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distance.jl
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distance.jl
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import Pkg; Pkg.activate("ComputeDistances",shared=true)
#First time only:
Pkg.add(["Chemfiles", "PDBTools", "Plots","CellListMap"])
# loading packages
using LinearAlgebra: norm
using StaticArrays
using PDBTools
using Plots
import CellListMap: wrap_relative_to
import Chemfiles
# function that computes the distance between atoms for each frame
function compute_distance(;pdbname, trajectory_name, selection1, selection2)
pdb = readPDB(pdbname)
dcd = Chemfiles.Trajectory(trajectory_name)
atom1 = select(pdb, selection1)
atom2 = select(pdb, selection2)
distances = Float64[]
for frame in dcd
# read unit cell matrix from trajectory
matrix_read = Chemfiles.matrix(Chemfiles.UnitCell(frame))
unit_cell = SMatrix{3,3}(transpose(matrix_read))
# read coordinates, convert them to small static vectors
coordinates = Chemfiles.positions(frame)
x = SVector{3}(@view(coordinates[:,atom1[1].index]))
y = SVector{3}(@view(coordinates[:,atom2[1].index]))
# wrap coordinates according to PBC. Note that here we use an
# internal function of `CellListMap`.
y_wrapped = wrap_relative_to(y,x,unit_cell)
# compute distance
d = norm(y_wrapped-x)
# add data to distance array
push!(distances, d)
end
return distances
end
#
# Examples
#
# NAMD trajectory file
function run_namd()
distances = compute_distance(
pdbname = "./data/structure.pdb",
trajectory_name ="./data/trajectory.dcd",
selection1 = "residue 1 and name CA",
selection2 = "residue 8000 and name OH2",
)
Plots.default(fontfamily="Computer Modern")
plt = plot(distances,
xlabel = "frame",
ylabel = "distance / Å",
framestyle=:box,
linewidth=2,
label=nothing
)
# savefig("./plot.svg") # to save the figure
display(plt)
return plt, distances
end
# Gromacs trajectory file
function run_gromacs()
distances = compute_distance(
pdbname = "./data/system.pdb",
trajectory_name ="./data/trajectory.xtc",
selection1 = "index 81044",
selection2 = "index 78821",
)
Plots.default(fontfamily="Computer Modern")
plt = plot(distances,
xlabel = "frame",
ylabel = "distance / Å",
framestyle=:box,
linewidth=2,
label=nothing
)
# savefig("./plot.svg") # to save the figure
display(plt)
return plt, distances
end