Add forcecomponents, generalize features
#19
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This breaking change adds a 3rd argument to the functions that compute `σ` and `ϕ`, requiring the feature name as an argument. This allows one to tune the decay-length or amplitude based on specific atom, residue, and/or field-type. This also establishes defaults for different fields that attempt to be a bit more physically realistic. These have not, however, been investigated in great detail. Finally, `forcecomponents` can be used to compute the net force on a residue, broken down by field. This is useful for tuning the amplitude, using the condition that a realistic structure is in equilibrium.
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Will require release of a new version of https://github.com/tmcgrath325/GaussianMixtureAlignment.jl to pass tests. Let's wait on @tmcgrath325 for that. |
tmcgrath325
approved these changes
May 28, 2024
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In line behind tmcgrath325/GaussianMixtureAlignment.jl#45 |
timholy
commented
May 29, 2024
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In light of #20, let's rerun the tests. |
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Looks good! Neither here nor there, but I appreciate the example of using |
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This breaking change adds a 3rd argument to the functions that compute
σandϕ, requiring the feature name as an argument. This allows oneto tune the decay-length or amplitude based on specific atom, residue,
and/or field-type.
This also establishes defaults for different fields that attempt to be a
bit more physically realistic. These have not, however, been
investigated in great detail.
Finally,
forcecomponentscan be used to compute the net force on aresidue, broken down by field. This is useful for tuning the amplitude,
using the condition that a realistic structure is in equilibrium.