Some auxiliary functions to quickly retrieve some data

getseq(AbstractVector{<:Atom} or filename; selection, code)

Returns the sequence of aminoacids from the vector of atoms or file name. Selections may be applied. Code defines if the output will be a one-letter, three-letter or full-residue name array.

Example

julia> using PDBTools

julia> protein = read_pdb(PDBTools.TESTPDB);

julia> getseq(protein,"residue < 3")
2-element Vector{String}:
 "A"
 "C"

julia> getseq(protein,"residue < 3", code=2)
2-element Vector{String}:
 "ALA"
 "CYS"

julia> getseq(protein,"residue < 3",code=3)
2-element Vector{String}:
 "Alanine"
 "Cysteine"

Sequence

Wrapper for strings, or vectors of chars, strings, or residue names, to dispatch on functions that operate on amino acid sequences.

Example

julia> seq = ["Alanine", "Glutamic acid", "Glycine"];

julia> mass(Sequence(seq))
257.2432

julia> seq = "AEG";

julia> mass(Sequence(seq))
257.2432

distance(x,y)

Computes the minimum distance between two sets of atoms, between an atom and a set of atoms, or simply the distance between two atoms. The input may be a vector of Atoms, or the coordinates that are output of the coor function.

Examples

julia> model = wget("1BSX");

julia> protein = select(model,"protein");

julia> ligand = select(model,"resname T3");

julia> distance(protein,ligand)
2.7775834820937417

julia> distance(protein[1],ligand[3])
36.453551075306784

julia> distance(coor(ligand),protein)
2.7775834820937417

closest(x,y)

Computes the minimum distance between two sets of atoms and returns the indices of the atoms and their distance. Both vector of atoms or vectors of coordinates can be used as input.

Examples

julia> model = wget("1BSX");

julia> protein = select(model,"protein");

julia> ligand = select(model,"resname T3");

julia> closest(ligand,protein)
(43, 3684, 2.7775834820937417)

julia> ligand[43]
    4037   O1      T3     B        2      512  -22.568   81.625    3.159 36.59  1.00     1       -      4041

julia> closest(ligand[43],protein)
(1, 3684, 2.7775834820937417)

julia> x = coor(protein)
3994-element Vector{SVector{3, Float64}}:
 [52.884, 24.022, 35.587]
 [52.916, 24.598, 36.993]
 ⋮
 [-46.887, 86.925, 13.235]
 [-47.164, 83.593, 15.25]

julia> closest(ligand,x)
(43, 3684, 2.7775834820937417)

coor(atoms; selection)

Returns the coordinates of the atoms. The input may be one atom (type Atom), a vector of atoms, or a Residue. The coordinates are returned as a vector of static vectors (from StaticArrays), more specifically as a Vector{SVector{3,Float64}}.

Examples

julia> using PDBTools, StaticArrays 

julia> protein = wget("1LBD");

julia> coor(protein[1])
3-element SVector{3, Float64} with indices SOneTo(3):
 45.228
 84.358
 70.638

julia> coor(protein[1],as=SVector{3,Float32})
3-element SVector{3, Float32} with indices SOneTo(3):
 45.228
 84.358
 70.638

julia> coor(protein, "index <= 2")
2-element Vector{SVector{3, Float64}}:
 [45.228, 84.358, 70.638]
 [46.08, 83.165, 70.327]

julia> coor(protein, only = at -> at.resname == "ALA")
110-element Vector{SVector{3, Float64}}:
 [43.94, 81.982, 70.474]
 [43.02, 80.825, 70.455]
 [41.996, 80.878, 69.34]
 ⋮
 [-17.866, 84.088, 51.741]
 [-18.496, 83.942, 52.777]
 [-15.888, 82.583, 51.706]
  
julia> residues = collect(eachresidue(protein));

julia> coor(residues[1])
6-element Vector{SVector{3, Float64}}:
 [45.228, 84.358, 70.638]
 [46.08, 83.165, 70.327]
 [45.257, 81.872, 70.236]
 [45.823, 80.796, 69.974]
 [47.147, 82.98, 71.413]
 [46.541, 82.639, 72.662]

maxmin(atoms::AbstractVector{<:Atom}; selection)

Returns the maximum and minimum coordinates of an atom vector, and the length (maximum minus minimum) in each direction.

Example

julia> protein = wget("1LBD");

julia> maxmin(protein)
 
 Minimum atom coordinates: xmin = [-29.301, 57.178, 45.668]
 Maximum atom coordinates: xmax = [47.147, 99.383, 86.886]
 Length in each direction: xlength = [76.448, 42.205, 41.217999999999996]

residue_ticks(
    atoms (or) residues (or) residue iterator; 
    first=nothing, last=nothing, stride=1, oneletter=true, serial=false
)

Returns a tuple with residue numbers and residue names for the given atoms, to be used as tick labels in plots.

The structure data can be provided a vector of Atoms, a vector of Residues or an EachResidue iterator.

first and last optional keyword parameters are integers that refer to the residue numbers to be included. The stride option can be used to skip residues and declutter the tick labels.

If oneletter is false, three-letter residue codes are returned. Residues with unknown names will be named X or XXX.

If serial=true the sequential residue index will be used as the index of the ticks. If instead serial=false, the positions will be set to the residue numbers.

Examples

julia> using PDBTools

julia> atoms = wget("1LBD", "protein");

julia> residue_ticks(atoms; stride=50) # Vector{<:Atom} as input
(Int32[225, 275, 325, 375, 425], ["S225", "Q275", "L325", "L375", "L425"])

julia> residue_ticks(atoms; first=235, last=240) # first=10
(Int32[235, 236, 237, 238, 239, 240], ["I235", "L236", "E237", "A238", "E239", "L240"])

julia> residue_ticks(eachresidue(atoms); stride=50) # residue iterator as input
(Int32[225, 275, 325, 375, 425], ["S225", "Q275", "L325", "L375", "L425"])

julia> residue_ticks(collect(eachresidue(atoms)); stride=50) # Vector{Residue} as input
(Int32[225, 275, 325, 375, 425], ["S225", "Q275", "L325", "L375", "L425"])

julia> residue_ticks(atoms; first=10, stride=50, serial=true) # using serial=true
(10:50:210, ["R234", "K284", "R334", "S384", "E434"])

The resulting tuple of residue numbers and labels can be used as xticks in Plots.plot, for example.

oneletter(residue::Union{AbstractString,Char})

Function to return a one-letter residue code from the three letter code or residue name. The function is case-insensitive.

Examples

julia> oneletter("ALA")
"A"

julia> oneletter("Glutamic acid")
"E"

threeletter(residue::String)

Function to return the three-letter natural-amino acid residue code from the one-letter code or residue name. The function is case-insensitive.

Examples

julia> threeletter("A")
"ALA"

julia> threeletter("Aspartic acid")
"ASP"

julia> threeletter("HSD")
"HIS"