mythos.energy.dna2.base_functions
Base energy functions for DNA2 model.
This function is based on the oxDNA2 model paper found here: https://ora.ox.ac.uk/objects/uuid:241ae8d5-2092-4b24-b1d0-3fb7482b7bcd/files/m7422ee58d9747bbd7af00d6435b570e6
Functions
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The radial part of the stacking and hydrogen-bonding potentials. |
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The radial part of the cross-stacking and coaxial stacking potentials. |
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The radial part of the excluded volume potential. |
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The angular modulation factor used in stacking, hydrogen-bonding, cross-stacking and coaxial stacking. |
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Another modulating term which is used to impose right-handedness (effectively a one-sided modulation). |
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Replaces a coaxial stacking potential in the DNA1 model. |
Module Contents
- mythos.energy.dna2.base_functions.f1(r: mythos.utils.types.ARR_OR_SCALAR, r_low: mythos.utils.types.Scalar, r_high: mythos.utils.types.Scalar, r_c_low: mythos.utils.types.Scalar, r_c_high: mythos.utils.types.Scalar, eps: mythos.utils.types.Scalar, a: mythos.utils.types.Scalar, r0: mythos.utils.types.Scalar, r_c: mythos.utils.types.Scalar, b_low: mythos.utils.types.Scalar, b_high: mythos.utils.types.Scalar) mythos.utils.types.ARR_OR_SCALAR[source]
The radial part of the stacking and hydrogen-bonding potentials.
This is based on equation 2.7 from the oxDNA paper.
- mythos.energy.dna2.base_functions.f2(r: mythos.utils.types.ARR_OR_SCALAR, r_low: mythos.utils.types.Scalar, r_high: mythos.utils.types.Scalar, r_c_low: mythos.utils.types.Scalar, r_c_high: mythos.utils.types.Scalar, k: mythos.utils.types.Scalar, r0: mythos.utils.types.Scalar, r_c: mythos.utils.types.Scalar, b_low: mythos.utils.types.Scalar, b_high: mythos.utils.types.Scalar) mythos.utils.types.ARR_OR_SCALAR[source]
The radial part of the cross-stacking and coaxial stacking potentials.
This is based on equation 2.8 from the oxDNA paper.
- mythos.energy.dna2.base_functions.f3(r: mythos.utils.types.ARR_OR_SCALAR, r_star: mythos.utils.types.Scalar, r_c: mythos.utils.types.Scalar, eps: mythos.utils.types.Scalar, sigma: mythos.utils.types.Scalar, b: mythos.utils.types.Scalar) mythos.utils.types.ARR_OR_SCALAR[source]
The radial part of the excluded volume potential.
This is based on equation 2.9 from the oxDNA paper.
- mythos.energy.dna2.base_functions.f4(theta: mythos.utils.types.ARR_OR_SCALAR, theta0: mythos.utils.types.Scalar, delta_theta_star: mythos.utils.types.Scalar, delta_theta_c: mythos.utils.types.Scalar, a: mythos.utils.types.Scalar, b: mythos.utils.types.Scalar) mythos.utils.types.ARR_OR_SCALAR[source]
The angular modulation factor used in stacking, hydrogen-bonding, cross-stacking and coaxial stacking.
This is based on equation 2.10 from the oxDNA paper.
- mythos.energy.dna2.base_functions.f5(x: mythos.utils.types.ARR_OR_SCALAR, x_star: mythos.utils.types.Scalar, x_c: mythos.utils.types.Scalar, a: mythos.utils.types.Scalar, b: mythos.utils.types.Scalar) mythos.utils.types.ARR_OR_SCALAR[source]
Another modulating term which is used to impose right-handedness (effectively a one-sided modulation).
This is based on equation 2.11 from the oxDNA paper.