Utility functions

GeometryBasics.Rect(model::Model{T, Triangle{T}})

Creates and returns a bounding box for the given model.

Supported keyword arguments

• padding::T = 0 Adds padding to each side of the (otherwise flush) bounding box, effectively increasing its size by 2 ⋅ padding in each direction.

Return type

GeometryBasics.Rect3{T}

GeometryBasics.mesh(model::Model{T, Triangle{T}})

Converts the given model into a GeometryBasics.jl-compatible mesh, e.g., for visualization through Makie.jl.

Return type

GeometryBasics.Mesh

guess_domain(ξ::Vector{T}, model::Model{T, Triangle{T}})

Make an educated guess whether the given observation point ξ is located in the protein domain Ω, the solvent domain Σ, or the surface domain Γ.

The domain is determined based on the relative position to the triangle with the closest centroid.

Supported keyword arguments

• surface_margin::T = 1e-3 maximum |cos| ⋅ norm allowed between the vector from the closest triangle's centroid to ξ and the triangle's unit normal vector before ξ is no longer considered to be part of the Γ domain.

Return type

Symbol (:Ω, :Σ, or :Γ)

Alias

guess_domain(Ξ::Vector{Vector{T}}, model::Model{T, Triangle{T}})

Determines the domain of each observation point ξ ∈ Ξ.

meshunion(
    model1::Model{T, Tetrahedron{T}},
    model2::Model{T, Tetrahedron{T}}
)

Merges two volume models, e.g., the models of a protein and the solvent. Duplicate nodes (e.g., the nodes on the protein surface) are merged into a single node, duplicate elements and charges (if any) are retained as well as the system constants of the first model.

Return type

Model{T, Tetrahedron{T}}

nessie_data_path(parts::AbstractString...)

Returns the absolute path to NESSie's "data" directory, if used without arguments, or to the location relative to that, specified by parts (e.g., a directory within "data").

Return type

String

obspoints_plane(
    a  ::AbstractVector{T},
    b  ::AbstractVector{T},
    c  ::AbstractVector{T},
    nba::Int,
    nbc::Int
)

Generates nba ⋅ nbc evenly distributed observation points on the parallelogram with the sides $\overline{BA}$ and $\overline{BC}$ and a, b, c being the location vectors to the points $A$, $B$, and $C$, respectively.

Arguments

• nba Number of observation points along $\overline{BA}$
• nbc Number of observation points along $\overline{BC}$

Return type

Generator -> Vector{T}

Example

for Ξ in obspoints_plane(...)
    for ξ in Ξ
        ...
    end
end