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MolSimToolkitShared.jl

MolSimToolkitShared.jl is a low-level package defining a series of functions and function names that are shared among other packages, such as MolSimToolkit.jl, PDBTools.jl, and ComplexMixtures.jl.

Normally this package won't be used by the end-user, but as a dependency of other packages.

API

Function name placeholders

These function names are considered public:

distance, distances
coordination_number, bulk_coordination
center_of_mass
wrap, wrap_to_first
align, align!, rmsd

Methods

MolSimToolkitShared.align — Function
align(x, y; mass = nothing)
align!(x, y; mass = nothing)

Aligns two structures (sets of points in 3D space). Solves the "Procrustes" problem, which is to find the best translation, and rotation, that aligns the two structures, minimizing the RMSD between them.

Structures are expected to be of the same size, and the correspondence is assumed from the vector indices.

align returns a new vector containing the coordinates of x aligned to y. align! modifies the input vector x in place.

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MolSimToolkitShared.align! — Function
align(x, y; mass = nothing)
align!(x, y; mass = nothing)

Aligns two structures (sets of points in 3D space). Solves the "Procrustes" problem, which is to find the best translation, and rotation, that aligns the two structures, minimizing the RMSD between them.

Structures are expected to be of the same size, and the correspondence is assumed from the vector indices.

align returns a new vector containing the coordinates of x aligned to y. align! modifies the input vector x in place.

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MolSimToolkitShared.center_of_mass — Method
center_of_mass(x::AbstractVector{<:AbstractVector}[, mass::AbstractVector=nothing])

Calculate the center of mass of a set of points.

Arguments

  • x::AbstractVector{<:AbstractVector}: A vector of coordinates.
  • mass::AbstractVector: A vector of masses. If not provided, all masses are assumed to be equal.

Example

julia> import MolSimToolkitShared: center_of_mass

julia> x = [ [1.0, 2.0, 3.0], [4.0, 5.0, 6.0], [7.0, 8.0, 9.0] ];

julia> center_of_mass(x)
3-element Vector{Float64}:
 4.0
 5.0
 6.0

julia> center_of_mass(x, [1.0, 2.0, 3.0]) # providing masses
3-element Vector{Float64}:
 5.0
 6.0
 7.0
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MolSimToolkitShared.rmsd — Method
rmsd(x::AbstractVector,y::AbstractVector)

Calculate the root mean square deviation between two vectors of coordinates.

Arguments

  • x::AbstractVector: A vector of coordinates.
  • y::AbstractVector: A vector of coordinates.

Returns

  • rmsd::Real: The root mean square deviation between the two vectors.
julia> import MolSimToolkitShared: rmsd

julia> x = [ [1.0, 2.0, 3.0], [4.0, 5.0, 6.0], [7.0, 8.0, 9.0] ];

julia> y = [ [2.0, 3.0, 4.0], [4.0, 5.0, 6.0], [7.0, 8.0, 9.0] ];

julia> rmsd(x, y)
1.0
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MolSimToolkitShared.wrap — Function
wrap(x, xref, unit_cell_matrix::SMatrix{N,N,T}) where {N,T}
wrap(x, xref, sides::AbstractVector)

Wraps the coordinates of point x such that it is the minimum image relative to xref. The unit cell may be given a a static matrix of size (N,N) or as a vector of length N.

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MolSimToolkitShared.wrap_to_first — Function
wrap_to_first(x, unit_cell_matrix)

Wraps the coordinates of point x such that the returning coordinates are in the first unit cell with all-positive coordinates. The unit cell has to be a matrix of size (N,N).

Example

julia> using MolSimToolkitShared: wrap_to_first

julia> uc = [10.0 0.0 0.0; 0.0 10.0 0.0; 0.0 0.0 10.0]
3×3 Matrix{Float64}:
 10.0   0.0   0.0
  0.0  10.0   0.0
  0.0   0.0  10.0

julia> wrap_to_first([15.0, 13.0, 2.0], uc)
3-element Vector{Float64}:
 5.0
 3.0000000000000004
 2.0
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