Solvent Accessible Surface Area (SASA)

sasa_particles(atoms; probe_radius, n_dots)

Calculates the Solvent Accessible Surface Area (SASA) for a vector of Atoms.

Main argument

• atoms::Vector{PDBTools.Atom}: A vector of atoms in the molecule.

Returns

PDBTools.SASA structure, containing the vector of atoms, the SASA of each atom (in Ų) and, optionally, the solvent accessible dots that define the surface.

The sasa function computes the total SASA or the SASA of a subset of the atoms in the structure.

Optional arguments

• probe_radius::Real=1.4f0: The radius of the solvent probe in Angstroms.
• n_dots::Int=512: The number of grid points along one axis for dot generation. Higher values lead to more accurate but slower calculations.
• unitcell=nothing: if periodic boundary conditions are used, provide a 3x3 matrix with the unitcell, or alternatively a vector of length 3 with the sides, for orthorhombic cells.
• parallel::Bool=true: Control if the computation runs in parallel (requires running Julia with multiple threads).

Example

julia> using PDBTools

julia> prot = select(read_pdb(PDBTools.TESTPDB), "protein");

julia> at_sasa = sasa_particles(prot);

julia> sasa(at_sasa) # total sasa of prot
5389.0146f0

julia> sasa(at_sasa, "backbone") # backbone sasa in prot
988.7648f0

julia> sasa(at_sasa, "not backbone") # other atoms
4400.246f0

julia> sasa(at_sasa, "resname ARG GLU") # some residue types
543.29846f0

Additional control:

Two arguments can control the atom radii used for computing the SASA. These arguments are functions:

• atom_type: Function that given each atom of the array of atoms, returns the atom "type".
• atom_radius_from_type: Given the atom "type", returns the vdW radius of the atom.
• output_dots::Bool=false: If true, the resulting SASA structure will contain the solvent accessible dots per particle in the dots field.

By default, atom_type = PDBTools.element, a function that just returns the element symbol of the atom, and atom_radius_from_type obtains the vdW radius from the PDBTools.elements list given the element symbol. Here, the atomic radii of https://en.wikipedia.org/wiki/Atomicradiioftheelements(datapage) are used. Atoms with missing radius have a NaN value, and the computation will not return meaningful values.

sasa(s::SASA)
sasa(s::SASA{<:AbstractVector{<:PDBTools.Atom}})
sasa(atoms::SASA{<:AbstractVector{PDBTools.Atom}}, selection::Union{Function,String})

Given the output of sasa_particles, sums up contributions of atoms to compute the SASA of the full structure, an atom, or a subset of atoms. The function can be called with only a SASA object (in which case the full SASA is returned), or with the object and a selection, given by a function or selection string.

Example

julia> using PDBTools

julia> prot = select(read_pdb(PDBTools.TESTPDB), "protein");

julia> at_sasa = sasa_particles(prot);

julia> sasa(at_sasa) # total sasa of prot
5389.0146f0

julia> sasa(at_sasa, "backbone") # selection string
988.7648f0

julia> sasa(at_sasa, at -> name(at) == "CA") # selection function
44.078426f0

julia> sasa(at_sasa[1]) # single atom SASA
5.467941f0