Simple structures and functions to read and write PDB files
The documentation can be found at: https://m3g.github.io/PDBTools.jl/stable/
julia> import Pkg; Pkg.add("PDBTools")Simple data structure:
atoms = readPDB("./structure.pdb")
Array{PDBTools.Atom,1} 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 CAAllows use of Julia (possibly user-defined) functions for selection:
atom -> ( atom.resname == "ARG" && atom.x < 10 ) || atom.name == "N"We do not aim to provide the fastest PDB parsing methods. If speed in reading files, returning subsets of the structures, etc., is critical to you, probably you will do better with some packages of BioJulia, BioStructures in particular.