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julia> ? mass
search: mass mapslices MathConstants makedocs set_zero_subnormals get_zero_subnormals mutable struct

  mass(name::String or atom::Atom or Vector{Atom})

  Returns the mass of an atom given its name, or Atom structure, or the total mass of a vector of Atoms.

  Example
  –––––––––

  julia> atoms = [ Atom(name="NT3"), Atom(name="CA") ];
  
  julia> mass(atoms[1])
  14.0067
  
  julia> mass("CA")
  12.011
  
  julia> mass(atoms)
  26.017699999999998

PDBTools.Atom — Type

Atom::DataType

Structure that contains the atom properties. It is mutable, so it can be edited. Fields:

mutable struct Atom
    index::Int # The sequential index of the atoms in the file
    index_pdb::Int # The index as written in the PDB file (might be anything)
    name::String # Atom name
    resname::String # Residue name
    chain::String # Chain identifier
    resnum::Int # Number of residue as written in PDB file
    residue::Int # Sequential residue (molecule) number in file
    x::Float64 # x coordinate
    y::Float64 # y coordinate
    z::Float64 # z coordinate
    beta::Float64 # temperature factor
    occup::Float64 # occupancy
    model::Int # model number
    segname::String # Segment name (cols 73:76)
    pdb_element::String # Element symbol string (cols 77:78)
    charge::String # Charge (cols: 79:80)
    custom::Dict{Symbol, Any} # Custom fields
end

Example

julia> using PDBTools

julia> atoms = readPDB(PDBTools.SMALLPDB)
   Array{Atoms,1} with 35 atoms with fields:
   index name resname chain   resnum  residue        x        y        z occup  beta model segname index_pdb
       1    N     ALA     A        1        1   -9.229  -14.861   -5.481  0.00  0.00     1    PROT         1
       2 1HT1     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
                                                       ⋮
      33  OD2     ASP     A        3        3   -6.974  -11.289   -9.300  1.00  0.00     1    PROT        33
      34    C     ASP     A        3        3   -2.626  -10.480   -7.749  1.00  0.00     1    PROT        34
      35    O     ASP     A        3        3   -1.940  -10.014   -8.658  1.00  0.00     1    PROT        35

julia> resname(atoms[1])
"ALA"

julia> chain(atoms[1])
"A"

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

julia> mass(atoms[1])
14.0067

julia> position(atoms[1])
3-element StaticArraysCore.SVector{3, Float64} with indices SOneTo(3):
  -9.229
 -14.861
  -5.481

The pdb_element and charge fields, which are frequently left empty in PDB files, are not printed. The direct access to the fields is considered part of the interface.

Custom fields can be set on Atom construction with the custom keyword argument, which receives a Dict{Symbol,Any} as parameter. They can be retrieved with the custom_field function or, if the custom field names does not overlap with an existing field, with the dot syntax. Requires PDBTools > 0.14.3.

Example

julia> using PDBTools

julia> atom = Atom(index = 0; custom=Dict(:c => "c", :index => 1));

julia> atom.c
"c"

julia> index(atom)
0

julia> custom_field(atom, :index)
1