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)
    pdb_element::String = "X"
    charge::Union{Nothing,String} = nothing
    custom::Dict{Symbol, Any} = Dict{Symbol,Any}()
end

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

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

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

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.

Read from string buffer

In some cases a PDB file data may be available as a string and not a regular file. For example, when reading the output of a zipped file. In these cases, it is possible to obtain the array of atoms by reading directly the string buffer with, for example:

julia> pdbdata = read(pdb_file, String); # returns a string with the PDB data, to exemplify

julia> atoms = readPDB(IOBuffer(pdbdata), "protein and name CA")
   Array{Atoms,1} with 104 atoms with fields:
   index name resname chain   resnum  residue        x        y        z occup  beta model segname index_pdb
       5   CA     ALA     A        1        1   -8.483  -14.912   -6.726  1.00  0.00     1    PROT         5
      15   CA     CYS     A        2        2   -5.113  -13.737   -5.466  1.00  0.00     1    PROT        15
      26   CA     ASP     A        3        3   -3.903  -11.262   -8.062  1.00  0.00     1    PROT        26
                                                       ⋮ 
    1425   CA     GLU     A      102      102    4.414   -4.302   -7.734  1.00  0.00     1    PROT      1425
    1440   CA     CYS     A      103      103    4.134   -7.811   -6.344  1.00  0.00     1    PROT      1440
    1454   CA     THR     A      104      104    3.244  -10.715   -8.603  1.00  0.00     1    PROT      1454