Read and write files

Read a PDB file

To read a PDB file and return a vector of atoms of type Atom, do:

atoms = readPDB("file.pdb")

Atom is the structure of data containing the atom index, name, residue, coordinates, etc. For example, after reading a file (as shown bellow), a list of atoms with the following structure will be generated:

julia> printatom(atoms[1])
   index name resname chain   resnum  residue        x        y        z  beta occup model segname index_pdb
       1    N     ALA     A        1        1   -9.229  -14.861   -5.481  0.00  1.00     1    PROT         1

The data in the Atom structure is organized as follows:

mutable struct Atom
    index::Int = 0 # The sequential index of the atoms in the file
    index_pdb::Int = 0 # The index as written in the PDB file (might be anything)
    name::String = "X"
    resname::String = "XXX"
    chain::String = "X"
    resnum::Int = 0 # Number of residue as written in PDB file
    residue::Int = 0 # Sequential residue (molecule) number in file
    x::Float64 = 0.0
    y::Float64 = 0.0
    z::Float64 = 0.0
    beta::Float64 = 0.0
    occup::Float64 = 0.0
    model::Int = 0
    segname::String = "XXXX" # Segment name (cols 73:76)
    element::String = "X"
    charge::Union{Nothing,String} = nothing
    custom::Dict{Symbol, Any} = Dict{Symbol,Any}()
end

Tip

For all these reading and writting functions, a final argument can be provided to read or write a subset of the atoms, following the selection syntax described in the Selection section. For example:

protein = readPDB("file.pdb","protein")

arginines = readPDB("file.pdb","resname ARG")

The only difference is that, if using Julia anonymous functions, the keyword is only:

arginines = readPDB("file.pdb",only = atom -> atom.resname == "ARG")

The same is valid for the write function, below.

Retrive from Protein Data Bank

Use the wget function to retrieve the atom data directly from the PDB database, optionally filtering the atoms with a selection:

julia> atoms = wget("1LBD","name CA")
   index name resname chain   resnum  residue        x        y        z  beta occup model segname index_pdb
       2   CA     SER     A      225        1   46.080   83.165   70.327 68.73  1.00     1       -         2
       8   CA     ALA     A      226        2   43.020   80.825   70.455 63.69  1.00     1       -         8
      13   CA     ASN     A      227        3   41.052   82.178   67.504 53.45  1.00     1       -        13
                                                       ⋮
    1847   CA     GLN     A      460      236  -22.650   79.082   50.023 71.46  1.00     1       -      1847
    1856   CA     MET     A      461      237  -25.561   77.191   51.710 78.41  1.00     1       -      1856
    1864   CA     THR     A      462      238  -26.915   73.645   51.198 82.96  1.00     1       -      1864

Edit a PDB file

The Atom structure is mutable, meaning that the fields can be edited. For example:

julia> atoms = readPDB("file.pdb")
   Array{PDBTools.Atom,1} with 62026 atoms with fields:
   index name resname chain   resnum  residue        x        y        z  beta occup model segname index_pdb
       1    N     ALA     A        1        1   -9.229  -14.861   -5.481  0.00  1.00     1    PROT         1
       2  HT1     ALA     A        1        1  -10.048  -15.427   -5.569  0.00  0.00     1    PROT         2
       3  HT2     ALA     A        1        1   -9.488  -13.913   -5.295  0.00  0.00     1    PROT         3

julia> atoms[1].segname = "ABCD"
"ABCD"

julia> printatom(atoms[1])
   index name resname chain   resnum  residue        x        y        z  beta occup model segname index_pdb
       1    N     ALA     A        1        1   -9.229  -14.861   -5.481  0.00  1.00     1    ABCD         1

Additionally, With the edit! function, you can directly edit or view the data in a vector of Atoms in your preferred text editor.

julia> edit!(atoms)

This will open a text editor. Here, we modified the data in the resname field of the first atom to ABC. Saving and closing the file will update the atoms array:

julia> printatom(atoms[1])
   index name resname chain   resnum  residue        x        y        z  beta occup model segname index_pdb
       1    N     ABC     A        1        1   -9.229  -14.861   -5.481  0.00  1.00     1    PROT         1

Write a PDB file

To write a PDB file use the writePDB function, as:

writePDB(atoms,"file.pdb")

where atoms contain a list of atoms with the Atom structures.

Read and write single-atom lines

PDBTools.read_atom(pdb_line): Given a line of a PDB file containing atom data, returns the data in a Atom structure.

PDBTools.write_atom(atom::Atom): Given an atom in the Atom structure, returns a string formatted in the PDB format, to be written to a file.