils.types.Scalar[source]
Excluded volume energy for unbonded interactions.
- mythos.energy.dna1.interactions.stacking(r_stack: mythos.utils.types.ARR_OR_SCALAR, theta4: mythos.utils.types.ARR_OR_SCALAR, theta5: mythos.utils.types.ARR_OR_SCALAR, theta6: mythos.utils.types.ARR_OR_SCALAR, cosphi1: mythos.utils.types.ARR_OR_SCALAR, cosphi2: mythos.utils.types.ARR_OR_SCALAR, dr_low_stack: mythos.utils.types.Scalar, dr_high_stack: mythos.utils.types.Scalar, eps_stack: mythos.utils.types.Scalar, a_stack: mythos.utils.types.Scalar, dr0_stack: mythos.utils.types.Scalar, dr_c_stack: mythos.utils.types.Scalar, dr_c_low_stack: mythos.utils.types.Scalar, dr_c_high_stack: mythos.utils.types.Scalar, b_low_stack: mythos.utils.types.Scalar, b_high_stack: mythos.utils.types.Scalar, theta0_stack_4: mythos.utils.types.Scalar, delta_theta_star_stack_4: mythos.utils.types.Scalar, a_stack_4: mythos.utils.types.Scalar, delta_theta_stack_4_c: mythos.utils.types.Scalar, b_stack_4: mythos.utils.types.Scalar, theta0_stack_5: mythos.utils.types.Scalar, delta_theta_star_stack_5: mythos.utils.types.Scalar, a_stack_5: mythos.utils.types.Scalar, delta_theta_stack_5_c: mythos.utils.types.Scalar, b_stack_5: mythos.utils.types.Scalar, theta0_stack_6: mythos.utils.types.Scalar, delta_theta_star_stack_6: mythos.utils.types.Scalar, a_stack_6: mythos.utils.types.Scalar, delta_theta_stack_6_c: mythos.utils.types.Scalar, b_stack_6: mythos.utils.types.Scalar, neg_cos_phi1_star_stack: mythos.utils.types.Scalar, a_stack_1: mythos.utils.types.Scalar, neg_cos_phi1_c_stack: mythos.utils.types.Scalar, b_neg_cos_phi1_stack: mythos.utils.types.Scalar, neg_cos_phi2_star_stack: mythos.utils.types.Scalar, a_stack_2: mythos.utils.types.Scalar, neg_cos_phi2_c_stack: mythos.utils.types.Scalar, b_neg_cos_phi2_stack: mythos.utils.types.Scalar) mythos.utils.types.Scalar[source]
Stacking energy.
- mythos.energy.dna1.interactions.cross_stacking(r_hb: mythos.utils.types.ARR_OR_SCALAR, theta1: mythos.utils.types.ARR_OR_SCALAR, theta2: mythos.utils.types.ARR_OR_SCALAR, theta3: mythos.utils.types.ARR_OR_SCALAR, theta4: mythos.utils.types.ARR_OR_SCALAR, theta7: mythos.utils.types.ARR_OR_SCALAR, theta8: mythos.utils.types.ARR_OR_SCALAR, dr_low_cross: mythos.utils.types.Scalar, dr_high_cross: mythos.utils.types.Scalar, dr_c_low_cross: mythos.utils.types.Scalar, dr_c_high_cross: mythos.utils.types.Scalar, k_cross: mythos.utils.types.Scalar, r0_cross: mythos.utils.types.Scalar, dr_c_cross: mythos.utils.types.Scalar, b_low_cross: mythos.utils.types.Scalar, b_high_cross: mythos.utils.types.Scalar, theta0_cross_1: mythos.utils.types.Scalar, delta_theta_star_cross_1: mythos.utils.types.Scalar, delta_theta_cross_1_c: mythos.utils.types.Scalar, a_cross_1: mythos.utils.types.Scalar, b_cross_1: mythos.utils.types.Scalar, theta0_cross_2: mythos.utils.types.Scalar, delta_theta_star_cross_2: mythos.utils.types.Scalar, delta_theta_cross_2_c: mythos.utils.types.Scalar, a_cross_2: mythos.utils.types.Scalar, b_cross_2: mythos.utils.types.Scalar, theta0_cross_3: mythos.utils.types.Scalar, delta_theta_star_cross_3: mythos.utils.types.Scalar, delta_theta_cross_3_c: mythos.utils.types.Scalar, a_cross_3: mythos.utils.types.Scalar, b_cross_3: mythos.utils.types.Scalar, theta0_cross_4: mythos.utils.types.Scalar, delta_theta_star_cross_4: mythos.utils.types.Scalar, delta_theta_cross_4_c: mythos.utils.types.Scalar, a_cross_4: mythos.utils.types.Scalar, b_cross_4: mythos.utils.types.Scalar, theta0_cross_7: mythos.utils.types.Scalar, delta_theta_star_cross_7: mythos.utils.types.Scalar, delta_theta_cross_7_c: mythos.utils.types.Scalar, a_cross_7: mythos.utils.types.Scalar, b_cross_7: mythos.utils.types.Scalar, theta0_cross_8: mythos.utils.types.Scalar, delta_theta_star_cross_8: mythos.utils.types.Scalar, delta_theta_cross_8_c: mythos.utils.types.Scalar, a_cross_8: mythos.utils.types.Scalar, b_cross_8: mythos.utils.types.Scalar) mythos.utils.types.Scalar[source]
Cross-stacking energy.
