README.md

PDBTools.jl

Read, write and manipulate atomic systems in PDB and mmCIF formats in Julia.

Documentation

The documentation can be found at: https://m3g.github.io/PDBTools.jl/stable/

Installing:

julia> import Pkg; Pkg.add("PDBTools")

Features:

Simple data structure:

atoms = read_pdb("./structure.pdb")
   Vector{Atom{Nothing}} with 62026 atoms with fields:
   index name resname chain   resnum  residue        x        y        z     b 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
                                                       ⋮ 
   62023   H2    TIP3     C     9338    19637  -18.014   16.666   11.615  0.00  1.00     1    WAT2     62023
   62024  OH2    TIP3     C     9339    19638   13.485   -4.534  -34.438  0.00  1.00     1    WAT2     62024
   62025   H1    TIP3     C     9339    19638   13.218   -3.647  -34.453  0.00  1.00     1    WAT2     62025
   62026   H2    TIP3     C     9339    19638   12.618   -4.977  -34.303  0.00  1.00     1    WAT2     62026
 

Selection syntax:

resname ARG and name CA

Allows use of Julia (possibly user-defined) functions for selection:

atom -> ( atom.resname == "ARG" && atom.x < 10 ) || atom.name == "N"

Not indicated for:

The purpose of PDBTools.jl is mostly to provide support for atomic structure manipulations in the context of Molecular Dynamics Simulations. Thus, it allows reading and writing flexibilities and limitations deviating from standard PDB directives (as VMD and other MD visualization packages do). For more standard support of the PDB and CIF formats use the packages of BioJulia, BioStructures in particular.