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.

PDBTools.hydrogen_bonds — Function

hydrogen_bonds(sim::Simulation, sel1, sel1 => sel2,...; kargs...)

Function to compute the number of hydrogen bonds per frame in a simulation.

Arguments

sim::Simulation: The Simulation object.

and, optionally,

a list of selections, or pairs of selections, given as selection strings. Examples: "protein", "protein" => "water", etc.

If no selection is provided, the hydrogen bonds among all atoms are computed. If two selections of a pair are different, their atoms must not overlap (an error will be thrown).

Returns

An ordered dictionary in which the key specifies the selections and the values are vectors with the number of hydrogen bonds in each frame.

Optional keyword arguments

parallel::Bool=true: Defines if the calculation is run in parallel. Requires starting Julia with multi-threading.
donnor_acceptor_distance::Real=3.5f0: Maximum distance between donnor and acceptor to consider a hydrogen bond.
angle_cutoff::Real=30: Maximum angle (in degrees) between donnor-hydrogen-acceptor to consider a hydrogen bond.
electronegative_elements=("N", "O", "F", "S"): Elements considered electronegative for hydrogen bonding.
d_covalent_bond::Real=1.2f0: Maximum distance between donnor and hydrogen to consider a covalent bond.

Example

julia> using MolSimToolkit, MolSimToolkit.Testing

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

julia> hbs = hydrogen_bonds(sim, "protein")
OrderedCollections.OrderedDict{String, Vector{Int64}} with 1 entry:
  "protein => protein" => [32, 28, 27, 27, 26]

julia> hbs = hydrogen_bonds(sim, "protein" => "water")
OrderedCollections.OrderedDict{String, Vector{Int64}} with 1 entry:
  "protein => water" => [75, 81, 76, 68, 80]

julia> hbs = hydrogen_bonds(sim, "protein", "protein" => "water", "water" => "resname POPC")
OrderedCollections.OrderedDict{String, Vector{Int64}} with 3 entries:
  "protein => protein"    => [32, 28, 27, 27, 26]
  "protein => water"      => [75, 81, 76, 68, 80]
  "water => resname POPC" => [413, 403, 406, 392, 376]

Note

This function does not use topology information. It identified polar hydrogens based on distance criteria only, where d_covalent_bond is the criterium for identifying covalent bonds between donnor and hydrogen atoms.

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["protein => protein"] hbs_prot_water["protein => water"]];
    xlabel="frame",
    ylabel="number of hydrogen bonds",
    label=["protein-protein" "protein-water"],
    legend=:outertopright,
)

Alternativelly, multiple selections, or pairs of selections can be provided, for faster computations,

hbs = hydrogen_bonds(sim,
        "protein",
        "protein" => "water",
        "protein" => "resname POPC",
)

OrderedCollections.OrderedDict{String, Vector{Int64}} with 3 entries:
  "protein => protein"      => [32, 28, 27, 27, 26]
  "protein => water"        => [75, 81, 76, 68, 80]
  "protein => resname POPC" => [0, 1, 4, 5, 6]

The result can be converted directly to a DataFrame

using DataFrames, CSV
df = DataFrame(hbs)

5×3 DataFrame

Row	protein => protein	protein => water	protein => resname POPC
	Int64	Int64	Int64
1	32	75	0
2	28	81	1
3	27	76	4
4	27	68	5
5	26	80	6

and saved to CSV file with CSV.write("hbonds.csv", df).

Note

The order of the pairs, e. g. "protein" => "water" or "water" => "protein", does not affect the result, as electronegative atoms of both groups will be considered as possible hydrogen bond donnors and/or acceptors.

When a single selection is provided, e. g. "protein", the hydrogen bonds within that selection are computed, with no repetitions.