- mythos.energy.dna1.interactions.coaxial_stacking(dr_stack: mythos.utils.types.ARR_OR_SCALAR, theta4: mythos.utils.types.ARR_OR_SCALAR, theta1: mythos.utils.types.ARR_OR_SCALAR, theta5: mythos.utils.types.ARR_OR_SCALAR, theta6: mythos.utils.types.ARR_OR_SCALAR, cosphi3: mythos.utils.types.ARR_OR_SCALAR, cosphi4: mythos.utils.types.ARR_OR_SCALAR, dr_low_coax: mythos.utils.types.Scalar, dr_high_coax: mythos.utils.types.Scalar, dr_c_low_coax: mythos.utils.types.Scalar, dr_c_high_coax: mythos.utils.types.Scalar, k_coax: mythos.utils.types.Scalar, dr0_coax: mythos.utils.types.Scalar, dr_c_coax: mythos.utils.types.Scalar, b_low_coax: mythos.utils.types.Scalar, b_high_coax: mythos.utils.types.Scalar, theta0_coax_4: mythos.utils.types.Scalar, delta_theta_star_coax_4: mythos.utils.types.Scalar, delta_theta_coax_4_c: mythos.utils.types.Scalar, a_coax_4: mythos.utils.types.Scalar, b_coax_4: mythos.utils.types.Scalar, theta0_coax_1: mythos.utils.types.Scalar, delta_theta_star_coax_1: mythos.utils.types.Scalar, delta_theta_coax_1_c: mythos.utils.types.Scalar, a_coax_1: mythos.utils.types.Scalar, b_coax_1: mythos.utils.types.Scalar, theta0_coax_5: mythos.utils.types.Scalar, delta_theta_star_coax_5: mythos.utils.types.Scalar, delta_theta_coax_5_c: mythos.utils.types.Scalar, a_coax_5: mythos.utils.types.Scalar, b_coax_5: mythos.utils.types.Scalar, theta0_coax_6: mythos.utils.types.Scalar, delta_theta_star_coax_6: mythos.utils.types.Scalar, delta_theta_coax_6_c: mythos.utils.types.Scalar, a_coax_6: mythos.utils.types.Scalar, b_coax_6: mythos.utils.types.Scalar, cos_phi3_star_coax: mythos.utils.types.Scalar, cos_phi3_c_coax: mythos.utils.types.Scalar, a_coax_3p: mythos.utils.types.Scalar, b_cos_phi3_coax: mythos.utils.types.Scalar, cos_phi4_star_coax: mythos.utils.types.Scalar, cos_phi4_c_coax: mythos.utils.types.Scalar, a_coax_4p: mythos.utils.types.Scalar, b_cos_phi4_coax: mythos.utils.types.Scalar) mythos.utils.types.Scalar[source]
Coaxial stacking energy.
- mythos.energy.dna1.interactions.hydrogen_bonding(dr_hb: mythos.utils.types.ARR_OR_SCALAR, theta1: mythos.utils.types.ARR_OR_SCALAR, theta2: mythos.utils.types.ARR_OR_SCALAR, theta3: mythos.utils.types.ARR_OR_SCALAR, theta4: mythos.utils.types.ARR_OR_SCALAR, theta7: mythos.utils.types.ARR_OR_SCALAR, theta8: mythos.utils.types.ARR_OR_SCALAR, dr_low_hb: mythos.utils.types.Scalar, dr_high_hb: mythos.utils.types.Scalar, dr_c_low_hb: mythos.utils.types.Scalar, dr_c_high_hb: mythos.utils.types.Scalar, eps_hb: mythos.utils.types.Scalar, a_hb: mythos.utils.types.Scalar, dr0_hb: mythos.utils.types.Scalar, dr_c_hb: mythos.utils.types.Scalar, b_low_hb: mythos.utils.types.Scalar, b_high_hb: mythos.utils.types.Scalar, theta0_hb_1: mythos.utils.types.Scalar, delta_theta_star_hb_1: mythos.utils.types.Scalar, a_hb_1: mythos.utils.types.Scalar, delta_theta_hb_1_c: mythos.utils.types.Scalar, b_hb_1: mythos.utils.types.Scalar, theta0_hb_2: mythos.utils.types.Scalar, delta_theta_star_hb_2: mythos.utils.types.Scalar, a_hb_2: mythos.utils.types.Scalar, delta_theta_hb_2_c: mythos.utils.types.Scalar, b_hb_2: mythos.utils.types.Scalar, theta0_hb_3: mythos.utils.types.Scalar, delta_theta_star_hb_3: mythos.utils.types.Scalar, a_hb_3: mythos.utils.types.Scalar, delta_theta_hb_3_c: mythos.utils.types.Scalar, b_hb_3: mythos.utils.types.Scalar, theta0_hb_4: mythos.utils.types.Scalar, delta_theta_star_hb_4: mythos.utils.types.Scalar, a_hb_4: mythos.utils.types.Scalar, delta_theta_hb_4_c: mythos.utils.types.Scalar, b_hb_4: mythos.utils.types.Scalar, theta0_hb_7: mythos.utils.types.Scalar, delta_theta_star_hb_7: mythos.utils.types.Scalar, a_hb_7: mythos.utils.types.Scalar, delta_theta_hb_7_c: mythos.utils.types.Scalar, b_hb_7: mythos.utils.types.Scalar, theta0_hb_8: mythos.utils.types.Scalar, delta_theta_star_hb_8: mythos.utils.types.Scalar, a_hb_8: mythos.utils.types.Scalar, delta_theta_hb_8_c: mythos.utils.types.Scalar, b_hb_8: mythos.utils.types.Scalar) mythos.utils.types.Scalar[source]
Hydrogen bonding energy.