Some auxiliary functions to quickly retrieve some data
Get the protein sequence
To obtain a list of the residue names of the protein with three- and one-letter codes, use
julia> seq = getseq("file.pdb")
+76-element Vector{String}:
+ "V"
+ "K"
+ ⋮
+ "R"
+ "G"
+Use getseq(atoms,code=2) to get the sequence as three-letter residue codes, or code=3 to get full natural-aminoacid names, like "Alanine", "Proline", etc.
If there is some non-standard protein residue in the sequence, inform the getseq function by adding a selection:
julia> getseq("file.pdb","protein or resname NEW")
+77-element Vector{String}:
+ "V"
+ "N"
+ ⋮
+ "R"
+ "G"By default the selection will only return the sequence of natural amino acids.
The getseq function can of course be used on an Atom list, accepts selections as the last argument, as well as the reading and writing functions:
atoms = readPDB("file.pdb")
+seq = getseq(atoms,"chain A")
+Distance between sets of atoms
The distance between atoms, or sets of atoms, can be computed with the distance function. This function returns the minimum distance between the atoms of the sets involved. For example:
julia> model = wget("1BSX");
+
+julia> protein = select(model,"protein");
+
+julia> ligand = select(model,"resname T3");
+
+julia> distance(protein,ligand)
+2.7775834820937417
+ Closest atoms and their distance
A function similar to the one above is closest, which returns the shortest distance between atoms but also the identity of the atom or pair of atoms that satisfy that shortest distance:
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> protein[3684]
+ 3684 NE2 HIS B 435 472 -21.539 82.145 5.686 44.44 1.00 1 - 3686
+
+julia> distance(ligand[43],protein[3684])
+2.7775834820937417
+ Obtain arrays with coordinates
All atoms:
julia> x = coor(atoms)
+1463-element Vector{SVector{3, Float64}}:
+ [-9.229, -14.861, -5.481]
+ [-10.048, -15.427, -5.569]
+ [-9.488, -13.913, -5.295]
+ ⋮
+ [5.772, -10.399, -8.044]
+ [6.408, -12.034, -8.343]
+ [6.017, -10.967, -9.713]
+Or use selections to retrieve the coordinates of subsets of atoms:
C$\alpha$ coordinates:
julia> xCA = coor(protein,"name CA")
+104-element Vector{SVector{3, Float64}}:
+ [-8.483, -14.912, -6.726]
+ [-5.113, -13.737, -5.466]
+ [-3.903, -11.262, -8.062]
+ ⋮
+ 7.836, -2.933, -6.873]
+ [4.414, -4.302, -7.734]
+ [4.134, -7.811, -6.344]
+ [3.244, -10.715, -8.603]
+The coordinates are output as arrays of static arrays (more specifically, as a Vector{SVector{3,Float64}}, from StaticArrays).
Maximum and minimum coordinates of the atoms
Use maxmin(atoms), or maxmin(atoms,"resname CA"), for example:
julia> m = maxmin(atoms,"chain A")
+
+ Minimum atom coordinates: xmin = [-41.5, -41.526, -41.517]
+ Maximum atom coordinates: xmax = [41.583, 41.502, 41.183]
+ Length in each direction: xlength = [83.083, 83.028, 82.7]
+m is a structure containing the three vectors with minimum and maximum coordinates, and lengths.