Hydrogen bonds

Computes the number of hydrogen bonds of a set of atoms, or between two sets of atoms, for each frame in a simulation.

Warning

This is an experimental feature. Breaking changes may occur without a breaking package release.

PDBTools.hydrogen_bonds — Function

hydrogen_bonds(
    sim::Simulation, 
    sel1::Union{String,Function}=at -> true, 
    sel2::Union{Nothing,String,Function}=nothing; 
    nthreads=Threads.nthreads(),
    show_progress::Bool=true,
    parallel::Bool=true,
    kargs...
)

Compute the number of hydrogen bonds for each frame of a simulation.

For further details on kargs... see the help entry of PDBTools.hydrogen_bonds.

Warning

Experimental feature: interface may change without breaking package release.

Example

julia> using MolSimToolkit, MolSimToolkit.Testing

julia> sim = Simulation(Testing.namd_pdb, Testing.namd_traj);

julia> hbs = hydrogen_bonds(sim, "protein")
5-element Vector{Int64}:
 32
 28
 27
 27
 26

julia> hbs = hydrogen_bonds(sim, "protein", "water")
5-element Vector{Int64}:
 75
 81
 76
 68
 80

source

Example

using MolSimToolkit, PDBTools
using MolSimToolkit.Testing # to load test files
using Plots
# Build Simulation object
sim = Simulation(Testing.namd_pdb, Testing.namd_traj)
# Compute h-bonds of the protein with itself
hbs_prot = hydrogen_bonds(sim, "protein")
# Compute h-bonds between protein and water
hbs_prot_water = hydrogen_bonds(sim, "protein", "water")
# Plot
plot(MolSimStyle,
    [hbs_prot hbs_prot_water];
    xlabel="frame",
    ylabel="number of hydrogen bonds",
    label=["protein-protein" "protein-water"],
    legend=:outertopright,
)