Structs

This struct corresponding to MD trajectory. This contains 4 fields like below.

• coordinates : AbstractArray{Coordinate, 2}
• attributes : Vector{Attribute}
• natom : Number of atoms.
• nframe : Number of frames in the trajectory.
• box : Vector{Coordinate} of periodic box size for each frame

The column of coordinates matrix means one snapshot. The row of coordinates matrix means time series of one atom.

[ a d g j
  b e h k
  c f i l ]

In this case, one snapshot correspond to [a b c].

The constructor is below.

function Trajectory(coordinates::Array{Coordinate, 2};
                    attributes::Vector{Attribute} = [Attribute() for i=1:length(coordinates)],
                    box::Vector{Coordinate} = Vector{Coordinate}())

This correspond to coordinate of atom. This contain 3 fields like below.

• x <: Real
• y <: Real
• z <: Real

Some operators and functions were overloaded to make Coordinate objects broadcastable.

This struct mean all atomic information other than coordinates. This contains 5 fields like below.

• resname : Union{String, Nothing}
• resid : Union{Int64, Nothing}
• atomname : Union{String, Nothing}
• atomid : Union{Int64, Nothing}
• mass : Union{Float32, Nothing}

The constructor is below.

function Attribute(;resname = nothing, resid = nothing,
                   atomname = nothing, atomid = nothing, mass = nothing)

This struct correspond to one snapshot of trajectory. This contains 3 fields like below.

• coordinates : Vector{Coordinate}
• attribute : Vector{Attribute}
• natom : Number of atoms.

This struct have all information of corresponding atom. This contains 2 fields like below.

• coordinate : Reference to Coordinate object.
• attribute : Reference to Attribute object.