PDB Utilities

The PDB module provides utility functions to deal with PDB (Protein Data Bank) files by thinly wrapping BioPython's PDB Parser.

Exported functions

get_structure

get_structure(filename::String)

Parses a PDB file and returns a structure PyObject.

filename Path/Filename of a PDB file.

get_chains

get_chains(structure::PyObject)

Gets the chains of a protein structure from a BioPython PyObject and returns an Array of Array{Float64,2} matrices of Cα atomic coordinates.

structure A protein structure.

structure_to_matrix

structure_to_matrix(structure::PyObject)

Converts a BioPython structure to a Array{Float64,2} matrix of Cα atomic coordinates.

structure A protein structure

export_pdb (experimental)

export_to_pdb(residueName::String,chainID::String,matrix::Array{Float64,2}, filename::String)

Exports a matrix of Cα atomic coordinates to a PDB File. As of now, it produces files as defined in the PDB specification (Section ATOM) with one minor difference: The atom name is right-aligned, because Formatting.jl does not support center-aligning (yet). This isn't in the specification, but some descriptions include it.

residueName residue name to write to the file

chainID chain ID (e.g. "A", "B", "C"..)

matrix the matrix to export.

filename Path/filename to export to.

get_remote_pdb

get_remote_pdb(id::String)

Downloads and caches a PDB from rcsb.org

id a PDB ID