Selection functions

The select function can be used to select subsets of atoms from a vector of atoms. A simple selection syntax can be used, for example:

atoms = select(atoms, "protein and resnum < 30")

or standard Julia function can be provided as the second argument:

atoms = select(atoms, at -> isprotein(at) && resnum(at) < 30)

General selection syntax

Accepted Boolean operators: and, or, and not.

The accepted keywords for the selection are:

Special macros: proteins, water

Just use these keywords to select the residues matching the properties desired.

Examples:

aromatic = select(atoms,"aromatic")

aromatic = select(atoms,"charged")

Available keywords:

select(atoms::AbstractVector{<:Atom}, by::String)

Select

julia> using PDBTools

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

julia> findfirst(Select("name CA"), atoms)
5

julia> filter(Select("name CA and residue 1"), atoms)
   Vector{Atom{Nothing}} with 1 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

Retrieving indices, filtering, etc

If only the indices of the atoms are of interest, the Julia findall function can be used, by passing a Select object, or a regular function, to select the atoms:

julia> using PDBTools

julia> atoms = read_pdb(PDBTools.TESTPDB, "protein and residue <= 3");

julia> findall(Select("name CA"), atoms)
3-element Vector{Int64}:
  5
 15
 26

julia> findall(at -> name(at) == "CA", atoms)
3-element Vector{Int64}:
  5
 15
 26

The Select constructor can be used to feed simple selection syntax entries to other Julia functions, such as findfirst, findlast, or filter:

julia> using PDBTools

julia> atoms = read_pdb(PDBTools.TESTPDB, "protein and residue <= 3");

julia> filter(Select("name CA"), atoms)
   Vector{Atom{Nothing}} with 3 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

julia> findfirst(Select("beta = 0.00"), atoms)
1

julia> using PDBTools

julia> atoms = read_pdb(PDBTools.TESTPDB, "protein and residue <= 3");

julia> name.(filter(sel"name CA", atoms))
3-element Vector{InlineStrings.String7}:
 "CA"
 "CA"
 "CA"

julia> findfirst(sel"name CA", atoms)
5

Use Julia functions directly

Selections can be done using Julia functions directly, providing a greater control over the selection and, possibly, the use of user defined selection functions. For example:

myselection(atom) = (atom.x < 10.0 && atom.resname == "GLY") || (atom.name == "CA") 
atoms = select(atoms, myselection)

or, for example, using Julia anonymous functions

select(atoms, at -> isprotein(at) && name(at) == "O" && atom.x < 10.0)

The only requirement is that the function defining the selection receives an PDBTools.Atom as input, and returns true or false depending on the conditions required for the atom.

select(atoms, at -> isprotein(at) && resnum(at) in [ 1, 5, 7 ])

Using VMD

VMD is a very popular and powerful package for visualization of simulations. It contains a very versatile library to read topologies and trajectory files, and a powerful selection syntax. We provide here a wrapper to VMD which enables using its capabilities.

For example, the solute can be defined with:

indices, names = select_with_vmd("./system.gro","protein",vmd="/usr/bin/vmd")

The output will contain two lists, one of atom indices (one-based) and atom names. The indices correspond to sequential indices in the input, not the indices written in the PDB file, for example.

The input may also be a vector of atoms of type PDBTools.Atom:

atoms = read_pdb("mypdbfile.pdb")
indices, names = select_with_vmd(atoms,"protein",vmd="/usr/bin/vmd")

The main advantage here is that all the file types and the complete selection syntax that VMD supports are supported. But VMD needs to be installed and is run in background, and it takes a few seconds to run.

select_with_vmd(inputfile::String, selection::String; vmd="vmd", srcload=nothing)
select_with_vmd(atoms::AbstractVector{<:Atom}, selection::String; vmd="vmd", srcload=nothing)

Loading vmd scripts

The select_with_vmd function also accepts an optional keyword parameter srcload, which can be used to load custom scripts within vmd before running setting the selection. This enables the definition of tcl scripts with custom selection macros, for instance. The usage would be:

sel = select_with_vmd("file.pdb", "resname MYRES"; srcload = [ "mymacros1.tcl", "mymacros2.tcl" ])

Which corresponds to sourceing each of the macro files in VMD before defining the selection with the custom MYRES name.