PDBTools

PDBTools is a simple package to read and write Protein Data Bank files, select atoms, and work with their coordinates. It is aimed to provide support for the typical uses of structure files in the context of molecular dynamics simulations.

As of version 2.0, PDBTools is able to read and write the atomic data from PDB and mmCIF structure files.

Features:

Simple data structure:

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

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:

PDBTools is not very strict in following the PDB or mmCIF formats. In particular, it does not read any of the meta-data of these files, only ATOM and HETATM fields are of interest. Also, it supports repeated atom entries, as each atom is read as an independent object. This flexibility provides support for common structure formats occurring in the Molecular Dynamics Simulations field.

If more comprehensive (and strict) support for these files is necessary, use the packages of BioJulia, BioStructures in particular.