Atomic and molecular properties

Some simple atom properties can be retrieved using special functions, which operate on atoms of the type Atom. For example:

julia> atoms = readPDB("./file.pdb");

julia> printatom(atoms[1])
   index name resname chain   resnum  residue        x        y        z  beta occup model segname index_pdb
       1   OW     SOL     X        1        1   54.370   45.310   33.970  0.00  0.00     1       -         1

julia> mass(atoms[1])
14.0067

julia> atomic_number(atoms[1])
7

julia> element(atoms[1])
"N"

julia> element_name(atoms[1])
"Nitrogen"

The formula or stoichiometry of a selection can also be retrieved:

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

julia> f = formula(atoms)
C₃N₁O₂

julia> stoichiometry(select(atoms,"water"))
H₂O₁

AtomsBase compatibility

The following functions are supported as part of the API, to conform the AtomsBase interface:

Custom Atom fields

Custom atom fields can be added to an Atom object by defining the custom dictionary. The fields can be accessed by the standard dot syntax if the field name does not clash with an existing Atom field, or by the custom_field getter function.

For example:

julia> atom = Atom(index = 0; custom=Dict(:c => "c", :index => 1))
       0    X     XXX     X        0        0    0.000    0.000    0.000  0.00  0.00     0    XXXX         0

julia> atom.c
"c"

julia> atom.index
0

julia> custom_field(atom, :index)
1

Setting new custom fields follow the standard Julia dictionary syntax:

julia> atom.custom[:new] = "NEW"
"NEW"

julia> atom.new
"NEW"

julia> custom_field(atom, :new)
"NEW"

If a custom field with the :mass key is added to the atom, the mass function returns the mass set at that field:

julia> using PDBTools

julia> atom = Atom();

julia> atom.custom[:mass] = 10.0
10.0

julia> mass(atom)
10.0

Elements for custom atom types

The types of atoms that PDBTools recognizes is defined in the PDBTools.elements dictionary. If new atom types are defined, it is possible to add these types to the dictionary, such that other functions work for the new types. The function to be used is add_element!.

add_element!(symbol::String, reference_element::PDBTools.Element; elements=PDBTools.elements)

julia> using PDBTools

julia> remove_custom_elements!(); # if any

julia> atoms = [ Atom(name="A1"), Atom(name="A2") ];

julia> add_element!("A1", PDBTools.elements["C"])
PDBTools.Element(:C, "C", "Carbon", 6, 12.011, true)

julia> add_element!("A2", PDBTools.elements["N"])
PDBTools.Element(:N, "N", "Nitrogen", 7, 14.0067, true)

julia> element(atoms[1])
"C"

julia> element(atoms[2])
"N"

julia> mass(atoms)
26.017699999999998

julia> remove_custom_elements!(); 

remove_custom_elements!()

julia> using PDBTools

julia> remove_custom_elements!();

julia> add_element!("GN", PDBTools.elements["N"])
PDBTools.Element(:N, "N", "Nitrogen", 7, 14.0067, true)

julia> element(Atom(name="GN"))
"N"

julia> remove_custom_elements!();

julia> element(Atom(name="GN")) # returns `nothing`